JoaoJunior/formatted-java-code-APR · Datasets at Hugging Face

public void initialize(int aType, String aName) throws Exception { this.itsType = aType; this.itsName = aName; props.put($Name, aName); }

public void initialize(int aType, String aName) throws Exception { int itsType = aType; this.itsName = aName; props.put($Name, aName); }

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public void setArguments(String args) { this.itsArguments = args; props.put($Arguments, args); }

public void setArguments(String args) { String itsArguments = args; props.put($Arguments, args); }

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public void setDescription(String description) { this.itsDescription = description; props.put($Comment, description); }

public void setDescription(String description) { String itsDescription = description; props.put($Comment, description); }

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public void setIconLocation(String path, int index) { this.itsIconPath = path; this.itsIconIndex = index; props.put($Icon, path); // }

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public void setLinkType(int aType) throws IllegalArgumentException { this.itsType = aType; }

public void setLinkType(int aType) throws IllegalArgumentException { int itsType = aType; }

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public void setShowCommand(int show) { this.itsShow = show; }

public void setShowCommand(int show) { int itsShow = show; }

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public void setTargetPath(String aPath) { this.itsTargetPath = aPath; StringTokenizer whiteSpaceTester = new StringTokenizer( aPath ); if( whiteSpaceTester.countTokens() > 1 ) props.put( $E_QUOT,QM ); props.put($Exec, aPath); }

public void setTargetPath(String aPath) { String itsTargetPath = aPath; StringTokenizer whiteSpaceTester = new StringTokenizer( aPath ); if( whiteSpaceTester.countTokens() > 1 ) props.put( $E_QUOT,QM ); props.put($Exec, aPath); }

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public void setWorkingDirectory(String aDirectory) { this.itsWorkingDirectory = aDirectory; StringTokenizer whiteSpaceTester = new StringTokenizer( aDirectory ); if( whiteSpaceTester.countTokens() > 1 ) props.put( $P_QUOT,QM ); props.put($Path, aDirectory); }

public void setWorkingDirectory(String aDirectory) { String itsWorkingDirectory = aDirectory; StringTokenizer whiteSpaceTester = new StringTokenizer( aDirectory ); if( whiteSpaceTester.countTokens() > 1 ) props.put( $P_QUOT,QM ); props.put($Path, aDirectory); }

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private File writeShortCut(String target, String shortCutDef) { File targetPath = new File(target.toString().substring(0, target.toString().lastIndexOf(File.separatorChar))); if (!targetPath.exists()) { targetPath.mkdirs(); this.createdDirectory = targetPath.toString(); } File targetFileName = new File( target ); File backupFile = new File( targetPath + File.separator + "." + targetFileName.getName() + System.currentTimeMillis() ); if( targetFileName.exists() ) { try { // create a hidden backup.file of the existing shortcut with a timestamp name. copyTo( targetFileName, backupFile );// + System.e ); targetFileName.delete(); } catch (IOException e3) { System.out.println("cannot create backup file " + backupFile + " of " + targetFileName );// e3.printStackTrace(); } } FileWriter fileWriter = null; try { fileWriter = new FileWriter( targetFileName ); } catch (IOException e1) { System.out.println( e1.getMessage() ); } try { fileWriter.write(shortCutDef); } catch (IOException e) { e.printStackTrace(); } try { fileWriter.close(); } catch (IOException e2) { e2.printStackTrace(); } return targetFileName; }

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public GenericObjectPool() { this(null,DEFAULT_MAX_ACTIVE,DEFAULT_WHEN_EXHAUSTED_ACTION,DEFAULT_MAX_WAIT,DEFAULT_MAX_IDLE,DEFAULT_TEST_ON_BORROW,DEFAULT_TEST_ON_RETURN,DEFAULT_TIME_BETWEEN_EVICTION_RUNS_MILLIS,DEFAULT_NUM_TESTS_PER_EVICTION_RUN,DEFAULT_MIN_EVICTABLE_IDLE_TIME_MILLIS,DEFAULT_TEST_WHILE_IDLE); }

public GenericObjectPool() { this(null,DEFAULT_MAX_ACTIVE,DEFAULT_WHEN_EXHAUSTED_ACTION,DEFAULT_MAX_WAIT,DEFAULT_MAX_IDLE,DEFAULT_MIN_IDLE,DEFAULT_TEST_ON_BORROW,DEFAULT_TEST_ON_RETURN,DEFAULT_TIME_BETWEEN_EVICTION_RUNS_MILLIS,DEFAULT_NUM_TESTS_PER_EVICTION_RUN,DEFAULT_MIN_EVICTABLE_IDLE_TIME_MILLIS,DEFAULT_TEST_WHILE_IDLE); }

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public XInfoPanel(InstallerFrame parent, InstallData idata) { super(parent, idata); // We initialize our layout layout = new GridBagLayout(); gbConstraints = new GridBagConstraints(); setLayout(layout); // We add the components infoLabel = new JLabel(parent.langpack.getString("InfoPanel.info"), parent.icons.getImageIcon("edit"), JLabel.TRAILING); parent.buildConstraints(gbConstraints, 0, 0, 1, 1, 1.0, 0.0); gbConstraints.insets = new Insets(5, 5, 5, 5); gbConstraints.fill = GridBagConstraints.BOTH; gbConstraints.anchor = GridBagConstraints.SOUTHWEST; layout.addLayoutComponent(infoLabel, gbConstraints); add(infoLabel); textArea = new JTextArea(); textArea.setEditable(false); JScrollPane scroller = new JScrollPane(textArea); parent.buildConstraints(gbConstraints, 0, 1, 1, 1, 1.0, 0.9); gbConstraints.anchor = GridBagConstraints.CENTER; layout.addLayoutComponent(scroller, gbConstraints); add(scroller); }

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private void loadInfo() { try { // We read it info = ResourceManager.getInstance().getTextResource("XInfoPanel.info"); } catch (Exception err) { info = "Error : could not load the info text !"; } }

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private void parseText() { try { // Initialize the variable substitutor VariableSubstitutor vs = new VariableSubstitutor (idata.getVariableValueMap()); // Parses the info text info = vs.substitute(info, null); } catch (Exception err) { err.printStackTrace(); } }

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private void parseText() { try { // Initialize the variable substitutor VariableSubstitutor vs = new VariableSubstitutor (idata.getVariableValueMap()); // Parses the info text info = vs.substitute(info, null); } catch (Exception err) { err.printStackTrace(); } }

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private void buildGUI() { setLayout(new BoxLayout(this, BoxLayout.Y_AXIS)); add(buildChannelGraphicsPanel()); add(new JSeparator()); add(buildControlsPane()); add(new JSeparator()); add(buildPane()); }

private void buildGUI() { setLayout(new BoxLayout(this, BoxLayout.Y_AXIS)); add(buildChannelGraphicsPanel()); add(new JSeparator()); add(buildControlsPane()); add(new JSeparator()); JPanel p = new JPanel(); p.setLayout(new BoxLayout(p,BoxLayout.X_AXIS)); p.add(buildPane()); p.add(Box.createHorizontalStrut(300)); add(p); }

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private JPanel buildPane() { JPanel p = new JPanel(); p.setLayout(new BoxLayout(p,BoxLayout.Y_AXIS)); p.add(noiseReduction); p.add(histogramButton); return p; }

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void viewHierarchy(Set images, int index) { HiViewerUIF presentation = HiViewerUIF.getInstance(control); HiViewer hiViewer = presentation.createHiViewer(); HiLoader loader = null; switch (index) { case HiViewerCtrl.VIEW_IN_PDI: loader = new CGCILoader(this, hiViewer, images); break; case HiViewerCtrl.VIEW_IN_CGCI: loader = new PDILoader(this, hiViewer, images); } if (loader != null) loader.load(); }

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public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged) { //#[ operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,Temperature,Pressure,boolean) ReactionTime rt = p_beginStatus.getTime(); if (!rt.equals(p_beginTime)) throw new InvalidBeginStatusException(); // set time double tBegin = p_beginTime.getStandardTime(); double tEnd = p_endTime.getStandardTime(); // set reaction set //if (p_initialization || p_reactionChanged || p_conditionChanged) { generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedList rList = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateAllODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //p_reactionChanged = true; //} // set numbers System.out.println("Total number of reactions to Daspk is "+rList.size()); int nState = p_reactionModel.getSpeciesNumber(); int nParameter = 0; LinkedList initialSpecies = new LinkedList();// if (parameterInfor!=null) nParameter = parameterInfor.length; if (parameterInfor != 0) { nParameter = rList.size(); //svp if (initialStatus == null) System.out.println("initialStatus = null"); Iterator spe_iter = initialStatus.getSpeciesStatus(); while (spe_iter.hasNext()) { SpeciesStatus ss = (SpeciesStatus) spe_iter.next(); String name = ss.getSpecies().getName(); initialSpecies.add(name); nParameter++; } } int neq = nState*(nParameter+1); // set temperature and pressure double T = p_temperature.getK(); double P = p_pressure.getAtm(); // set initial value of y and yprime; double [] y = new double[neq]; double [] yprime = new double[neq]; //double numberOfReactedSpecies=0; // get the present status at t_begin, and set y and y' accordingly System.out.println("Before ODE: " + String.valueOf(tBegin) + "SEC"); System.out.println("End at : " + String.valueOf(tEnd) + "SEC"); for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) { SpeciesStatus ss = (SpeciesStatus)iter.next(); double conc = ss.getConcentration(); double flux = ss.getFlux(); if (ss.isReactedSpecies()) { Species spe = ss.getSpecies(); int id = getRealID(spe); System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getName() + '\t' + String.valueOf(conc) + '\t' + String.valueOf(flux)); y[id-1] = conc; yprime[id-1] = flux; } } if (nParameter != 0){//svp parameterInforArray = new ParameterInfor[nParameter]; for (int i = 1; i <= rList.size(); i++){ parameterInforArray[i-1] = new ParameterInfor("k",i,0.00); } for (int i=rList.size()+1; i<=nParameter;i++){ parameterInforArray[i - 1] = new ParameterInfor("CO", nParameter, 0.00); } if (p_beginTime.getTime() == 0 || p_beginTime.getTime() == 0.00) { LinkedList sensitivityStatus = new LinkedList(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber();// for (int i=0;i<reactionNumber*speciesNumber;i++){ for (int i=0; i<nParameter*speciesNumber;i++){ sensitivityStatus.add(i,null); } p_beginStatus.addSensitivity(sensitivityStatus); double sflux = 1; Iterator species_iter = p_reactionModel.getSpecies(); while (species_iter.hasNext()) { Species spe = (Species) species_iter.next(); int m = getRealID(spe); for (int p=0;p<nParameter;p++){ int k = m + (p+1) * speciesNumber - 1; if (p >= rList.size()){ int speciesNum = p-rList.size(); String name = (String)initialSpecies.get(speciesNum); sflux = 0; SensitivityStatus senStatus; if (name.equalsIgnoreCase(spe.getName())){ senStatus = new SensitivityStatus(1, sflux, m, p + 1); y[k] = 1; } else{ senStatus = new SensitivityStatus(0,sflux,m,p+1); y[k]=0; } sensitivityStatus.add(k - p_reactionModel.getSpeciesNumber(), senStatus); p_beginStatus.putSensitivityStatus(k - speciesNumber, senStatus); yprime[k] = sflux; } else{ Reaction rxn = (Reaction)rList.get(p); if (rxn.containsAsProduct(spe)) { sflux = 1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } if (rxn.containsAsReactant(spe)) { sflux = -1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } else { sflux = 0; } SensitivityStatus senStatus = new SensitivityStatus(0, sflux, m, p+1); sensitivityStatus.add(k-p_reactionModel.getSpeciesNumber(),senStatus); p_beginStatus.putSensitivityStatus(k-speciesNumber,senStatus); y[k] = 0; yprime[k] = sflux; } } } } else { for (int i = p_reactionModel.getSpeciesNumber(); i < y.length; i++) { SensitivityStatus ss = (SensitivityStatus) p_beginStatus. getSensitivityStatus(i-p_reactionModel.getSpeciesNumber()); double sens = ss.getSensitivity(); double sflux = ss.getSFlux(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber(); Iterator species_iter = p_reactionModel.getSpecies(); y[i] = sens; yprime[i] = sflux; } } } //System.out.println("Number of Reacted Species is " + numberOfReactedSpecies); int idid; HashMap speStatus = new HashMap(); LinkedList senStatus = new LinkedList(); double[] tPresent = {tBegin}; int temp = 1; if (nParameter==0) { idid = solveDAE(p_initialization, reactionList, true, thirdBodyReactionList, nState, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid !=1 && idid != 2 && idid != 3) { System.out.println("The idid from DASPK was "+idid + " at time "+tPresent[0]); throw new DynamicSimulatorException("DASPK: SA off."); } System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, 0); } else { idid = solveSEN(p_initialization, reactionList, p_reactionChanged, thirdBodyReactionList, nState, nParameter, this.parameterInforArray, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid != 2 && idid != 3) throw new DynamicSimulatorException("DASPK: SA on."); //speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); senStatus = generateSensitivityStatus(p_reactionModel,y,yprime,nParameter); SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, senStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); sss.setIDTranslator(IDTranslator); sss.setReactionList(rList); return sss; } SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CH4"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO2"), rList, sss, p_temperature); return sss; //#] }

public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged) { //#[ operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,Temperature,Pressure,boolean) ReactionTime rt = p_beginStatus.getTime(); if (!rt.equals(p_beginTime)) throw new InvalidBeginStatusException(); // set time double tBegin = p_beginTime.getStandardTime(); double tEnd = p_endTime.getStandardTime(); // set reaction set //if (p_initialization || p_reactionChanged || p_conditionChanged) { LinkedList rList = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateAllODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //p_reactionChanged = true; //} // set numbers System.out.println("Total number of reactions to Daspk is "+rList.size()); int nState = p_reactionModel.getSpeciesNumber(); int nParameter = 0; LinkedList initialSpecies = new LinkedList();// if (parameterInfor!=null) nParameter = parameterInfor.length; if (parameterInfor != 0) { nParameter = rList.size(); //svp if (initialStatus == null) System.out.println("initialStatus = null"); Iterator spe_iter = initialStatus.getSpeciesStatus(); while (spe_iter.hasNext()) { SpeciesStatus ss = (SpeciesStatus) spe_iter.next(); String name = ss.getSpecies().getName(); initialSpecies.add(name); nParameter++; } } int neq = nState*(nParameter+1); // set temperature and pressure double T = p_temperature.getK(); double P = p_pressure.getAtm(); // set initial value of y and yprime; double [] y = new double[neq]; double [] yprime = new double[neq]; //double numberOfReactedSpecies=0; // get the present status at t_begin, and set y and y' accordingly System.out.println("Before ODE: " + String.valueOf(tBegin) + "SEC"); System.out.println("End at : " + String.valueOf(tEnd) + "SEC"); for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) { SpeciesStatus ss = (SpeciesStatus)iter.next(); double conc = ss.getConcentration(); double flux = ss.getFlux(); if (ss.isReactedSpecies()) { Species spe = ss.getSpecies(); int id = getRealID(spe); System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getName() + '\t' + String.valueOf(conc) + '\t' + String.valueOf(flux)); y[id-1] = conc; yprime[id-1] = flux; } } if (nParameter != 0){//svp parameterInforArray = new ParameterInfor[nParameter]; for (int i = 1; i <= rList.size(); i++){ parameterInforArray[i-1] = new ParameterInfor("k",i,0.00); } for (int i=rList.size()+1; i<=nParameter;i++){ parameterInforArray[i - 1] = new ParameterInfor("CO", nParameter, 0.00); } if (p_beginTime.getTime() == 0 || p_beginTime.getTime() == 0.00) { LinkedList sensitivityStatus = new LinkedList(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber();// for (int i=0;i<reactionNumber*speciesNumber;i++){ for (int i=0; i<nParameter*speciesNumber;i++){ sensitivityStatus.add(i,null); } p_beginStatus.addSensitivity(sensitivityStatus); double sflux = 1; Iterator species_iter = p_reactionModel.getSpecies(); while (species_iter.hasNext()) { Species spe = (Species) species_iter.next(); int m = getRealID(spe); for (int p=0;p<nParameter;p++){ int k = m + (p+1) * speciesNumber - 1; if (p >= rList.size()){ int speciesNum = p-rList.size(); String name = (String)initialSpecies.get(speciesNum); sflux = 0; SensitivityStatus senStatus; if (name.equalsIgnoreCase(spe.getName())){ senStatus = new SensitivityStatus(1, sflux, m, p + 1); y[k] = 1; } else{ senStatus = new SensitivityStatus(0,sflux,m,p+1); y[k]=0; } sensitivityStatus.add(k - p_reactionModel.getSpeciesNumber(), senStatus); p_beginStatus.putSensitivityStatus(k - speciesNumber, senStatus); yprime[k] = sflux; } else{ Reaction rxn = (Reaction)rList.get(p); if (rxn.containsAsProduct(spe)) { sflux = 1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } if (rxn.containsAsReactant(spe)) { sflux = -1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } else { sflux = 0; } SensitivityStatus senStatus = new SensitivityStatus(0, sflux, m, p+1); sensitivityStatus.add(k-p_reactionModel.getSpeciesNumber(),senStatus); p_beginStatus.putSensitivityStatus(k-speciesNumber,senStatus); y[k] = 0; yprime[k] = sflux; } } } } else { for (int i = p_reactionModel.getSpeciesNumber(); i < y.length; i++) { SensitivityStatus ss = (SensitivityStatus) p_beginStatus. getSensitivityStatus(i-p_reactionModel.getSpeciesNumber()); double sens = ss.getSensitivity(); double sflux = ss.getSFlux(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber(); Iterator species_iter = p_reactionModel.getSpecies(); y[i] = sens; yprime[i] = sflux; } } } //System.out.println("Number of Reacted Species is " + numberOfReactedSpecies); int idid; HashMap speStatus = new HashMap(); LinkedList senStatus = new LinkedList(); double[] tPresent = {tBegin}; int temp = 1; if (nParameter==0) { idid = solveDAE(p_initialization, reactionList, true, thirdBodyReactionList, nState, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid !=1 && idid != 2 && idid != 3) { System.out.println("The idid from DASPK was "+idid + " at time "+tPresent[0]); throw new DynamicSimulatorException("DASPK: SA off."); } System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, 0); } else { idid = solveSEN(p_initialization, reactionList, p_reactionChanged, thirdBodyReactionList, nState, nParameter, this.parameterInforArray, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid != 2 && idid != 3) throw new DynamicSimulatorException("DASPK: SA on."); //speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); senStatus = generateSensitivityStatus(p_reactionModel,y,yprime,nParameter); SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, senStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); sss.setIDTranslator(IDTranslator); sss.setReactionList(rList); return sss; } SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CH4"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO2"), rList, sss, p_temperature); return sss; //#] }

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public synchronized Object borrowObject(Object key) throws Exception { long starttime = System.currentTimeMillis(); boolean newlyCreated = false; for(;;) { LinkedList pool = (LinkedList)(_poolMap.get(key)); if(null == pool) { pool = new LinkedList(); _poolMap.put(key,pool); } ObjectTimestampPair pair = null; // if there are any sleeping, just grab one of those try { pair = (ObjectTimestampPair)(pool.removeFirst()); if(null != pair) { _totalIdle--; } } catch(NoSuchElementException e) { /* ignored */ } // otherwise if(null == pair) { // if there is a totalMaxActive and we are at the limit then // we have to make room if ((_maxTotal > 0) && (_totalActive + _totalIdle >= _maxTotal)) { clearOldest(); } // check if we can create one // (note we know that the num sleeping is 0, else we wouldn't be here) int active = getActiveCount(key); if ((_maxActive < 0 || active < _maxActive) && (_maxTotal < 0 || _totalActive + _totalIdle < _maxTotal)) { Object obj = _factory.makeObject(key); pair = new ObjectTimestampPair(obj); newlyCreated = true; } else { // the pool is exhausted switch(_whenExhaustedAction) { case WHEN_EXHAUSTED_GROW: Object obj = _factory.makeObject(key); pair = new ObjectTimestampPair(obj); break; case WHEN_EXHAUSTED_FAIL: throw new NoSuchElementException(); case WHEN_EXHAUSTED_BLOCK: try { if(_maxWait <= 0) { wait(); } else { // this code may be executed again after a notify then continue cycle // so, need to calculate the amount of time to wait final long elapsed = (System.currentTimeMillis() - starttime); final long waitTime = _maxWait - elapsed; if (waitTime > 0) { wait(waitTime); } } } catch(InterruptedException e) { // ignored } if(_maxWait > 0 && ((System.currentTimeMillis() - starttime) >= _maxWait)) { throw new NoSuchElementException("Timeout waiting for idle object"); } else { continue; // keep looping } default: throw new IllegalArgumentException("whenExhaustedAction " + _whenExhaustedAction + " not recognized."); } } } _factory.activateObject(key,pair.value); if(_testOnBorrow && !_factory.validateObject(key,pair.value)) { _factory.destroyObject(key,pair.value); if(newlyCreated) { throw new NoSuchElementException("Could not create a validated object"); } // else keep looping } else { incrementActiveCount(key); return pair.value; } } }

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public synchronized void evict() throws Exception { Object key = null; if (_recentlyEvictedKeys == null) { _recentlyEvictedKeys = new HashSet(_poolMap.size()); } Set remainingKeys = new HashSet(_poolMap.keySet()); remainingKeys.removeAll(_recentlyEvictedKeys); Iterator keyIter = remainingKeys.iterator(); ListIterator objIter = null; for(int i=0,m=getNumTests();i<m;i++) { if(_poolMap.size() > 0) { // Find next idle object pool key to work on if (key == null) { if (!keyIter.hasNext()) { _recentlyEvictedKeys.clear(); remainingKeys = new HashSet(_poolMap.keySet()); keyIter = remainingKeys.iterator(); } if (!keyIter.hasNext()) { // done, there are no keyed pools return; } key = keyIter.next(); } // if we don't have a keyed object pool iterator if (objIter == null) { final LinkedList list = (LinkedList)_poolMap.get(key); if (_evictLastIndex < 0 || _evictLastIndex > list.size()) { _evictLastIndex = list.size(); } objIter = list.listIterator(_evictLastIndex); } // if the _evictionCursor has a previous object, then test it if(objIter.hasPrevious()) { ObjectTimestampPair pair = (ObjectTimestampPair)(objIter.previous()); boolean removeObject=false; if(_minEvictableIdleTimeMillis > 0 && System.currentTimeMillis() - pair.tstamp > _minEvictableIdleTimeMillis) { removeObject=true; } else if(_testWhileIdle) { boolean active = false; try { _factory.activateObject(key,pair.value); active = true; } catch(Exception e) { removeObject=true; } if(active) { if(!_factory.validateObject(key,pair.value)) { removeObject=true; } else { try { _factory.passivateObject(key,pair.value); } catch(Exception e) { removeObject=true; } } } } if(removeObject) { try { objIter.remove(); _totalIdle--; _factory.destroyObject(key,pair.value); // Do not remove the key from the _poolList or _poolmap, even if the list // stored in the _poolMap for this key is empty when the // {@link #getMinIdle <i>minIdle</i>} is > 0. // // Otherwise if it was the last object for that key, drop that pool if ((_minIdle == 0) && (((LinkedList)(_poolMap.get(key))).isEmpty())) { _poolMap.remove(key); } } catch(Exception e) { ; // ignored } } } else { // else done evicting keyed pool _recentlyEvictedKeys.add(key); _evictLastIndex = -1; objIter = null; } } } }

public synchronized void evict() throws Exception { Object key = null; if (_recentlyEvictedKeys == null) { _recentlyEvictedKeys = new HashSet(_poolMap.size()); } Set remainingKeys = new HashSet(_poolMap.keySet()); remainingKeys.removeAll(_recentlyEvictedKeys); Iterator keyIter = remainingKeys.iterator(); ListIterator objIter = null; for(int i=0,m=getNumTests();i<m;i++) { if(_poolMap.size() > 0) { // Find next idle object pool key to work on if (key == null) { if (!keyIter.hasNext()) { _recentlyEvictedKeys.clear(); remainingKeys = new HashSet(_poolMap.keySet()); keyIter = remainingKeys.iterator(); } if (!keyIter.hasNext()) { // done, there are no keyed pools return; } key = keyIter.next(); } // if we don't have a keyed object pool iterator if (objIter == null) { final LinkedList list = (LinkedList)_poolMap.get(key); if (_evictLastIndex < 0 || _evictLastIndex > list.size()) { _evictLastIndex = list.size(); } objIter = list.listIterator(_evictLastIndex); } // if the _evictionCursor has a previous object, then test it if(objIter.hasPrevious()) { ObjectTimestampPair pair = (ObjectTimestampPair)(objIter.previous()); boolean removeObject=false; if(_minEvictableIdleTimeMillis > 0 && System.currentTimeMillis() - pair.tstamp > _minEvictableIdleTimeMillis) { removeObject=true; } if(_testWhileIdle && removeObject == false) { boolean active = false; try { _factory.activateObject(key,pair.value); active = true; } catch(Exception e) { removeObject=true; } if(active) { if(!_factory.validateObject(key,pair.value)) { removeObject=true; } else { try { _factory.passivateObject(key,pair.value); } catch(Exception e) { removeObject=true; } } } } if(removeObject) { try { objIter.remove(); _totalIdle--; _factory.destroyObject(key,pair.value); // Do not remove the key from the _poolList or _poolmap, even if the list // stored in the _poolMap for this key is empty when the // {@link #getMinIdle <i>minIdle</i>} is > 0. // // Otherwise if it was the last object for that key, drop that pool if ((_minIdle == 0) && (((LinkedList)(_poolMap.get(key))).isEmpty())) { _poolMap.remove(key); } } catch(Exception e) { ; // ignored } } } else { // else done evicting keyed pool _recentlyEvictedKeys.add(key); _evictLastIndex = -1; objIter = null; } } } }

3,240,305

private void analyzeShortcutSpec() { if (!haveShortcutSpec) { shortcutsToCreate = false; return; } XMLElement skipper = spec.getFirstChildNamed(SPEC_KEY_SKIP_IFNOT_SUPPORTED); skipIfNotSupported = (skipper != null); // ---------------------------------------------------- // find out if we should simulate a not supported // scenario // ---------------------------------------------------- XMLElement support = spec.getFirstChildNamed(SPEC_KEY_NOT_SUPPORTED); if (support != null) { simulteNotSupported = true; } // ---------------------------------------------------- // find out in which program group the shortcuts should // be placed and where this program group should be // located // ---------------------------------------------------- XMLElement group = spec.getFirstChildNamed(SPEC_KEY_PROGRAM_GROUP); String location = null; hasDesktopShortcuts = false; if (group != null) { suggestedProgramGroup = group.getAttribute(SPEC_ATTRIBUTE_DEFAULT_GROUP, ""); location = group.getAttribute(SPEC_ATTRIBUTE_LOCATION, SPEC_VALUE_APPLICATIONS); } else { suggestedProgramGroup = ""; location = SPEC_VALUE_APPLICATIONS; } if (location.equals(SPEC_VALUE_APPLICATIONS)) { groupLocation = Shortcut.APPLICATIONS; } else if (location.equals(SPEC_VALUE_START_MENU)) { groupLocation = Shortcut.START_MENU; } // ---------------------------------------------------- // create a list of all shortcuts that need to be // created, containing all details about each shortcut // ---------------------------------------------------- VariableSubstitutor substitutor = new VariableSubstitutor(idata.getVariables()); String temp; Vector shortcutSpecs = spec.getChildrenNamed(SPEC_KEY_SHORTCUT); XMLElement shortcutSpec; ShortcutData data; for (int i = 0; i < shortcutSpecs.size(); i++) { shortcutSpec = (XMLElement) shortcutSpecs.elementAt(i); if (!OsConstraint.oneMatchesCurrentSystem(shortcutSpec)) continue; data = new ShortcutData(); data.name = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_NAME); data.subgroup = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_SUBGROUP); data.description = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_DESCRIPTION, ""); //** Linux **// data.deskTopEntryLinux_Encoding = shortcutSpec .getAttribute(SPEC_ATTRIBUTE_ENCODING, ""); data.deskTopEntryLinux_MimeType = shortcutSpec .getAttribute(SPEC_ATTRIBUTE_MIMETYPE, ""); data.deskTopEntryLinux_Terminal = shortcutSpec .getAttribute(SPEC_ATTRIBUTE_TERMINAL, ""); data.deskTopEntryLinux_TerminalOptions = shortcutSpec.getAttribute( SPEC_ATTRIBUTE_TERMINAL_OPTIONS, ""); data.deskTopEntryLinux_Type = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_TYPE, ""); data.deskTopEntryLinux_URL = substitutor.substitute(shortcutSpec.getAttribute( SPEC_ATTRIBUTE_URL, ""), null); data.deskTopEntryLinux_X_KDE_SubstituteUID = shortcutSpec.getAttribute( SPEC_ATTRIBUTE_KDE_SUBST_UID, ""); data.createForAll = new Boolean(shortcutSpec.getAttribute(CREATE_FOR_ALL, "false")); //** EndOf LINUX **// temp = fixSeparatorChar(shortcutSpec.getAttribute(SPEC_ATTRIBUTE_TARGET, "")); data.target = substitutor.substitute(temp, null); temp = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_COMMAND, ""); data.commandLine = substitutor.substitute(temp, null); temp = fixSeparatorChar(shortcutSpec.getAttribute(SPEC_ATTRIBUTE_ICON, "")); data.iconFile = substitutor.substitute(temp, null); data.iconIndex = Integer.parseInt(shortcutSpec.getAttribute(SPEC_ATTRIBUTE_ICON_INDEX, "0")); temp = fixSeparatorChar(shortcutSpec.getAttribute(SPEC_ATTRIBUTE_WORKING_DIR, "")); data.workingDirectory = substitutor.substitute(temp, null); String initialState = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_INITIAL_STATE, ""); if (initialState.equals(SPEC_VALUE_NO_SHOW)) { data.initialState = Shortcut.HIDE; } else if (initialState.equals(SPEC_VALUE_NORMAL)) { data.initialState = Shortcut.NORMAL; } else if (initialState.equals(SPEC_VALUE_MAXIMIZED)) { data.initialState = Shortcut.MAXIMIZED; } else if (initialState.equals(SPEC_VALUE_MINIMIZED)) { data.initialState = Shortcut.MINIMIZED; } else { data.initialState = Shortcut.NORMAL; } // -------------------------------------------------- // if the minimal data requirements are met to create // the shortcut, create one entry each for each of // the requested types. // Eventually this will cause the creation of one // shortcut in each of the associated locations. // -------------------------------------------------- // without a name we can not create a shortcut if (data.name == null) { continue; } //1. Elmar: "Without a target we can not create a shortcut." //2. Marc: "No, Even on Linux a Link can be an URL and has no target." if (data.target == null) { continue; } // the shortcut is not actually required for any of the selected packs Vector forPacks = shortcutSpec.getChildrenNamed(SPEC_KEY_PACKS); if (!shortcutRequiredFor(forPacks)) { continue; } // -------------------------------------------------- // This section is executed if we don't skip. // -------------------------------------------------- // For each of the categories set the type and if // the link should be placed in the program group, // then clone the data set to obtain an independent // instance and add this to the list of shortcuts // to be created. In this way, we will set up an // identical copy for each of the locations at which // a shortcut should be placed. Therefore you must // not use 'else if' statements! // -------------------------------------------------- { if (attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_DESKTOP)) { hasDesktopShortcuts = true; data.addToGroup = false; data.type = Shortcut.DESKTOP; shortcuts.add(data.clone()); } if (attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_APPLICATIONS)) { data.addToGroup = false; data.type = Shortcut.APPLICATIONS; shortcuts.add(data.clone()); } if (attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_START_MENU)) { data.addToGroup = false; data.type = Shortcut.START_MENU; shortcuts.add(data.clone()); } if (attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_STARTUP)) { data.addToGroup = false; data.type = Shortcut.START_UP; shortcuts.add(data.clone()); } if (attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_PROGRAM_GROUP)) { data.addToGroup = true; data.type = Shortcut.APPLICATIONS; shortcuts.add(data.clone()); } } } // ---------------------------------------------------- // signal if there are any shortcuts to create // ---------------------------------------------------- if (shortcuts.size() > 0) { shortcutsToCreate = true; } }

private void analyzeShortcutSpec() { if (!haveShortcutSpec) { shortcutsToCreate = false; return; } XMLElement skipper = spec.getFirstChildNamed(SPEC_KEY_SKIP_IFNOT_SUPPORTED); skipIfNotSupported = (skipper != null); // ---------------------------------------------------- // find out if we should simulate a not supported // scenario // ---------------------------------------------------- XMLElement support = spec.getFirstChildNamed(SPEC_KEY_NOT_SUPPORTED); if (support != null) { simulteNotSupported = true; } // ---------------------------------------------------- // find out in which program group the shortcuts should // be placed and where this program group should be // located // ---------------------------------------------------- XMLElement group = spec.getFirstChildNamed(SPEC_KEY_PROGRAM_GROUP); String location = null; hasDesktopShortcuts = false; if (group != null) { suggestedProgramGroup = group.getAttribute(SPEC_ATTRIBUTE_DEFAULT_GROUP, ""); location = group.getAttribute(SPEC_ATTRIBUTE_LOCATION, SPEC_VALUE_APPLICATIONS); } else { suggestedProgramGroup = ""; location = SPEC_VALUE_APPLICATIONS; } if (location.equals(SPEC_VALUE_APPLICATIONS)) { groupLocation = Shortcut.APPLICATIONS; } else if (location.equals(SPEC_VALUE_START_MENU)) { groupLocation = Shortcut.START_MENU; } // ---------------------------------------------------- // create a list of all shortcuts that need to be // created, containing all details about each shortcut // ---------------------------------------------------- VariableSubstitutor substitutor = new VariableSubstitutor(idata.getVariables()); String temp; Vector shortcutSpecs = spec.getChildrenNamed(SPEC_KEY_SHORTCUT); XMLElement shortcutSpec; ShortcutData data; for (int i = 0; i < shortcutSpecs.size(); i++) { shortcutSpec = (XMLElement) shortcutSpecs.elementAt(i); if (!OsConstraint.oneMatchesCurrentSystem(shortcutSpec)) continue; data = new ShortcutData(); data.name = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_NAME); data.subgroup = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_SUBGROUP); data.description = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_DESCRIPTION, ""); //** Linux **// data.deskTopEntryLinux_Encoding = shortcutSpec .getAttribute(SPEC_ATTRIBUTE_ENCODING, ""); data.deskTopEntryLinux_MimeType = shortcutSpec .getAttribute(SPEC_ATTRIBUTE_MIMETYPE, ""); data.deskTopEntryLinux_Terminal = shortcutSpec .getAttribute(SPEC_ATTRIBUTE_TERMINAL, ""); data.deskTopEntryLinux_TerminalOptions = shortcutSpec.getAttribute( SPEC_ATTRIBUTE_TERMINAL_OPTIONS, ""); data.deskTopEntryLinux_Type = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_TYPE, ""); data.deskTopEntryLinux_URL = substitutor.substitute(shortcutSpec.getAttribute( SPEC_ATTRIBUTE_URL, ""), null); data.deskTopEntryLinux_X_KDE_SubstituteUID = shortcutSpec.getAttribute( SPEC_ATTRIBUTE_KDE_SUBST_UID, ""); data.createForAll = Boolean.valueOf(shortcutSpec.getAttribute(CREATE_FOR_ALL, "false")); //** EndOf LINUX **// temp = fixSeparatorChar(shortcutSpec.getAttribute(SPEC_ATTRIBUTE_TARGET, "")); data.target = substitutor.substitute(temp, null); temp = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_COMMAND, ""); data.commandLine = substitutor.substitute(temp, null); temp = fixSeparatorChar(shortcutSpec.getAttribute(SPEC_ATTRIBUTE_ICON, "")); data.iconFile = substitutor.substitute(temp, null); data.iconIndex = Integer.parseInt(shortcutSpec.getAttribute(SPEC_ATTRIBUTE_ICON_INDEX, "0")); temp = fixSeparatorChar(shortcutSpec.getAttribute(SPEC_ATTRIBUTE_WORKING_DIR, "")); data.workingDirectory = substitutor.substitute(temp, null); String initialState = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_INITIAL_STATE, ""); if (initialState.equals(SPEC_VALUE_NO_SHOW)) { data.initialState = Shortcut.HIDE; } else if (initialState.equals(SPEC_VALUE_NORMAL)) { data.initialState = Shortcut.NORMAL; } else if (initialState.equals(SPEC_VALUE_MAXIMIZED)) { data.initialState = Shortcut.MAXIMIZED; } else if (initialState.equals(SPEC_VALUE_MINIMIZED)) { data.initialState = Shortcut.MINIMIZED; } else { data.initialState = Shortcut.NORMAL; } // -------------------------------------------------- // if the minimal data requirements are met to create // the shortcut, create one entry each for each of // the requested types. // Eventually this will cause the creation of one // shortcut in each of the associated locations. // -------------------------------------------------- // without a name we can not create a shortcut if (data.name == null) { continue; } //1. Elmar: "Without a target we can not create a shortcut." //2. Marc: "No, Even on Linux a Link can be an URL and has no target." if (data.target == null) { continue; } // the shortcut is not actually required for any of the selected packs Vector forPacks = shortcutSpec.getChildrenNamed(SPEC_KEY_PACKS); if (!shortcutRequiredFor(forPacks)) { continue; } // -------------------------------------------------- // This section is executed if we don't skip. // -------------------------------------------------- // For each of the categories set the type and if // the link should be placed in the program group, // then clone the data set to obtain an independent // instance and add this to the list of shortcuts // to be created. In this way, we will set up an // identical copy for each of the locations at which // a shortcut should be placed. Therefore you must // not use 'else if' statements! // -------------------------------------------------- { if (attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_DESKTOP)) { hasDesktopShortcuts = true; data.addToGroup = false; data.type = Shortcut.DESKTOP; shortcuts.add(data.clone()); } if (attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_APPLICATIONS)) { data.addToGroup = false; data.type = Shortcut.APPLICATIONS; shortcuts.add(data.clone()); } if (attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_START_MENU)) { data.addToGroup = false; data.type = Shortcut.START_MENU; shortcuts.add(data.clone()); } if (attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_STARTUP)) { data.addToGroup = false; data.type = Shortcut.START_UP; shortcuts.add(data.clone()); } if (attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_PROGRAM_GROUP)) { data.addToGroup = true; data.type = Shortcut.APPLICATIONS; shortcuts.add(data.clone()); } } } // ---------------------------------------------------- // signal if there are any shortcuts to create // ---------------------------------------------------- if (shortcuts.size() > 0) { shortcutsToCreate = true; } }

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private boolean attributeIsTrue(XMLElement element, String name) { String value = element.getAttribute(name, "").toUpperCase(); if (value.equals("YES")) { return (true); } else if (value.equals("TRUE")) { return (true); } else if (value.equals("ON")) { return (true); } else if (value.equals("1")) { return (true); } return (false); }

private boolean attributeIsTrue(XMLElement element, String name) { String value = element.getAttribute(name, "").toUpperCase(); if ("YES".equals(value)) { return (true); } else if (value.equals("TRUE")) { return (true); } else if (value.equals("ON")) { return (true); } else if (value.equals("1")) { return (true); } return (false); }

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private boolean attributeIsTrue(XMLElement element, String name) { String value = element.getAttribute(name, "").toUpperCase(); if (value.equals("YES")) { return (true); } else if (value.equals("TRUE")) { return (true); } else if (value.equals("ON")) { return (true); } else if (value.equals("1")) { return (true); } return (false); }

private boolean attributeIsTrue(XMLElement element, String name) { String value = element.getAttribute(name, "").toUpperCase(); if (value.equals("YES")) { return (true); } else if ("TRUE".equals(value)) { return (true); } else if (value.equals("ON")) { return (true); } else if (value.equals("1")) { return (true); } return (false); }

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private boolean attributeIsTrue(XMLElement element, String name) { String value = element.getAttribute(name, "").toUpperCase(); if (value.equals("YES")) { return (true); } else if (value.equals("TRUE")) { return (true); } else if (value.equals("ON")) { return (true); } else if (value.equals("1")) { return (true); } return (false); }

private boolean attributeIsTrue(XMLElement element, String name) { String value = element.getAttribute(name, "").toUpperCase(); if (value.equals("YES")) { return (true); } else if (value.equals("TRUE")) { return (true); } else if ("ON".equals(value)) { return (true); } else if (value.equals("1")) { return (true); } return (false); }

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private boolean attributeIsTrue(XMLElement element, String name) { String value = element.getAttribute(name, "").toUpperCase(); if (value.equals("YES")) { return (true); } else if (value.equals("TRUE")) { return (true); } else if (value.equals("ON")) { return (true); } else if (value.equals("1")) { return (true); } return (false); }

private boolean attributeIsTrue(XMLElement element, String name) { String value = element.getAttribute(name, "").toUpperCase(); if (value.equals("YES")) { return (true); } else if (value.equals("TRUE")) { return (true); } else if (value.equals("ON")) { return (true); } else if ("1".equals(value)) { return (true); } return (false); }

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private void buildAlternateUI() { layout = new GridBagLayout(); constraints = new GridBagConstraints(); setLayout(layout); // ---------------------------------------------------- // static text a the top of the panel, that apologizes // about the fact that we can not create shortcuts on // this particular target OS. // ---------------------------------------------------- MultiLineLabel apologyLabel = new MultiLineLabel(parent.langpack .getString("ShortcutPanel.alternate.apology"), 0, 0); constraints.gridx = 0; constraints.gridy = 0; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.weightx = 1.0; constraints.weighty = 1.0; constraints.insets = new Insets(5, 5, 5, 5); constraints.fill = GridBagConstraints.HORIZONTAL; constraints.anchor = GridBagConstraints.WEST; layout.addLayoutComponent(apologyLabel, constraints); add(apologyLabel); // ---------------------------------------------------- // label that explains the significance ot the list box // ---------------------------------------------------- MultiLineLabel listLabel = new MultiLineLabel(parent.langpack .getString("ShortcutPanel.alternate.targetsLabel"), 0, 0); constraints.gridx = 0; constraints.gridy = 1; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.weightx = 1.0; constraints.weighty = 1.0; layout.addLayoutComponent(listLabel, constraints); add(listLabel); // ---------------------------------------------------- // list box to list all of the intended shortcut targets // ---------------------------------------------------- Vector targets = new Vector(); for (int i = 0; i < shortcuts.size(); i++) { targets.add(((ShortcutData) shortcuts.elementAt(i)).target); } targetList = new JList(targets); JScrollPane scrollPane = new JScrollPane(targetList); constraints.gridx = 0; constraints.gridy = 2; constraints.fill = GridBagConstraints.BOTH; layout.addLayoutComponent(scrollPane, constraints); add(scrollPane); // ---------------------------------------------------- // static text that explains about the text file // ---------------------------------------------------- MultiLineLabel fileExplanation = new MultiLineLabel(parent.langpack .getString("ShortcutPanel.alternate.textFileExplanation"), 0, 0); constraints.gridx = 0; constraints.gridy = 3; constraints.weightx = 1.0; constraints.weighty = 1.0; constraints.fill = GridBagConstraints.HORIZONTAL; layout.addLayoutComponent(fileExplanation, constraints); add(fileExplanation); // ---------------------------------------------------- // button to save the text file // ---------------------------------------------------- saveButton = ButtonFactory.createButton(parent.langpack .getString("ShortcutPanel.alternate.saveButton"), idata.buttonsHColor); saveButton.addActionListener(this); constraints.gridx = 0; constraints.gridy = 4; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.fill = GridBagConstraints.NONE; constraints.anchor = GridBagConstraints.CENTER; layout.addLayoutComponent(saveButton, constraints); add(saveButton); }

private void buildAlternateUI() { layout = new GridBagLayout(); constraints = new GridBagConstraints(); setLayout(layout); // ---------------------------------------------------- // static text a the top of the panel, that apologizes // about the fact that we can not create shortcuts on // this particular target OS. // ---------------------------------------------------- MultiLineLabel apologyLabel = new MultiLineLabel(parent.langpack .getString("ShortcutPanel.alternate.apology"), 0, 0); constraints.gridx = 0; constraints.gridy = 0; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.weightx = 1.0; constraints.weighty = 1.0; constraints.insets = new Insets(5, 5, 5, 5); constraints.fill = GridBagConstraints.HORIZONTAL; constraints.anchor = GridBagConstraints.WEST; layout.addLayoutComponent(apologyLabel, constraints); add(apologyLabel); // ---------------------------------------------------- // label that explains the significance ot the list box // ---------------------------------------------------- MultiLineLabel listLabel = new MultiLineLabel(parent.langpack .getString("ShortcutPanel.alternate.targetsLabel"), 0, 0); constraints.gridx = 0; constraints.gridy = 1; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.weightx = 1.0; constraints.weighty = 1.0; layout.addLayoutComponent(listLabel, constraints); add(listLabel); // ---------------------------------------------------- // list box to list all of the intended shortcut targets // ---------------------------------------------------- Vector targets = new Vector(); for (int i = 0; i < shortcuts.size(); i++) { targets.add(((ShortcutData) shortcuts.elementAt(i)).target); } JList targetList = new JList(targets); JScrollPane scrollPane = new JScrollPane(targetList); constraints.gridx = 0; constraints.gridy = 2; constraints.fill = GridBagConstraints.BOTH; layout.addLayoutComponent(scrollPane, constraints); add(scrollPane); // ---------------------------------------------------- // static text that explains about the text file // ---------------------------------------------------- MultiLineLabel fileExplanation = new MultiLineLabel(parent.langpack .getString("ShortcutPanel.alternate.textFileExplanation"), 0, 0); constraints.gridx = 0; constraints.gridy = 3; constraints.weightx = 1.0; constraints.weighty = 1.0; constraints.fill = GridBagConstraints.HORIZONTAL; layout.addLayoutComponent(fileExplanation, constraints); add(fileExplanation); // ---------------------------------------------------- // button to save the text file // ---------------------------------------------------- saveButton = ButtonFactory.createButton(parent.langpack .getString("ShortcutPanel.alternate.saveButton"), idata.buttonsHColor); saveButton.addActionListener(this); constraints.gridx = 0; constraints.gridy = 4; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.fill = GridBagConstraints.NONE; constraints.anchor = GridBagConstraints.CENTER; layout.addLayoutComponent(saveButton, constraints); add(saveButton); }

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private void buildUI(File groups) { itsProgramFolder = groups; constraints.gridx = 0; constraints.gridy = 0; constraints.gridwidth = 3; constraints.gridheight = 1; constraints.weightx = 1.0; constraints.weighty = 1.0; constraints.fill = GridBagConstraints.HORIZONTAL; constraints.anchor = GridBagConstraints.WEST; /**/ // Add a CheckBox which enables the user to entirely supress shortcut creation. String menuKind = parent.langpack.getString("ShortcutPanel.regular.StartMenu:Start-Menu"); if( OsVersion.IS_UNIX && UnixHelper.kdeIsInstalled() ) menuKind = parent.langpack.getString("ShortcutPanel.regular.StartMenu:K-Menu"); createShortcuts = new JCheckBox( StringTool.replace( parent.langpack.getString("ShortcutPanel.regular.create"), "StartMenu", menuKind ), true); createShortcuts.addActionListener(this); constraints.gridx = 0; constraints.gridy = 1; constraints.gridwidth = 2; constraints.gridheight = 1; constraints.weighty = 0.2; layout.addLayoutComponent(createShortcuts, constraints); add(createShortcuts); // ---------------------------------------------------- // check box to allow the user to decide if a desktop // shortcut should be created. // this should only be created if needed and requested // in the definition file. // ---------------------------------------------------- if (hasDesktopShortcuts) { String initialAllowedValue = idata.getVariable( "DesktopShortcutCheckboxEnabled" ); boolean initialAllowedFlag = false; if( initialAllowedValue==null) initialAllowedFlag= false; else if( Boolean.TRUE.toString().equals(initialAllowedValue) ) initialAllowedFlag=true; allowDesktopShortcut = new JCheckBox(parent.langpack .getString("ShortcutPanel.regular.desktop"), initialAllowedFlag); constraints.gridx = 0; constraints.gridy = 2; constraints.gridwidth = 3; constraints.gridheight = 1; constraints.weighty = 0.2; layout.addLayoutComponent(allowDesktopShortcut, constraints); add(allowDesktopShortcut); } listLabel = LabelFactory.create(parent.langpack.getString("ShortcutPanel.regular.list"), JLabel.LEADING); constraints.gridx = 0; constraints.gridy = 3; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.weightx = 0.2; constraints.weighty = 0.2; constraints.fill = GridBagConstraints.NONE; constraints.anchor = GridBagConstraints.WEST; layout.addLayoutComponent(listLabel, constraints); add(listLabel); // ---------------------------------------------------- // list box to list all of already existing folders as program groups // at the intended destination // ---------------------------------------------------- addSelectionList( groups, 0, 4, 2, 1, GridBagConstraints.BOTH ); // ---------------------------------------------------- // radio buttons to select current user or all users. // ---------------------------------------------------- if (shortcut.multipleUsers()) { JPanel usersPanel = new JPanel(new GridLayout(2, 1)); ButtonGroup usersGroup = new ButtonGroup(); currentUser = new JRadioButton(parent.langpack .getString("ShortcutPanel.regular.currentUser"), !isRootUser); currentUser.addActionListener(this); usersGroup.add(currentUser); usersPanel.add(currentUser); allUsers = new JRadioButton( parent.langpack.getString("ShortcutPanel.regular.allUsers"), isRootUser); if (!isRootUser) allUsers.setEnabled(false); allUsers.addActionListener(this); usersGroup.add(allUsers); usersPanel.add(allUsers); TitledBorder border = new TitledBorder(new EmptyBorder(2, 2, 2, 2), parent.langpack .getString("ShortcutPanel.regular.userIntro")); usersPanel.setBorder(border); constraints.gridx = 2; constraints.gridy = 4; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.weighty = 1.0; constraints.weightx = 1.0; constraints.fill = GridBagConstraints.NONE; layout.addLayoutComponent(usersPanel, constraints); add(usersPanel); } // ---------------------------------------------------- // edit box that contains the suggested program group // name, which can be modfied or substituted from the // list by the user // ---------------------------------------------------- programGroup = new JTextField(suggestedProgramGroup, 40); // 40? constraints.gridx = 0; constraints.gridy = 5; constraints.gridwidth = 2; constraints.gridheight = 1; constraints.weighty = 1.0; constraints.weightx = 10.0; constraints.fill = GridBagConstraints.HORIZONTAL; layout.addLayoutComponent(programGroup, constraints); add(programGroup); // ---------------------------------------------------- // reset button that allows the user to revert to the // original suggestion for the program group // ---------------------------------------------------- defaultButton = ButtonFactory.createButton(parent.langpack .getString("ShortcutPanel.regular.default"), idata.buttonsHColor); defaultButton.addActionListener(this); constraints.gridx = 2; constraints.gridy = 5; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.fill = GridBagConstraints.NONE; layout.addLayoutComponent(defaultButton, constraints); add(defaultButton); }

private void buildUI(File groups) { File itsProgramFolder = groups; constraints.gridx = 0; constraints.gridy = 0; constraints.gridwidth = 3; constraints.gridheight = 1; constraints.weightx = 1.0; constraints.weighty = 1.0; constraints.fill = GridBagConstraints.HORIZONTAL; constraints.anchor = GridBagConstraints.WEST; /**/ // Add a CheckBox which enables the user to entirely supress shortcut creation. String menuKind = parent.langpack.getString("ShortcutPanel.regular.StartMenu:Start-Menu"); if( OsVersion.IS_UNIX && UnixHelper.kdeIsInstalled() ) menuKind = parent.langpack.getString("ShortcutPanel.regular.StartMenu:K-Menu"); createShortcuts = new JCheckBox( StringTool.replace( parent.langpack.getString("ShortcutPanel.regular.create"), "StartMenu", menuKind ), true); createShortcuts.addActionListener(this); constraints.gridx = 0; constraints.gridy = 1; constraints.gridwidth = 2; constraints.gridheight = 1; constraints.weighty = 0.2; layout.addLayoutComponent(createShortcuts, constraints); add(createShortcuts); // ---------------------------------------------------- // check box to allow the user to decide if a desktop // shortcut should be created. // this should only be created if needed and requested // in the definition file. // ---------------------------------------------------- if (hasDesktopShortcuts) { String initialAllowedValue = idata.getVariable( "DesktopShortcutCheckboxEnabled" ); boolean initialAllowedFlag = false; if( initialAllowedValue==null) initialAllowedFlag= false; else if( Boolean.TRUE.toString().equals(initialAllowedValue) ) initialAllowedFlag=true; allowDesktopShortcut = new JCheckBox(parent.langpack .getString("ShortcutPanel.regular.desktop"), initialAllowedFlag); constraints.gridx = 0; constraints.gridy = 2; constraints.gridwidth = 3; constraints.gridheight = 1; constraints.weighty = 0.2; layout.addLayoutComponent(allowDesktopShortcut, constraints); add(allowDesktopShortcut); } listLabel = LabelFactory.create(parent.langpack.getString("ShortcutPanel.regular.list"), JLabel.LEADING); constraints.gridx = 0; constraints.gridy = 3; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.weightx = 0.2; constraints.weighty = 0.2; constraints.fill = GridBagConstraints.NONE; constraints.anchor = GridBagConstraints.WEST; layout.addLayoutComponent(listLabel, constraints); add(listLabel); // ---------------------------------------------------- // list box to list all of already existing folders as program groups // at the intended destination // ---------------------------------------------------- addSelectionList( groups, 0, 4, 2, 1, GridBagConstraints.BOTH ); // ---------------------------------------------------- // radio buttons to select current user or all users. // ---------------------------------------------------- if (shortcut.multipleUsers()) { JPanel usersPanel = new JPanel(new GridLayout(2, 1)); ButtonGroup usersGroup = new ButtonGroup(); currentUser = new JRadioButton(parent.langpack .getString("ShortcutPanel.regular.currentUser"), !isRootUser); currentUser.addActionListener(this); usersGroup.add(currentUser); usersPanel.add(currentUser); allUsers = new JRadioButton( parent.langpack.getString("ShortcutPanel.regular.allUsers"), isRootUser); if (!isRootUser) allUsers.setEnabled(false); allUsers.addActionListener(this); usersGroup.add(allUsers); usersPanel.add(allUsers); TitledBorder border = new TitledBorder(new EmptyBorder(2, 2, 2, 2), parent.langpack .getString("ShortcutPanel.regular.userIntro")); usersPanel.setBorder(border); constraints.gridx = 2; constraints.gridy = 4; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.weighty = 1.0; constraints.weightx = 1.0; constraints.fill = GridBagConstraints.NONE; layout.addLayoutComponent(usersPanel, constraints); add(usersPanel); } // ---------------------------------------------------- // edit box that contains the suggested program group // name, which can be modfied or substituted from the // list by the user // ---------------------------------------------------- programGroup = new JTextField(suggestedProgramGroup, 40); // 40? constraints.gridx = 0; constraints.gridy = 5; constraints.gridwidth = 2; constraints.gridheight = 1; constraints.weighty = 1.0; constraints.weightx = 10.0; constraints.fill = GridBagConstraints.HORIZONTAL; layout.addLayoutComponent(programGroup, constraints); add(programGroup); // ---------------------------------------------------- // reset button that allows the user to revert to the // original suggestion for the program group // ---------------------------------------------------- defaultButton = ButtonFactory.createButton(parent.langpack .getString("ShortcutPanel.regular.default"), idata.buttonsHColor); defaultButton.addActionListener(this); constraints.gridx = 2; constraints.gridy = 5; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.fill = GridBagConstraints.NONE; layout.addLayoutComponent(defaultButton, constraints); add(defaultButton); }

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private void buildUI(File groups) { itsProgramFolder = groups; constraints.gridx = 0; constraints.gridy = 0; constraints.gridwidth = 3; constraints.gridheight = 1; constraints.weightx = 1.0; constraints.weighty = 1.0; constraints.fill = GridBagConstraints.HORIZONTAL; constraints.anchor = GridBagConstraints.WEST; /**/ // Add a CheckBox which enables the user to entirely supress shortcut creation. String menuKind = parent.langpack.getString("ShortcutPanel.regular.StartMenu:Start-Menu"); if( OsVersion.IS_UNIX && UnixHelper.kdeIsInstalled() ) menuKind = parent.langpack.getString("ShortcutPanel.regular.StartMenu:K-Menu"); createShortcuts = new JCheckBox( StringTool.replace( parent.langpack.getString("ShortcutPanel.regular.create"), "StartMenu", menuKind ), true); createShortcuts.addActionListener(this); constraints.gridx = 0; constraints.gridy = 1; constraints.gridwidth = 2; constraints.gridheight = 1; constraints.weighty = 0.2; layout.addLayoutComponent(createShortcuts, constraints); add(createShortcuts); // ---------------------------------------------------- // check box to allow the user to decide if a desktop // shortcut should be created. // this should only be created if needed and requested // in the definition file. // ---------------------------------------------------- if (hasDesktopShortcuts) { String initialAllowedValue = idata.getVariable( "DesktopShortcutCheckboxEnabled" ); boolean initialAllowedFlag = false; if( initialAllowedValue==null) initialAllowedFlag= false; else if( Boolean.TRUE.toString().equals(initialAllowedValue) ) initialAllowedFlag=true; allowDesktopShortcut = new JCheckBox(parent.langpack .getString("ShortcutPanel.regular.desktop"), initialAllowedFlag); constraints.gridx = 0; constraints.gridy = 2; constraints.gridwidth = 3; constraints.gridheight = 1; constraints.weighty = 0.2; layout.addLayoutComponent(allowDesktopShortcut, constraints); add(allowDesktopShortcut); } listLabel = LabelFactory.create(parent.langpack.getString("ShortcutPanel.regular.list"), JLabel.LEADING); constraints.gridx = 0; constraints.gridy = 3; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.weightx = 0.2; constraints.weighty = 0.2; constraints.fill = GridBagConstraints.NONE; constraints.anchor = GridBagConstraints.WEST; layout.addLayoutComponent(listLabel, constraints); add(listLabel); // ---------------------------------------------------- // list box to list all of already existing folders as program groups // at the intended destination // ---------------------------------------------------- addSelectionList( groups, 0, 4, 2, 1, GridBagConstraints.BOTH ); // ---------------------------------------------------- // radio buttons to select current user or all users. // ---------------------------------------------------- if (shortcut.multipleUsers()) { JPanel usersPanel = new JPanel(new GridLayout(2, 1)); ButtonGroup usersGroup = new ButtonGroup(); currentUser = new JRadioButton(parent.langpack .getString("ShortcutPanel.regular.currentUser"), !isRootUser); currentUser.addActionListener(this); usersGroup.add(currentUser); usersPanel.add(currentUser); allUsers = new JRadioButton( parent.langpack.getString("ShortcutPanel.regular.allUsers"), isRootUser); if (!isRootUser) allUsers.setEnabled(false); allUsers.addActionListener(this); usersGroup.add(allUsers); usersPanel.add(allUsers); TitledBorder border = new TitledBorder(new EmptyBorder(2, 2, 2, 2), parent.langpack .getString("ShortcutPanel.regular.userIntro")); usersPanel.setBorder(border); constraints.gridx = 2; constraints.gridy = 4; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.weighty = 1.0; constraints.weightx = 1.0; constraints.fill = GridBagConstraints.NONE; layout.addLayoutComponent(usersPanel, constraints); add(usersPanel); } // ---------------------------------------------------- // edit box that contains the suggested program group // name, which can be modfied or substituted from the // list by the user // ---------------------------------------------------- programGroup = new JTextField(suggestedProgramGroup, 40); // 40? constraints.gridx = 0; constraints.gridy = 5; constraints.gridwidth = 2; constraints.gridheight = 1; constraints.weighty = 1.0; constraints.weightx = 10.0; constraints.fill = GridBagConstraints.HORIZONTAL; layout.addLayoutComponent(programGroup, constraints); add(programGroup); // ---------------------------------------------------- // reset button that allows the user to revert to the // original suggestion for the program group // ---------------------------------------------------- defaultButton = ButtonFactory.createButton(parent.langpack .getString("ShortcutPanel.regular.default"), idata.buttonsHColor); defaultButton.addActionListener(this); constraints.gridx = 2; constraints.gridy = 5; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.fill = GridBagConstraints.NONE; layout.addLayoutComponent(defaultButton, constraints); add(defaultButton); }

private void buildUI(File groups) { itsProgramFolder = groups; constraints.gridx = 0; constraints.gridy = 0; constraints.gridwidth = 3; constraints.gridheight = 1; constraints.weightx = 1.0; constraints.weighty = 1.0; constraints.fill = GridBagConstraints.HORIZONTAL; constraints.anchor = GridBagConstraints.WEST; /**/ // Add a CheckBox which enables the user to entirely supress shortcut creation. String menuKind = parent.langpack.getString("ShortcutPanel.regular.StartMenu:Start-Menu"); if( OsVersion.IS_UNIX && UnixHelper.kdeIsInstalled() ) menuKind = parent.langpack.getString("ShortcutPanel.regular.StartMenu:K-Menu"); createShortcuts = new JCheckBox( StringTool.replace( parent.langpack.getString("ShortcutPanel.regular.create"), "StartMenu", menuKind ), true); createShortcuts.addActionListener(this); constraints.gridx = 0; constraints.gridy = 1; constraints.gridwidth = 2; constraints.gridheight = 1; constraints.weighty = 0.2; layout.addLayoutComponent(createShortcuts, constraints); add(createShortcuts); // ---------------------------------------------------- // check box to allow the user to decide if a desktop // shortcut should be created. // this should only be created if needed and requested // in the definition file. // ---------------------------------------------------- if (hasDesktopShortcuts) { String initialAllowedValue = idata.getVariable( "DesktopShortcutCheckboxEnabled" ); boolean initialAllowedFlag = false; if( initialAllowedValue==null) initialAllowedFlag= false; else if( Boolean.TRUE.toString().equals(initialAllowedValue) ) initialAllowedFlag=true; allowDesktopShortcut = new JCheckBox(parent.langpack .getString("ShortcutPanel.regular.desktop"), initialAllowedFlag); constraints.gridx = 0; constraints.gridy = 2; constraints.gridwidth = 3; constraints.gridheight = 1; constraints.weighty = 0.2; layout.addLayoutComponent(allowDesktopShortcut, constraints); add(allowDesktopShortcut); } JLabel listLabel = LabelFactory.create(parent.langpack.getString("ShortcutPanel.regular.list"), JLabel.LEADING); constraints.gridx = 0; constraints.gridy = 3; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.weightx = 0.2; constraints.weighty = 0.2; constraints.fill = GridBagConstraints.NONE; constraints.anchor = GridBagConstraints.WEST; layout.addLayoutComponent(listLabel, constraints); add(listLabel); // ---------------------------------------------------- // list box to list all of already existing folders as program groups // at the intended destination // ---------------------------------------------------- addSelectionList( groups, 0, 4, 2, 1, GridBagConstraints.BOTH ); // ---------------------------------------------------- // radio buttons to select current user or all users. // ---------------------------------------------------- if (shortcut.multipleUsers()) { JPanel usersPanel = new JPanel(new GridLayout(2, 1)); ButtonGroup usersGroup = new ButtonGroup(); currentUser = new JRadioButton(parent.langpack .getString("ShortcutPanel.regular.currentUser"), !isRootUser); currentUser.addActionListener(this); usersGroup.add(currentUser); usersPanel.add(currentUser); allUsers = new JRadioButton( parent.langpack.getString("ShortcutPanel.regular.allUsers"), isRootUser); if (!isRootUser) allUsers.setEnabled(false); allUsers.addActionListener(this); usersGroup.add(allUsers); usersPanel.add(allUsers); TitledBorder border = new TitledBorder(new EmptyBorder(2, 2, 2, 2), parent.langpack .getString("ShortcutPanel.regular.userIntro")); usersPanel.setBorder(border); constraints.gridx = 2; constraints.gridy = 4; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.weighty = 1.0; constraints.weightx = 1.0; constraints.fill = GridBagConstraints.NONE; layout.addLayoutComponent(usersPanel, constraints); add(usersPanel); } // ---------------------------------------------------- // edit box that contains the suggested program group // name, which can be modfied or substituted from the // list by the user // ---------------------------------------------------- programGroup = new JTextField(suggestedProgramGroup, 40); // 40? constraints.gridx = 0; constraints.gridy = 5; constraints.gridwidth = 2; constraints.gridheight = 1; constraints.weighty = 1.0; constraints.weightx = 10.0; constraints.fill = GridBagConstraints.HORIZONTAL; layout.addLayoutComponent(programGroup, constraints); add(programGroup); // ---------------------------------------------------- // reset button that allows the user to revert to the // original suggestion for the program group // ---------------------------------------------------- defaultButton = ButtonFactory.createButton(parent.langpack .getString("ShortcutPanel.regular.default"), idata.buttonsHColor); defaultButton.addActionListener(this); constraints.gridx = 2; constraints.gridy = 5; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.fill = GridBagConstraints.NONE; layout.addLayoutComponent(defaultButton, constraints); add(defaultButton); }

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private void createShortcuts() { if (!create) return; ShortcutData data; String tmpgn; for (int i = 0; i < shortcuts.size(); i++) { data = (ShortcutData) shortcuts.elementAt(i); try { //The cloning guarantees that data.subgroup will not be null. //See ShortcutData.cloneString if (data.subgroup.length() > 0 && (data.subgroup.charAt(0) == '/' || data.subgroup.charAt(0) == '\\')) { tmpgn = groupName + data.subgroup; } else { tmpgn = groupName + File.separator + data.subgroup; } shortcut.setUserType(itsUserType); shortcut.setLinkName(data.name); shortcut.setLinkType(data.type); shortcut.setArguments(data.commandLine); shortcut.setDescription(data.description); shortcut.setIconLocation(data.iconFile, data.iconIndex); shortcut.setShowCommand(data.initialState); shortcut.setTargetPath(data.target); shortcut.setWorkingDirectory(data.workingDirectory); shortcut.setEncoding(data.deskTopEntryLinux_Encoding); shortcut.setMimetype(data.deskTopEntryLinux_MimeType); shortcut.setTerminal(data.deskTopEntryLinux_Terminal); shortcut.setTerminalOptions(data.deskTopEntryLinux_TerminalOptions); shortcut.setType(data.deskTopEntryLinux_Type); shortcut.setKdeSubstUID(data.deskTopEntryLinux_X_KDE_SubstituteUID); shortcut.setURL(data.deskTopEntryLinux_URL); shortcut.setCreateForAll(data.createForAll); if (data.addToGroup) { shortcut.setProgramGroup(tmpgn); } else { shortcut.setProgramGroup(""); } try { // ---------------------------------------------- // save the shortcut only if it is either not on // the desktop or if it is on the desktop and // the user has signalled that it is ok to place // shortcuts on the desktop. // ---------------------------------------------- if ((data.type != Shortcut.DESKTOP) || ((data.type == Shortcut.DESKTOP) && allowDesktopShortcut .isSelected())) { // save the shortcut shortcut.save(); // add the file and directory name to the file list String fileName = shortcut.getFileName(); files.add(0, fileName); File file = new File(fileName); File base = new File(shortcut.getBasePath()); Vector intermediates = new Vector(); //String directoryName = shortcut.getDirectoryCreated (); execFiles.add(new ExecutableFile(fileName, 2, ExecutableFile.WARN, new ArrayList(), false)); files.add(fileName); while ((file = file.getParentFile()) != null) { if (file.equals(base)) break; intermediates.add(file); } if (file != null) { for (Iterator iter = intermediates.iterator(); iter.hasNext();) files.add(0, iter.next().toString()); } } } catch (Exception exception) {} } catch (Throwable exception) { continue; } } // try { if (execFiles != null) { FileExecutor executor = new FileExecutor(execFiles); // // TODO: Hi Guys, // TODO The following commented-out line sometimes produces an uncatchable // nullpointer Exception! // TODO evaluate for what reason the files should exec. // TODO if there is a serious explanation, why to do that, // TODO the code must be more robust //evaluate executor.executeFiles( ExecutableFile.NEVER, null ); } } catch (NullPointerException nep) { nep.printStackTrace(); } catch (RuntimeException cannot) { cannot.printStackTrace(); } parent.unlockNextButton(); }

private void createShortcuts() { if (!create) return; ShortcutData data; String tmpgn; for (int i = 0; i < shortcuts.size(); i++) { data = (ShortcutData) shortcuts.elementAt(i); try { //The cloning guarantees that data.subgroup will not be null. //See ShortcutData.cloneString if (data.subgroup.length() > 0 && (data.subgroup.charAt(0) == '/' || data.subgroup.charAt(0) == '\\')) { tmpgn = groupName + data.subgroup; } else { tmpgn = groupName + File.separator + data.subgroup; } shortcut.setUserType(itsUserType); shortcut.setLinkName(data.name); shortcut.setLinkType(data.type); shortcut.setArguments(data.commandLine); shortcut.setDescription(data.description); shortcut.setIconLocation(data.iconFile, data.iconIndex); shortcut.setShowCommand(data.initialState); shortcut.setTargetPath(data.target); shortcut.setWorkingDirectory(data.workingDirectory); shortcut.setEncoding(data.deskTopEntryLinux_Encoding); shortcut.setMimetype(data.deskTopEntryLinux_MimeType); shortcut.setTerminal(data.deskTopEntryLinux_Terminal); shortcut.setTerminalOptions(data.deskTopEntryLinux_TerminalOptions); shortcut.setType(data.deskTopEntryLinux_Type); shortcut.setKdeSubstUID(data.deskTopEntryLinux_X_KDE_SubstituteUID); shortcut.setURL(data.deskTopEntryLinux_URL); shortcut.setCreateForAll(data.createForAll); if (data.addToGroup) { shortcut.setProgramGroup(tmpgn); } else { shortcut.setProgramGroup(""); } try { // ---------------------------------------------- // save the shortcut only if it is either not on // the desktop or if it is on the desktop and // the user has signalled that it is ok to place // shortcuts on the desktop. // ---------------------------------------------- if ((data.type != Shortcut.DESKTOP) || ((data.type == Shortcut.DESKTOP) && allowDesktopShortcut .isSelected())) { // save the shortcut shortcut.save(); // add the file and directory name to the file list String fileName = shortcut.getFileName(); files.add(0, fileName); File file = new File(fileName); File base = new File(shortcut.getBasePath()); Vector intermediates = new Vector(); //String directoryName = shortcut.getDirectoryCreated (); execFiles.add(new ExecutableFile(fileName, 2, ExecutableFile.WARN, new ArrayList(), false)); files.add(fileName); while ((file = file.getParentFile()) != null) { if (file.equals(base)) break; intermediates.add(file); } if (file != null) { for (Iterator iter = intermediates.iterator(); iter.hasNext();) files.add(0, iter.next().toString()); } } } catch (Exception exception) {} } catch (Throwable exception) { } } // try { if (execFiles != null) { FileExecutor executor = new FileExecutor(execFiles); // // TODO: Hi Guys, // TODO The following commented-out line sometimes produces an uncatchable // nullpointer Exception! // TODO evaluate for what reason the files should exec. // TODO if there is a serious explanation, why to do that, // TODO the code must be more robust //evaluate executor.executeFiles( ExecutableFile.NEVER, null ); } } catch (NullPointerException nep) { nep.printStackTrace(); } catch (RuntimeException cannot) { cannot.printStackTrace(); } parent.unlockNextButton(); }

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public void actionPerformed(ActionEvent event) { Object eventSource = event.getSource(); /*if (eventSource != null) { System.out.println("Instance Of : " + eventSource.getClass().getName()); }*/ // ---------------------------------------------------- // create shortcut for the current user was selected // refresh the list of program groups accordingly and // reset the program group to the default setting. // ---------------------------------------------------- if (eventSource.equals(currentUser)) { groupList.setListData(shortcut.getProgramGroups(Shortcut.CURRENT_USER)); programGroup.setText(suggestedProgramGroup); shortcut.setUserType(itsUserType = Shortcut.CURRENT_USER); return; } // ---------------------------------------------------- // create shortcut for all users was selected // refresh the list of program groups accordingly and // reset the program group to the default setting. // ---------------------------------------------------- else if (eventSource.equals(allUsers)) { groupList.setListData(shortcut.getProgramGroups(Shortcut.ALL_USERS)); programGroup.setText(suggestedProgramGroup); shortcut.setUserType(itsUserType = Shortcut.ALL_USERS); return; } // ---------------------------------------------------- // The reset button was pressed. // - clear the selection in the list box, because the // selection is no longer valid // - refill the program group edit control with the // suggested program group name // ---------------------------------------------------- else if (eventSource.equals(defaultButton)) { groupList.getSelectionModel().clearSelection(); programGroup.setText(suggestedProgramGroup); return; } // ---------------------------------------------------- // the save button was pressed. This is a request to // save shortcut information to a text file. // ---------------------------------------------------- else if (eventSource.equals(saveButton)) { saveToFile(); // add the file to the uninstaller addToUninstaller(); return; } else if (eventSource.equals(createShortcuts)) { create = createShortcuts.isSelected(); if (groupList != null) { groupList.setEnabled(create); } programGroup.setEnabled(create); currentUser.setEnabled(create); defaultButton.setEnabled(create); // ** There where no Desktop Links or not allowed, this may be null: **// if (allowDesktopShortcut != null) { allowDesktopShortcut.setEnabled(create); } if (isRootUser) { allUsers.setEnabled(create); } } }

3,240,315

private void analyzeShortcutSpec() { if (!haveShortcutSpec) { shortcutsToCreate = false; return; } XMLElement skipper = spec.getFirstChildNamed(SPEC_KEY_SKIP_IFNOT_SUPPORTED); skipIfNotSupported = (skipper != null); // ---------------------------------------------------- // find out if we should simulate a not supported // scenario // ---------------------------------------------------- XMLElement support = spec.getFirstChildNamed(SPEC_KEY_NOT_SUPPORTED); if (support != null) { simulteNotSupported = true; } // ---------------------------------------------------- // find out in which program group the shortcuts should // be placed and where this program group should be // located // ---------------------------------------------------- XMLElement group = spec.getFirstChildNamed(SPEC_KEY_PROGRAM_GROUP); String location = null; hasDesktopShortcuts = false; if (group != null) { suggestedProgramGroup = group.getAttribute(SPEC_ATTRIBUTE_DEFAULT_GROUP, ""); location = group.getAttribute(SPEC_ATTRIBUTE_LOCATION, SPEC_VALUE_APPLICATIONS); } else { suggestedProgramGroup = ""; location = SPEC_VALUE_APPLICATIONS; } if (location.equals(SPEC_VALUE_APPLICATIONS)) { groupLocation = Shortcut.APPLICATIONS; } else if (location.equals(SPEC_VALUE_START_MENU)) { groupLocation = Shortcut.START_MENU; } // ---------------------------------------------------- // create a list of all shortcuts that need to be // created, containing all details about each shortcut // ---------------------------------------------------- // String temp; Vector shortcutSpecs = spec.getChildrenNamed(SPEC_KEY_SHORTCUT); XMLElement shortcutSpec; ShortcutData data; shortCuts = new Vector(); for (int i = 0; i < shortcutSpecs.size(); i++) { // System.out.println( "Processing shortcut: " + i ); shortcutSpec = (XMLElement) shortcutSpecs.elementAt(i); if (!OsConstraint.oneMatchesCurrentSystem(shortcutSpec)) { continue; } // TODO: write log info INFO.info( "Checking Condition for " + // shortcutSpec.getAttribute( SPEC_ATTRIBUTE_NAME ) ); if (!checkConditions(shortcutSpec)) { continue; } // TODO write log info INFO.info( "Checked Condition for " + // shortcutSpec.getAttribute( SPEC_ATTRIBUTE_NAME ) ); data = new ShortcutData(); data.name = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_NAME); data.subgroup = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_SUBGROUP, ""); data.description = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_DESCRIPTION, ""); // ** Linux **// data.deskTopEntryLinux_Encoding = shortcutSpec .getAttribute(SPEC_ATTRIBUTE_ENCODING, ""); data.deskTopEntryLinux_MimeType = shortcutSpec .getAttribute(SPEC_ATTRIBUTE_MIMETYPE, ""); data.deskTopEntryLinux_Terminal = shortcutSpec .getAttribute(SPEC_ATTRIBUTE_TERMINAL, ""); data.deskTopEntryLinux_TerminalOptions = shortcutSpec.getAttribute( SPEC_ATTRIBUTE_TERMINAL_OPTIONS, ""); data.deskTopEntryLinux_Type = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_TYPE, ""); data.deskTopEntryLinux_URL = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_URL, ""); data.deskTopEntryLinux_X_KDE_SubstituteUID = shortcutSpec.getAttribute( SPEC_ATTRIBUTE_KDE_SUBST_UID, ""); data.createForAll = new Boolean(shortcutSpec.getAttribute(CREATE_FOR_ALL, "false")); // ** EndOf LINUX **// // temp = data.target = fixSeparatorChar(shortcutSpec.getAttribute(SPEC_ATTRIBUTE_TARGET, "")); // temp = data.commandLine = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_COMMAND, ""); // temp = data.iconFile = fixSeparatorChar(shortcutSpec.getAttribute(SPEC_ATTRIBUTE_ICON, "")); data.iconIndex = Integer.parseInt(shortcutSpec.getAttribute(SPEC_ATTRIBUTE_ICON_INDEX, "0")); // temp = data.workingDirectory = fixSeparatorChar(shortcutSpec.getAttribute( SPEC_ATTRIBUTE_WORKING_DIR, "")); String initialState = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_INITIAL_STATE, ""); if (initialState.equals(SPEC_VALUE_NO_SHOW)) { data.initialState = Shortcut.HIDE; } else if (initialState.equals(SPEC_VALUE_NORMAL)) { data.initialState = Shortcut.NORMAL; } else if (initialState.equals(SPEC_VALUE_MAXIMIZED)) { data.initialState = Shortcut.MAXIMIZED; } else if (initialState.equals(SPEC_VALUE_MINIMIZED)) { data.initialState = Shortcut.MINIMIZED; } else { data.initialState = Shortcut.NORMAL; } //LOG System.out.println("data.initialState: " + data.initialState); // -------------------------------------------------- // if the minimal data requirements are met to create // the shortcut, create one entry each for each of // the requested types. // Eventually this will cause the creation of one // shortcut in each of the associated locations. // -------------------------------------------------- // without a name we can not create a shortcut if (data.name == null) { continue; } // 1. Elmar: "Without a target we can not create a shortcut." // 2. Marc: "No, Even on Linux a Link can be an URL and has no target." if (data.target == null) { // TODO: write log info INFO.warn( "Shortcut: " + data + " has no target" ); data.target = ""; } // the shortcut is not actually required for any of the selected packs // the shortcut is not actually required for any of the selected packs // the shortcut is not actually required for any of the selected packs Vector forPacks = shortcutSpec.getChildrenNamed(SPEC_KEY_PACKS); if (!shortcutRequiredFor(forPacks)) { continue; } // -------------------------------------------------- // This section is executed if we don't skip. // -------------------------------------------------- // For each of the categories set the type and if // the link should be placed in the program group, // then clone the data set to obtain an independent // instance and add this to the list of shortcuts // to be created. In this way, we will set up an // identical copy for each of the locations at which // a shortcut should be placed. Therefore you must // not use 'else if' statements! // -------------------------------------------------- { if (XMLHelper.attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_DESKTOP)) { hasDesktopShortcuts = true; data.addToGroup = false; data.type = Shortcut.DESKTOP; shortcuts.add(data.clone()); } if (XMLHelper.attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_APPLICATIONS)) { data.addToGroup = false; data.type = Shortcut.APPLICATIONS; shortcuts.add(data.clone()); } if (XMLHelper.attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_START_MENU)) { data.addToGroup = false; data.type = Shortcut.START_MENU; shortcuts.add(data.clone()); } if (XMLHelper.attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_STARTUP)) { data.addToGroup = false; data.type = Shortcut.START_UP; shortcuts.add(data.clone()); } if (XMLHelper.attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_PROGRAM_GROUP)) { data.addToGroup = true; data.type = Shortcut.APPLICATIONS; shortcuts.add(data.clone()); } // / TODO: write log INFO.info( "data.name: " + data.name ); shortCuts.add((data.name == null) ? "" : data.name); // + " -> " + data.target + // " Type: " + data.type ); } } // ---------------------------------------------------- // signal if there are any shortcuts to create // ---------------------------------------------------- if (shortcuts.size() > 0) { shortcutsToCreate = true; } }

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private void analyzeShortcutSpec() { if (!haveShortcutSpec) { shortcutsToCreate = false; return; } XMLElement skipper = spec.getFirstChildNamed(SPEC_KEY_SKIP_IFNOT_SUPPORTED); skipIfNotSupported = (skipper != null); // ---------------------------------------------------- // find out if we should simulate a not supported // scenario // ---------------------------------------------------- XMLElement support = spec.getFirstChildNamed(SPEC_KEY_NOT_SUPPORTED); if (support != null) { simulteNotSupported = true; } // ---------------------------------------------------- // find out in which program group the shortcuts should // be placed and where this program group should be // located // ---------------------------------------------------- XMLElement group = spec.getFirstChildNamed(SPEC_KEY_PROGRAM_GROUP); String location = null; hasDesktopShortcuts = false; if (group != null) { suggestedProgramGroup = group.getAttribute(SPEC_ATTRIBUTE_DEFAULT_GROUP, ""); location = group.getAttribute(SPEC_ATTRIBUTE_LOCATION, SPEC_VALUE_APPLICATIONS); } else { suggestedProgramGroup = ""; location = SPEC_VALUE_APPLICATIONS; } if (location.equals(SPEC_VALUE_APPLICATIONS)) { groupLocation = Shortcut.APPLICATIONS; } else if (location.equals(SPEC_VALUE_START_MENU)) { groupLocation = Shortcut.START_MENU; } // ---------------------------------------------------- // create a list of all shortcuts that need to be // created, containing all details about each shortcut // ---------------------------------------------------- // String temp; Vector shortcutSpecs = spec.getChildrenNamed(SPEC_KEY_SHORTCUT); XMLElement shortcutSpec; ShortcutData data; shortCuts = new Vector(); for (int i = 0; i < shortcutSpecs.size(); i++) { // System.out.println( "Processing shortcut: " + i ); shortcutSpec = (XMLElement) shortcutSpecs.elementAt(i); if (!OsConstraint.oneMatchesCurrentSystem(shortcutSpec)) { continue; } // TODO: write log info INFO.info( "Checking Condition for " + // shortcutSpec.getAttribute( SPEC_ATTRIBUTE_NAME ) ); if (!checkConditions(shortcutSpec)) { continue; } // TODO write log info INFO.info( "Checked Condition for " + // shortcutSpec.getAttribute( SPEC_ATTRIBUTE_NAME ) ); data = new ShortcutData(); data.name = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_NAME); data.subgroup = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_SUBGROUP, ""); data.description = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_DESCRIPTION, ""); // ** Linux **// data.deskTopEntryLinux_Encoding = shortcutSpec .getAttribute(SPEC_ATTRIBUTE_ENCODING, ""); data.deskTopEntryLinux_MimeType = shortcutSpec .getAttribute(SPEC_ATTRIBUTE_MIMETYPE, ""); data.deskTopEntryLinux_Terminal = shortcutSpec .getAttribute(SPEC_ATTRIBUTE_TERMINAL, ""); data.deskTopEntryLinux_TerminalOptions = shortcutSpec.getAttribute( SPEC_ATTRIBUTE_TERMINAL_OPTIONS, ""); data.deskTopEntryLinux_Type = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_TYPE, ""); data.deskTopEntryLinux_URL = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_URL, ""); data.deskTopEntryLinux_X_KDE_SubstituteUID = shortcutSpec.getAttribute( SPEC_ATTRIBUTE_KDE_SUBST_UID, ""); data.createForAll = new Boolean(shortcutSpec.getAttribute(CREATE_FOR_ALL, "false")); // ** EndOf LINUX **// // temp = data.target = fixSeparatorChar(shortcutSpec.getAttribute(SPEC_ATTRIBUTE_TARGET, "")); // temp = data.commandLine = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_COMMAND, ""); // temp = data.iconFile = fixSeparatorChar(shortcutSpec.getAttribute(SPEC_ATTRIBUTE_ICON, "")); data.iconIndex = Integer.parseInt(shortcutSpec.getAttribute(SPEC_ATTRIBUTE_ICON_INDEX, "0")); // temp = data.workingDirectory = fixSeparatorChar(shortcutSpec.getAttribute( SPEC_ATTRIBUTE_WORKING_DIR, "")); String initialState = shortcutSpec.getAttribute(SPEC_ATTRIBUTE_INITIAL_STATE, ""); if (initialState.equals(SPEC_VALUE_NO_SHOW)) { data.initialState = Shortcut.HIDE; } else if (initialState.equals(SPEC_VALUE_NORMAL)) { data.initialState = Shortcut.NORMAL; } else if (initialState.equals(SPEC_VALUE_MAXIMIZED)) { data.initialState = Shortcut.MAXIMIZED; } else if (initialState.equals(SPEC_VALUE_MINIMIZED)) { data.initialState = Shortcut.MINIMIZED; } else { data.initialState = Shortcut.NORMAL; } //LOG System.out.println("data.initialState: " + data.initialState); // -------------------------------------------------- // if the minimal data requirements are met to create // the shortcut, create one entry each for each of // the requested types. // Eventually this will cause the creation of one // shortcut in each of the associated locations. // -------------------------------------------------- // without a name we can not create a shortcut if (data.name == null) { continue; } // 1. Elmar: "Without a target we can not create a shortcut." // 2. Marc: "No, Even on Linux a Link can be an URL and has no target." if (data.target == null) { // TODO: write log info INFO.warn( "Shortcut: " + data + " has no target" ); data.target = ""; } // the shortcut is not actually required for any of the selected packs // the shortcut is not actually required for any of the selected packs // the shortcut is not actually required for any of the selected packs Vector forPacks = shortcutSpec.getChildrenNamed(SPEC_KEY_PACKS); if (!shortcutRequiredFor(forPacks)) { continue; } // -------------------------------------------------- // This section is executed if we don't skip. // -------------------------------------------------- // For each of the categories set the type and if // the link should be placed in the program group, // then clone the data set to obtain an independent // instance and add this to the list of shortcuts // to be created. In this way, we will set up an // identical copy for each of the locations at which // a shortcut should be placed. Therefore you must // not use 'else if' statements! // -------------------------------------------------- { if (XMLHelper.attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_DESKTOP)) { hasDesktopShortcuts = true; data.addToGroup = false; data.type = Shortcut.DESKTOP; shortcuts.add(data.clone()); } if (XMLHelper.attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_APPLICATIONS)) { data.addToGroup = false; data.type = Shortcut.APPLICATIONS; shortcuts.add(data.clone()); } if (XMLHelper.attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_START_MENU)) { data.addToGroup = false; data.type = Shortcut.START_MENU; shortcuts.add(data.clone()); } if (XMLHelper.attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_STARTUP)) { data.addToGroup = false; data.type = Shortcut.START_UP; shortcuts.add(data.clone()); } if (XMLHelper.attributeIsTrue(shortcutSpec, SPEC_ATTRIBUTE_PROGRAM_GROUP)) { data.addToGroup = true; data.type = Shortcut.APPLICATIONS; shortcuts.add(data.clone()); } // / TODO: write log INFO.info( "data.name: " + data.name ); shortCuts.add((data.name == null) ? "" : data.name); // + " -> " + data.target + // " Type: " + data.type ); } } // ---------------------------------------------------- // signal if there are any shortcuts to create // ---------------------------------------------------- if (shortcuts.size() > 0) { shortcutsToCreate = true; } }

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private void buildUI(File groups) { itsProgramFolder = groups; // constraints.gridx = 1; // constraints.gridy = line+1; // constraints.gridwidth = 3; // constraints.gridheight = 1; constraints.insets = new Insets(10, 10, 0, 0); // Add a CheckBox which enables the user to entirely supress shortcut creation. String menuKind = parent.langpack.getString("ShortcutPanel.regular.StartMenu:Start-Menu"); if (OsVersion.IS_UNIX && UnixHelper.kdeIsInstalled()) { menuKind = parent.langpack.getString("ShortcutPanel.regular.StartMenu:K-Menu"); } createShortcuts = new JCheckBox(StringTool.replace(parent.langpack .getString("ShortcutPanel.regular.create"), "StartMenu", menuKind), true); createShortcuts.addActionListener(this); constraints.gridx = col; constraints.gridy = line + 1; constraints.gridwidth = 1; constraints.gridheight = 1; // constraints.weightx = 0.1; // constraints.weighty = 0.2; constraints.fill = GridBagConstraints.HORIZONTAL; constraints.anchor = GridBagConstraints.NORTHWEST; layout.addLayoutComponent(createShortcuts, constraints); add(createShortcuts); constraints.insets = new Insets(0, 10, 0, 0); // ---------------------------------------------------- // check box to allow the user to decide if a desktop // shortcut should be created. // this should only be created if needed and requested // in the definition file. // ---------------------------------------------------- if (hasDesktopShortcuts) { String initialAllowedValue = idata.getVariable("DesktopShortcutCheckboxEnabled"); boolean initialAllowedFlag = false; if (initialAllowedValue == null) { initialAllowedFlag = false; } else if (Boolean.TRUE.toString().equals(initialAllowedValue)) { initialAllowedFlag = true; } allowDesktopShortcut = new JCheckBox(parent.langpack .getString("ShortcutPanel.regular.desktop"), initialAllowedFlag); constraints.gridx = col; constraints.gridy = line + 2; constraints.gridwidth = 1; constraints.gridheight = 1; // constraints.weighty = 0.2; // constraints.weighty = 1.0; // constraints.weighty = 0.5; layout.addLayoutComponent(allowDesktopShortcut, constraints); add(allowDesktopShortcut); } listLabel = LabelFactory.create(parent.langpack.getString("ShortcutPanel.regular.list"), JLabel.LEADING); constraints.gridx = col; constraints.gridy = line + 3; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.insets = new Insets(10, 10, 0, 0); constraints.fill = GridBagConstraints.HORIZONTAL; constraints.anchor = GridBagConstraints.NORTHWEST; layout.addLayoutComponent(listLabel, constraints); add(listLabel); // ---------------------------------------------------- // list box to list all of already existing folders as program groups // at the intended destination // ---------------------------------------------------- Vector dirEntries = new Vector(); File[] entries = groups.listFiles(); // Quickfix prevent NullPointer on non default compliant Linux - KDEs // i.e Mandrake 2005 LE stores from now also in "applnk" instead in prior "applnk-mdk": if (entries != null) { for (int idx = 0; idx < entries.length; idx++) { if (entries[idx].isDirectory()) { dirEntries.add(entries[idx].getName()); } } } if (groupList == null) { groupList = new JList(); } groupList = addList(dirEntries, ListSelectionModel.SINGLE_SELECTION, groupList, col, line + 4, 1, 1, GridBagConstraints.BOTH); // ---------------------------------------------------- // radio buttons to select current user or all users. // ---------------------------------------------------- if (shortcut.multipleUsers()) { JPanel usersPanel = new JPanel(new GridLayout(2, 1)); ButtonGroup usersGroup = new ButtonGroup(); currentUser = new JRadioButton(parent.langpack .getString("ShortcutPanel.regular.currentUser"), !isRootUser); currentUser.addActionListener(this); usersGroup.add(currentUser); usersPanel.add(currentUser); allUsers = new JRadioButton( parent.langpack.getString("ShortcutPanel.regular.allUsers"), isRootUser); if (!isRootUser) { allUsers.setEnabled(false); } allUsers.addActionListener(this); usersGroup.add(allUsers); usersPanel.add(allUsers); TitledBorder border = new TitledBorder(new EmptyBorder(2, 2, 2, 2), parent.langpack .getString("ShortcutPanel.regular.userIntro")); usersPanel.setBorder(border); constraints.gridx = col + 1; constraints.gridy = line + 4; constraints.gridwidth = 1; constraints.gridheight = 1; // constraints.weighty = 1.0; // constraints.weightx = 1.0; constraints.fill = GridBagConstraints.HORIZONTAL; layout.addLayoutComponent(usersPanel, constraints); add(usersPanel); } // ---------------------------------------------------- // edit box that contains the suggested program group // name, which can be modfied or substituted from the // list by the user // ---------------------------------------------------- programGroup = new JTextField(suggestedProgramGroup, 40); // 40? constraints.gridx = col; constraints.gridy = line + 5; constraints.gridwidth = 1; constraints.gridheight = 1; // constraints.weighty = 1.0; // constraints.weightx = 1.0; constraints.fill = GridBagConstraints.HORIZONTAL; layout.addLayoutComponent(programGroup, constraints); add(programGroup); // ---------------------------------------------------- // reset button that allows the user to revert to the // original suggestion for the program group // ---------------------------------------------------- defaultButton = ButtonFactory.createButton(parent.langpack .getString("ShortcutPanel.regular.default"), idata.buttonsHColor); defaultButton.addActionListener(this); constraints.gridx = col + 1; constraints.gridy = line + 5; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.fill = GridBagConstraints.HORIZONTAL; layout.addLayoutComponent(defaultButton, constraints); add(defaultButton); }

private void buildUI(File groups) { // constraints.gridx = 1; // constraints.gridy = line+1; // constraints.gridwidth = 3; // constraints.gridheight = 1; constraints.insets = new Insets(10, 10, 0, 0); // Add a CheckBox which enables the user to entirely supress shortcut creation. String menuKind = parent.langpack.getString("ShortcutPanel.regular.StartMenu:Start-Menu"); if (OsVersion.IS_UNIX && UnixHelper.kdeIsInstalled()) { menuKind = parent.langpack.getString("ShortcutPanel.regular.StartMenu:K-Menu"); } createShortcuts = new JCheckBox(StringTool.replace(parent.langpack .getString("ShortcutPanel.regular.create"), "StartMenu", menuKind), true); createShortcuts.addActionListener(this); constraints.gridx = col; constraints.gridy = line + 1; constraints.gridwidth = 1; constraints.gridheight = 1; // constraints.weightx = 0.1; // constraints.weighty = 0.2; constraints.fill = GridBagConstraints.HORIZONTAL; constraints.anchor = GridBagConstraints.NORTHWEST; layout.addLayoutComponent(createShortcuts, constraints); add(createShortcuts); constraints.insets = new Insets(0, 10, 0, 0); // ---------------------------------------------------- // check box to allow the user to decide if a desktop // shortcut should be created. // this should only be created if needed and requested // in the definition file. // ---------------------------------------------------- if (hasDesktopShortcuts) { String initialAllowedValue = idata.getVariable("DesktopShortcutCheckboxEnabled"); boolean initialAllowedFlag = false; if (initialAllowedValue == null) { initialAllowedFlag = false; } else if (Boolean.TRUE.toString().equals(initialAllowedValue)) { initialAllowedFlag = true; } allowDesktopShortcut = new JCheckBox(parent.langpack .getString("ShortcutPanel.regular.desktop"), initialAllowedFlag); constraints.gridx = col; constraints.gridy = line + 2; constraints.gridwidth = 1; constraints.gridheight = 1; // constraints.weighty = 0.2; // constraints.weighty = 1.0; // constraints.weighty = 0.5; layout.addLayoutComponent(allowDesktopShortcut, constraints); add(allowDesktopShortcut); } listLabel = LabelFactory.create(parent.langpack.getString("ShortcutPanel.regular.list"), JLabel.LEADING); constraints.gridx = col; constraints.gridy = line + 3; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.insets = new Insets(10, 10, 0, 0); constraints.fill = GridBagConstraints.HORIZONTAL; constraints.anchor = GridBagConstraints.NORTHWEST; layout.addLayoutComponent(listLabel, constraints); add(listLabel); // ---------------------------------------------------- // list box to list all of already existing folders as program groups // at the intended destination // ---------------------------------------------------- Vector dirEntries = new Vector(); File[] entries = groups.listFiles(); // Quickfix prevent NullPointer on non default compliant Linux - KDEs // i.e Mandrake 2005 LE stores from now also in "applnk" instead in prior "applnk-mdk": if (entries != null) { for (int idx = 0; idx < entries.length; idx++) { if (entries[idx].isDirectory()) { dirEntries.add(entries[idx].getName()); } } } if (groupList == null) { groupList = new JList(); } groupList = addList(dirEntries, ListSelectionModel.SINGLE_SELECTION, groupList, col, line + 4, 1, 1, GridBagConstraints.BOTH); // ---------------------------------------------------- // radio buttons to select current user or all users. // ---------------------------------------------------- if (shortcut.multipleUsers()) { JPanel usersPanel = new JPanel(new GridLayout(2, 1)); ButtonGroup usersGroup = new ButtonGroup(); currentUser = new JRadioButton(parent.langpack .getString("ShortcutPanel.regular.currentUser"), !isRootUser); currentUser.addActionListener(this); usersGroup.add(currentUser); usersPanel.add(currentUser); allUsers = new JRadioButton( parent.langpack.getString("ShortcutPanel.regular.allUsers"), isRootUser); if (!isRootUser) { allUsers.setEnabled(false); } allUsers.addActionListener(this); usersGroup.add(allUsers); usersPanel.add(allUsers); TitledBorder border = new TitledBorder(new EmptyBorder(2, 2, 2, 2), parent.langpack .getString("ShortcutPanel.regular.userIntro")); usersPanel.setBorder(border); constraints.gridx = col + 1; constraints.gridy = line + 4; constraints.gridwidth = 1; constraints.gridheight = 1; // constraints.weighty = 1.0; // constraints.weightx = 1.0; constraints.fill = GridBagConstraints.HORIZONTAL; layout.addLayoutComponent(usersPanel, constraints); add(usersPanel); } // ---------------------------------------------------- // edit box that contains the suggested program group // name, which can be modfied or substituted from the // list by the user // ---------------------------------------------------- programGroup = new JTextField(suggestedProgramGroup, 40); // 40? constraints.gridx = col; constraints.gridy = line + 5; constraints.gridwidth = 1; constraints.gridheight = 1; // constraints.weighty = 1.0; // constraints.weightx = 1.0; constraints.fill = GridBagConstraints.HORIZONTAL; layout.addLayoutComponent(programGroup, constraints); add(programGroup); // ---------------------------------------------------- // reset button that allows the user to revert to the // original suggestion for the program group // ---------------------------------------------------- defaultButton = ButtonFactory.createButton(parent.langpack .getString("ShortcutPanel.regular.default"), idata.buttonsHColor); defaultButton.addActionListener(this); constraints.gridx = col + 1; constraints.gridy = line + 5; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.fill = GridBagConstraints.HORIZONTAL; layout.addLayoutComponent(defaultButton, constraints); add(defaultButton); }

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private void buildUI(File groups) { itsProgramFolder = groups; // constraints.gridx = 1; // constraints.gridy = line+1; // constraints.gridwidth = 3; // constraints.gridheight = 1; constraints.insets = new Insets(10, 10, 0, 0); // Add a CheckBox which enables the user to entirely supress shortcut creation. String menuKind = parent.langpack.getString("ShortcutPanel.regular.StartMenu:Start-Menu"); if (OsVersion.IS_UNIX && UnixHelper.kdeIsInstalled()) { menuKind = parent.langpack.getString("ShortcutPanel.regular.StartMenu:K-Menu"); } createShortcuts = new JCheckBox(StringTool.replace(parent.langpack .getString("ShortcutPanel.regular.create"), "StartMenu", menuKind), true); createShortcuts.addActionListener(this); constraints.gridx = col; constraints.gridy = line + 1; constraints.gridwidth = 1; constraints.gridheight = 1; // constraints.weightx = 0.1; // constraints.weighty = 0.2; constraints.fill = GridBagConstraints.HORIZONTAL; constraints.anchor = GridBagConstraints.NORTHWEST; layout.addLayoutComponent(createShortcuts, constraints); add(createShortcuts); constraints.insets = new Insets(0, 10, 0, 0); // ---------------------------------------------------- // check box to allow the user to decide if a desktop // shortcut should be created. // this should only be created if needed and requested // in the definition file. // ---------------------------------------------------- if (hasDesktopShortcuts) { String initialAllowedValue = idata.getVariable("DesktopShortcutCheckboxEnabled"); boolean initialAllowedFlag = false; if (initialAllowedValue == null) { initialAllowedFlag = false; } else if (Boolean.TRUE.toString().equals(initialAllowedValue)) { initialAllowedFlag = true; } allowDesktopShortcut = new JCheckBox(parent.langpack .getString("ShortcutPanel.regular.desktop"), initialAllowedFlag); constraints.gridx = col; constraints.gridy = line + 2; constraints.gridwidth = 1; constraints.gridheight = 1; // constraints.weighty = 0.2; // constraints.weighty = 1.0; // constraints.weighty = 0.5; layout.addLayoutComponent(allowDesktopShortcut, constraints); add(allowDesktopShortcut); } listLabel = LabelFactory.create(parent.langpack.getString("ShortcutPanel.regular.list"), JLabel.LEADING); constraints.gridx = col; constraints.gridy = line + 3; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.insets = new Insets(10, 10, 0, 0); constraints.fill = GridBagConstraints.HORIZONTAL; constraints.anchor = GridBagConstraints.NORTHWEST; layout.addLayoutComponent(listLabel, constraints); add(listLabel); // ---------------------------------------------------- // list box to list all of already existing folders as program groups // at the intended destination // ---------------------------------------------------- Vector dirEntries = new Vector(); File[] entries = groups.listFiles(); // Quickfix prevent NullPointer on non default compliant Linux - KDEs // i.e Mandrake 2005 LE stores from now also in "applnk" instead in prior "applnk-mdk": if (entries != null) { for (int idx = 0; idx < entries.length; idx++) { if (entries[idx].isDirectory()) { dirEntries.add(entries[idx].getName()); } } } if (groupList == null) { groupList = new JList(); } groupList = addList(dirEntries, ListSelectionModel.SINGLE_SELECTION, groupList, col, line + 4, 1, 1, GridBagConstraints.BOTH); // ---------------------------------------------------- // radio buttons to select current user or all users. // ---------------------------------------------------- if (shortcut.multipleUsers()) { JPanel usersPanel = new JPanel(new GridLayout(2, 1)); ButtonGroup usersGroup = new ButtonGroup(); currentUser = new JRadioButton(parent.langpack .getString("ShortcutPanel.regular.currentUser"), !isRootUser); currentUser.addActionListener(this); usersGroup.add(currentUser); usersPanel.add(currentUser); allUsers = new JRadioButton( parent.langpack.getString("ShortcutPanel.regular.allUsers"), isRootUser); if (!isRootUser) { allUsers.setEnabled(false); } allUsers.addActionListener(this); usersGroup.add(allUsers); usersPanel.add(allUsers); TitledBorder border = new TitledBorder(new EmptyBorder(2, 2, 2, 2), parent.langpack .getString("ShortcutPanel.regular.userIntro")); usersPanel.setBorder(border); constraints.gridx = col + 1; constraints.gridy = line + 4; constraints.gridwidth = 1; constraints.gridheight = 1; // constraints.weighty = 1.0; // constraints.weightx = 1.0; constraints.fill = GridBagConstraints.HORIZONTAL; layout.addLayoutComponent(usersPanel, constraints); add(usersPanel); } // ---------------------------------------------------- // edit box that contains the suggested program group // name, which can be modfied or substituted from the // list by the user // ---------------------------------------------------- programGroup = new JTextField(suggestedProgramGroup, 40); // 40? constraints.gridx = col; constraints.gridy = line + 5; constraints.gridwidth = 1; constraints.gridheight = 1; // constraints.weighty = 1.0; // constraints.weightx = 1.0; constraints.fill = GridBagConstraints.HORIZONTAL; layout.addLayoutComponent(programGroup, constraints); add(programGroup); // ---------------------------------------------------- // reset button that allows the user to revert to the // original suggestion for the program group // ---------------------------------------------------- defaultButton = ButtonFactory.createButton(parent.langpack .getString("ShortcutPanel.regular.default"), idata.buttonsHColor); defaultButton.addActionListener(this); constraints.gridx = col + 1; constraints.gridy = line + 5; constraints.gridwidth = 1; constraints.gridheight = 1; constraints.fill = GridBagConstraints.HORIZONTAL; layout.addLayoutComponent(defaultButton, constraints); add(defaultButton); }

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public void panelActivate() { try { readShortcutSpec(); } catch (Throwable exception) { System.out.println("could not read shortcut spec!"); exception.printStackTrace(); } // Create the UI elements try { shortcut = (Shortcut) (TargetFactory.getInstance() .makeObject("com.izforge.izpack.util.os.Shortcut")); shortcut.initialize(Shortcut.APPLICATIONS, "-"); } catch (Throwable exception) { System.out.println("could not create shortcut instance"); exception.printStackTrace(); } analyzeShortcutSpec(); if (shortcutsToCreate && !OsVersion.IS_OSX) { if (shortcut.supported() && !simulteNotSupported) { File allUsersProgramsFolder = getProgramsFolder(Shortcut.ALL_USERS); isRootUser = allUsersProgramsFolder.canWrite(); if (isRootUser) { itsUserType = Shortcut.ALL_USERS; } else { itsUserType = Shortcut.CURRENT_USER; } buildUI(getProgramsFolder(isRootUser ? Shortcut.ALL_USERS : Shortcut.CURRENT_USER)); // addSelectionList(); // add( shortCutsArea ); // JList shortCutList = null; // addList( shortCuts, ListSelectionModel.SINGLE_SELECTION, shortCutList, col, // line+6, 1, 1, GridBagConstraints.BOTH ); } else { // TODO MEP: Test buildAlternateUI(); // parent.unlockNextButton(); // parent.lockPrevButton(); } } else { ; // parent.skipPanel (); } }

public void panelActivate() { try { readShortcutSpec(); } catch (Throwable exception) { System.out.println("could not read shortcut spec!"); exception.printStackTrace(); } // Create the UI elements try { shortcut = (Shortcut) (TargetFactory.getInstance() .makeObject("com.izforge.izpack.util.os.Shortcut")); shortcut.initialize(Shortcut.APPLICATIONS, "-"); } catch (Throwable exception) { System.out.println("could not create shortcut instance"); exception.printStackTrace(); } analyzeShortcutSpec(); if (shortcutsToCreate && !OsVersion.IS_OSX) { if (shortcut.supported() && !simulteNotSupported) { File allUsersProgramsFolder = getProgramsFolder(Shortcut.ALL_USERS); Debug.log("All UsersProgramsFolder: '" + allUsersProgramsFolder + "'"); File forceTest = new File(allUsersProgramsFolder + File.separator + System.getProperty("user.name") + System.currentTimeMillis()); try { isRootUser = forceTest.createNewFile(); } catch (Exception e) { isRootUser = false; Debug.log("IOException: " + "'" + e.getLocalizedMessage() + "'"); Debug.log("You cannot create '" + forceTest + "'"); } if (forceTest.exists()) { Debug.log("Delete temporary File: '" + forceTest + "'"); forceTest.delete(); } String perm = isRootUser ? "can" : "cannot"; Debug.log("You " + perm + " write into '" + allUsersProgramsFolder + "'"); if (isRootUser) { itsUserType = Shortcut.ALL_USERS; } else { itsUserType = Shortcut.CURRENT_USER; } buildUI(getProgramsFolder(isRootUser ? Shortcut.ALL_USERS : Shortcut.CURRENT_USER)); // addSelectionList(); // add( shortCutsArea ); // JList shortCutList = null; // addList( shortCuts, ListSelectionModel.SINGLE_SELECTION, shortCutList, col, // line+6, 1, 1, GridBagConstraints.BOTH ); } else { // TODO MEP: Test buildAlternateUI(); // parent.unlockNextButton(); // parent.lockPrevButton(); } } else { ; // parent.skipPanel (); } }

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public void makeXMLData (XMLElement panelRoot) { // ---------------------------------------------------- // if there are no shortcuts to create, shortcuts are // not supported, or we should simulate that they are // not supported, then we have nothing to add. Just // return // ---------------------------------------------------- if (!shortcutsToCreate || !shortcut.supported () || simulteNotSupported ) { return; } ShortcutData data; XMLElement dataElement; // ---------------------------------------------------- // add the item that defines the name of the program group // ---------------------------------------------------- dataElement = new XMLElement (AUTO_KEY_PROGRAM_GROUP); dataElement.setAttribute (AUTO_ATTRIBUTE_NAME, groupName); panelRoot.addChild (dataElement); // ---------------------------------------------------- // add the details for each of the shortcuts // ---------------------------------------------------- for (int i = 0; i < shortcuts.size (); i++) { data = (ShortcutData)shortcuts.elementAt (i); dataElement = new XMLElement (AUTO_KEY_SHORTCUT); dataElement.setAttribute (AUTO_ATTRIBUTE_NAME, data.name); dataElement.setAttribute (AUTO_ATTRIBUTE_GROUP, new Boolean (data.addToGroup).toString ()); dataElement.setAttribute (AUTO_ATTRIBUTE_TYPE, Integer.toString (data.type)); dataElement.setAttribute (AUTO_ATTRIBUTE_COMMAND, data.commandLine); dataElement.setAttribute (AUTO_ATTRIBUTE_DESCRIPTION, data.description); dataElement.setAttribute (AUTO_ATTRIBUTE_ICON, data.iconFile); dataElement.setAttribute (AUTO_ATTRIBUTE_ICON_INDEX, Integer.toString (data.iconIndex)); dataElement.setAttribute (AUTO_ATTRIBUTE_INITIAL_STATE, Integer.toString (data.initialState)); dataElement.setAttribute (AUTO_ATTRIBUTE_TARGET, data.target); dataElement.setAttribute (AUTO_ATTRIBUTE_WORKING_DIR, data.workingDirectory); // ---------------------------------------------- // add the shortcut only if it is either not on // the desktop or if it is on the desktop and // the user has signalled that it is ok to place // shortcuts on the desktop. // ---------------------------------------------- if ( (data.type != Shortcut.DESKTOP) || ((data.type == Shortcut.DESKTOP) && allowDesktopShortcut.isSelected ()) ) { panelRoot.addChild (dataElement); } } }

public void makeXMLData (XMLElement panelRoot) { // ---------------------------------------------------- // if there are no shortcuts to create, shortcuts are // not supported, or we should simulate that they are // not supported, then we have nothing to add. Just // return // ---------------------------------------------------- if (!shortcutsToCreate || !shortcut.supported () || simulteNotSupported ) { return; } ShortcutData data; XMLElement dataElement; // ---------------------------------------------------- // add the item that defines the name of the program group // ---------------------------------------------------- dataElement = new XMLElement (AUTO_KEY_PROGRAM_GROUP); dataElement.setAttribute (AUTO_ATTRIBUTE_NAME, groupName); panelRoot.addChild (dataElement); // ---------------------------------------------------- // add the details for each of the shortcuts // ---------------------------------------------------- for (int i = 0; i < shortcuts.size (); i++) { data = (ShortcutData)shortcuts.elementAt (i); dataElement = new XMLElement (AUTO_KEY_SHORTCUT); dataElement.setAttribute (AUTO_ATTRIBUTE_NAME, data.name); dataElement.setAttribute (AUTO_ATTRIBUTE_GROUP, Boolean.valueOf(data.addToGroup).toString ()); dataElement.setAttribute (AUTO_ATTRIBUTE_TYPE, Integer.toString (data.type)); dataElement.setAttribute (AUTO_ATTRIBUTE_COMMAND, data.commandLine); dataElement.setAttribute (AUTO_ATTRIBUTE_DESCRIPTION, data.description); dataElement.setAttribute (AUTO_ATTRIBUTE_ICON, data.iconFile); dataElement.setAttribute (AUTO_ATTRIBUTE_ICON_INDEX, Integer.toString (data.iconIndex)); dataElement.setAttribute (AUTO_ATTRIBUTE_INITIAL_STATE, Integer.toString (data.initialState)); dataElement.setAttribute (AUTO_ATTRIBUTE_TARGET, data.target); dataElement.setAttribute (AUTO_ATTRIBUTE_WORKING_DIR, data.workingDirectory); // ---------------------------------------------- // add the shortcut only if it is either not on // the desktop or if it is on the desktop and // the user has signalled that it is ok to place // shortcuts on the desktop. // ---------------------------------------------- if ( (data.type != Shortcut.DESKTOP) || ((data.type == Shortcut.DESKTOP) && allowDesktopShortcut.isSelected ()) ) { panelRoot.addChild (dataElement); } } }

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private void parseText() { try { // Initialize the variable substitutor VariableSubstitutor vs = new VariableSubstitutor(idata.getVariableValueMap()); // Parses the info text info = vs.substitute(info, null); } catch (Exception err) { err.printStackTrace(); } }

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public Frontend() throws Exception { super(); // Sets the Kunststoff L&F as the right one KunststoffLookAndFeel klnf = new KunststoffLookAndFeel(); UIManager.setLookAndFeel(klnf); klnf.setCurrentTheme(new IzPackKMetalTheme()); // Shows the splash window splashWindow = new FrontendSplashWindow(); // We load the configuration Frontend.splashWindow.update(1, "Loading the configuration ..."); loadConfig(); // We load the localisation Frontend.splashWindow.update(2, "Loading the localisation ..."); loadLocalisation(); String title = langpack.getString("frontend.title"); // We launch the GUI FrontendFrame fef = new FrontendFrame(title, langpack); }

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public Frontend() throws Exception { super(); // Sets the Kunststoff L&F as the right one KunststoffLookAndFeel klnf = new KunststoffLookAndFeel(); UIManager.setLookAndFeel(klnf); klnf.setCurrentTheme(new IzPackKMetalTheme()); // Shows the splash window splashWindow = new FrontendSplashWindow(); // We load the configuration Frontend.splashWindow.update(1, "Loading the configuration ..."); loadConfig(); // We load the localisation Frontend.splashWindow.update(2, "Loading the localisation ..."); loadLocalisation(); String title = langpack.getString("frontend.title"); // We launch the GUI FrontendFrame fef = new FrontendFrame(title, langpack); }

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public synchronized Object borrowObject(Object key) throws Exception { long starttime = System.currentTimeMillis(); boolean newlyCreated = false; for(;;) { CursorableLinkedList pool = (CursorableLinkedList)(_poolMap.get(key)); if(null == pool) { pool = new CursorableLinkedList(); _poolMap.put(key,pool); _poolList.add(key); } ObjectTimestampPair pair = null; // if there are any sleeping, just grab one of those try { pair = (ObjectTimestampPair)(pool.removeFirst()); if(null != pair) { _totalIdle--; } } catch(NoSuchElementException e) { /* ignored */ } // otherwise if(null == pair) { // if there is a totalMaxActive and we are at the limit then // we have to make room if ((_maxTotal > 0) && (_totalActive + _totalIdle >= _maxTotal)) { clearOldest(); } // check if we can create one // (note we know that the num sleeping is 0, else we wouldn't be here) int active = getActiveCount(key); if ((_maxActive < 0 || active < _maxActive) && (_maxTotal < 0 || _totalActive + _totalIdle < _maxTotal)) { Object obj = _factory.makeObject(key); pair = new ObjectTimestampPair(obj); newlyCreated = true; } else { // the pool is exhausted switch(_whenExhaustedAction) { case WHEN_EXHAUSTED_GROW: Object obj = _factory.makeObject(key); pair = new ObjectTimestampPair(obj); break; case WHEN_EXHAUSTED_FAIL: throw new NoSuchElementException(); case WHEN_EXHAUSTED_BLOCK: try { if(_maxWait <= 0) { wait(); } else { wait(_maxWait); } } catch(InterruptedException e) { // ignored } if(_maxWait > 0 && ((System.currentTimeMillis() - starttime) >= _maxWait)) { throw new NoSuchElementException("Timeout waiting for idle object"); } else { continue; // keep looping } default: throw new IllegalArgumentException("whenExhaustedAction " + _whenExhaustedAction + " not recognized."); } } } _factory.activateObject(key,pair.value); if(_testOnBorrow && !_factory.validateObject(key,pair.value)) { _factory.destroyObject(key,pair.value); if(newlyCreated) { throw new NoSuchElementException("Could not create a validated object"); } // else keep looping } else { incrementActiveCount(key); return pair.value; } } }

public synchronized Object borrowObject(Object key) throws Exception { long starttime = System.currentTimeMillis(); boolean newlyCreated = false; for(;;) { CursorableLinkedList pool = (CursorableLinkedList)(_poolMap.get(key)); if(null == pool) { pool = new CursorableLinkedList(); _poolMap.put(key,pool); _poolList.add(key); } ObjectTimestampPair pair = null; // if there are any sleeping, just grab one of those try { pair = (ObjectTimestampPair)(pool.removeFirst()); if(null != pair) { _totalIdle--; } } catch(NoSuchElementException e) { /* ignored */ } // otherwise if(null == pair) { // if there is a totalMaxActive and we are at the limit then // we have to make room if ((_maxTotal > 0) && (_totalActive + _totalIdle >= _maxTotal)) { clearOldest(); } // check if we can create one // (note we know that the num sleeping is 0, else we wouldn't be here) int active = getActiveCount(key); if ((_maxActive < 0 || active < _maxActive) && (_maxTotal < 0 || _totalActive + _totalIdle < _maxTotal)) { Object obj = _factory.makeObject(key); pair = new ObjectTimestampPair(obj); newlyCreated = true; } else { // the pool is exhausted switch(_whenExhaustedAction) { case WHEN_EXHAUSTED_GROW: Object obj = _factory.makeObject(key); pair = new ObjectTimestampPair(obj); break; case WHEN_EXHAUSTED_FAIL: throw new NoSuchElementException(); case WHEN_EXHAUSTED_BLOCK: try { if(_maxWait <= 0) { wait(); } else { final long elapsed = (System.currentTimeMillis() - starttime); final long waitTime = _maxWait - elapsed; if (waitTime > 0) { wait(waitTime); } } } catch(InterruptedException e) { // ignored } if(_maxWait > 0 && ((System.currentTimeMillis() - starttime) >= _maxWait)) { throw new NoSuchElementException("Timeout waiting for idle object"); } else { continue; // keep looping } default: throw new IllegalArgumentException("whenExhaustedAction " + _whenExhaustedAction + " not recognized."); } } } _factory.activateObject(key,pair.value); if(_testOnBorrow && !_factory.validateObject(key,pair.value)) { _factory.destroyObject(key,pair.value); if(newlyCreated) { throw new NoSuchElementException("Could not create a validated object"); } // else keep looping } else { incrementActiveCount(key); return pair.value; } } }

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public void paintComponent(Graphics g) { super.paintComponent(g); Graphics2D g2D = (Graphics2D) g; g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); g2D.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY); g2D.setRenderingHint(RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_BILINEAR); BufferedImage img = model.getDisplayedImage(); if (img == null) return; //paintXYFrame(g2D); g2D.drawImage(img, null, 0, 0); double v = model.getPixelsSizeX()/model.getZoomFactor(); v *= model.getUnitBarSize(); int size = (int) model.getUnitBarSize(); if (v > 0 && model.isUnitBar()) { paintScaleBar(g2D, img.getWidth()-size-5, img.getHeight()-10, size, ""+v); } }

public void paintComponent(Graphics g) { super.paintComponent(g); Graphics2D g2D = (Graphics2D) g; g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); g2D.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY); g2D.setRenderingHint(RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_BILINEAR); BufferedImage img = model.getDisplayedImage(); if (img == null) return; //paintXYFrame(g2D); g2D.drawImage(img, null, 0, 0); double v = model.getPixelsSizeX()/model.getZoomFactor(); v *= model.getUnitBarSize(); int size = (int) model.getUnitBarSize(); if (v > 0 && model.isUnitBar()) { paintScaleBar(g2D, img.getWidth()-size-5, img.getHeight()-10, size, value); } }

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private void paintScaleBar(Graphics2D g2D, int x, int y, int l, String s) { FontMetrics fontMetrics = g2D.getFontMetrics(); int hFont = fontMetrics.getHeight()/3; int size = s.length()*charWidth; g2D.setColor(UNIT_BAR_COLOR); g2D.drawString(s, x+l/2-size/2+1, y-hFont); g2D.setStroke(UNIT_BAR_STROKE); g2D.drawLine(x, y, x+l, y); }

private void paintScaleBar(Graphics2D g2D, int x, int y, int l, String s) { FontMetrics fontMetrics = g2D.getFontMetrics(); int hFont = fontMetrics.getHeight()/3; g2D.setColor(UNIT_BAR_COLOR); g2D.drawString(s, x+l/2-size/2+1, y-hFont); g2D.setStroke(UNIT_BAR_STROKE); g2D.drawLine(x, y, x+l, y); }

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private void paintScaleBar(Graphics2D g2D, int x, int y, int l, String s) { FontMetrics fontMetrics = g2D.getFontMetrics(); int hFont = fontMetrics.getHeight()/3; int size = s.length()*charWidth; g2D.setColor(UNIT_BAR_COLOR); g2D.drawString(s, x+l/2-size/2+1, y-hFont); g2D.setStroke(UNIT_BAR_STROKE); g2D.drawLine(x, y, x+l, y); }

private void paintScaleBar(Graphics2D g2D, int x, int y, int l, String s) { FontMetrics fontMetrics = g2D.getFontMetrics(); int hFont = fontMetrics.getHeight()/3; int size = s.length()*charWidth; g2D.setColor(UNIT_BAR_COLOR); g2D.drawString(s, x+(l-fontMetrics.stringWidth(s))/2+1, y-hFont); g2D.setStroke(UNIT_BAR_STROKE); g2D.drawLine(x, y, x+l, y); }

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protected synchronized void startEvictor(long delay) { if(null != _evictor) { _evictor.cancel(); _evictor = null; } if(delay > 0) { _evictor = new Evictor(delay); Thread t = new Thread(_evictor); t.setDaemon(true); t.start(); } }

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public void actionPerformed(ActionEvent e) { Object src = e.getSource(); if (src == quitButton) System.exit(0); else if (src == destroyButton) { Destroyer destroyer = new Destroyer(installPath, targetDestroyCheckbox.isSelected(), new DestroyerHandler()); destroyer.start(); } }

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public void actionPerformed(ActionEvent e) { Object src = e.getSource(); if (src == quitButton) System.exit(0); else if (src == destroyButton) { Destroyer destroyer = new Destroyer(installPath, targetDestroyCheckbox.isSelected(), new DestroyerHandler()); destroyer.start(); } }

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public int askQuestion (String title, String question, int choices) { return askQuestion (title, question, choices, -1); }

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public void emitError(String title, String error) { progressBar.setString(error); JOptionPane.showMessageDialog(null, error, title, JOptionPane.OK_CANCEL_OPTION); }

public void emitError(String title, String error) { progressBar.setString(error); JOptionPane.showMessageDialog( null, error, title, JOptionPane.OK_CANCEL_OPTION); }

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public void emitNotification (String text) { }

public void emitNotification(String text) { }

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public boolean emitWarning (String title, String text) { return (JOptionPane.showConfirmDialog(null, text, title, JOptionPane.OK_CANCEL_OPTION, JOptionPane.WARNING_MESSAGE) == JOptionPane.OK_OPTION); }

public boolean emitWarning(String title, String text) { return (JOptionPane.showConfirmDialog(null, text, title, JOptionPane.OK_CANCEL_OPTION, JOptionPane.WARNING_MESSAGE) == JOptionPane.OK_OPTION); }

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public boolean emitWarning (String title, String text) { return (JOptionPane.showConfirmDialog(null, text, title, JOptionPane.OK_CANCEL_OPTION, JOptionPane.WARNING_MESSAGE) == JOptionPane.OK_OPTION); }

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public void nextStep (String step_name, int step_no, int no_of_substeps) { }

public void nextStep(String step_name, int step_no, int no_of_substeps) { }

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public void startAction (String name, int max) { progressBar.setMinimum(0); progressBar.setMaximum(max); blockGUI(); }

public void startAction(String name, int max) { progressBar.setMinimum(0); progressBar.setMaximum(max); blockGUI(); }

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public void stopAction () { progressBar.setString(langpack.getString("InstallPanel.finished")); targetDestroyCheckbox.setEnabled(false); destroyButton.setEnabled(false); releaseGUI(); }

public void stopAction() { progressBar.setString(langpack.getString("InstallPanel.finished")); targetDestroyCheckbox.setEnabled(false); destroyButton.setEnabled(false); releaseGUI(); }

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public UninstallerFrame() throws Exception { super("IzPack - Uninstaller"); // Initializations langpack = new LocaleDatabase(getClass().getResourceAsStream("/langpack.xml")); getInstallPath(); icons = new IconsDatabase(); loadIcons(); UIManager.put("OptionPane.yesButtonText", langpack.getString("installer.yes")); UIManager.put("OptionPane.noButtonText", langpack.getString("installer.no")); UIManager.put("OptionPane.cancelButtonText", langpack.getString("installer.cancel")); // Sets the frame icon setIconImage(icons.getImageIcon("JFrameIcon").getImage()); // We build the GUI & show it buildGUI(); addWindowListener(new WindowHandler()); pack(); centerFrame(this); setResizable(false); setVisible(true); }

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public UninstallerFrame() throws Exception { super("IzPack - Uninstaller"); // Initializations langpack = new LocaleDatabase(getClass().getResourceAsStream("/langpack.xml")); getInstallPath(); icons = new IconsDatabase(); loadIcons(); UIManager.put("OptionPane.yesButtonText", langpack.getString("installer.yes")); UIManager.put("OptionPane.noButtonText", langpack.getString("installer.no")); UIManager.put("OptionPane.cancelButtonText", langpack.getString("installer.cancel")); // Sets the frame icon setIconImage(icons.getImageIcon("JFrameIcon").getImage()); // We build the GUI & show it buildGUI(); addWindowListener(new WindowHandler()); pack(); centerFrame(this); setResizable(false); setVisible(true); }

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private void buildConstraints(GridBagConstraints gbc, int gx, int gy, int gw, int gh, double wx, double wy) { gbc.gridx = gx; gbc.gridy = gy; gbc.gridwidth = gw; gbc.gridheight = gh; gbc.weightx = wx; gbc.weighty = wy; }

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private void buildGUI() { // We initialize our layout JPanel contentPane = (JPanel) getContentPane(); layout = new GridBagLayout(); contentPane.setLayout(layout); gbConstraints = new GridBagConstraints(); gbConstraints.insets = new Insets(5, 5, 5, 5); // We prepare our action handler ActionsHandler handler = new ActionsHandler(); // Prepares the glass pane to block gui interaction when needed JPanel glassPane = (JPanel) getGlassPane(); glassPane.addMouseListener( new MouseAdapter() { }); glassPane.addMouseMotionListener( new MouseMotionAdapter() { }); glassPane.addKeyListener( new KeyAdapter() { }); // We set-up the buttons factory ButtonFactory.useButtonIcons(); ButtonFactory.useHighlightButtons(); // We put our components warningLabel = new JLabel(langpack.getString("uninstaller.warning"), icons.getImageIcon("warning"), JLabel.TRAILING); buildConstraints(gbConstraints, 0, 0, 2, 1, 1.0, 0.0); gbConstraints.anchor = GridBagConstraints.WEST; gbConstraints.fill = GridBagConstraints.NONE; layout.addLayoutComponent(warningLabel, gbConstraints); contentPane.add(warningLabel); targetDestroyCheckbox = new JCheckBox(langpack.getString("uninstaller.destroytarget") + installPath, false); buildConstraints(gbConstraints, 0, 1, 2, 1, 1.0, 0.0); layout.addLayoutComponent(targetDestroyCheckbox, gbConstraints); contentPane.add(targetDestroyCheckbox); gbConstraints.fill = GridBagConstraints.HORIZONTAL; progressBar = new JProgressBar(); progressBar.setStringPainted(true); progressBar.setString(langpack.getString("InstallPanel.begin")); buildConstraints(gbConstraints, 0, 2, 2, 1, 1.0, 0.0); layout.addLayoutComponent(progressBar, gbConstraints); contentPane.add(progressBar); destroyButton = ButtonFactory.createButton(langpack.getString("uninstaller.uninstall"), icons.getImageIcon("delete"), buttonsHColor); destroyButton.addActionListener(handler); buildConstraints(gbConstraints, 0, 3, 1, 1, 0.5, 0.0); gbConstraints.fill = GridBagConstraints.NONE; gbConstraints.anchor = GridBagConstraints.WEST; layout.addLayoutComponent(destroyButton, gbConstraints); contentPane.add(destroyButton); quitButton = ButtonFactory.createButton(langpack.getString("installer.quit"), icons.getImageIcon("stop"), buttonsHColor); quitButton.addActionListener(handler); buildConstraints(gbConstraints, 1, 3, 1, 1, 0.5, 0.0); gbConstraints.anchor = GridBagConstraints.EAST; layout.addLayoutComponent(quitButton, gbConstraints); contentPane.add(quitButton); }

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private void buildGUI() { // We initialize our layout JPanel contentPane = (JPanel) getContentPane(); layout = new GridBagLayout(); contentPane.setLayout(layout); gbConstraints = new GridBagConstraints(); gbConstraints.insets = new Insets(5, 5, 5, 5); // We prepare our action handler ActionsHandler handler = new ActionsHandler(); // Prepares the glass pane to block gui interaction when needed JPanel glassPane = (JPanel) getGlassPane(); glassPane.addMouseListener( new MouseAdapter() { }); glassPane.addMouseMotionListener( new MouseMotionAdapter() { }); glassPane.addKeyListener( new KeyAdapter() { }); // We set-up the buttons factory ButtonFactory.useButtonIcons(); ButtonFactory.useHighlightButtons(); // We put our components warningLabel = new JLabel(langpack.getString("uninstaller.warning"), icons.getImageIcon("warning"), JLabel.TRAILING); buildConstraints(gbConstraints, 0, 0, 2, 1, 1.0, 0.0); gbConstraints.anchor = GridBagConstraints.WEST; gbConstraints.fill = GridBagConstraints.NONE; layout.addLayoutComponent(warningLabel, gbConstraints); contentPane.add(warningLabel); targetDestroyCheckbox = new JCheckBox(langpack.getString("uninstaller.destroytarget") + installPath, false); buildConstraints(gbConstraints, 0, 1, 2, 1, 1.0, 0.0); layout.addLayoutComponent(targetDestroyCheckbox, gbConstraints); contentPane.add(targetDestroyCheckbox); gbConstraints.fill = GridBagConstraints.HORIZONTAL; progressBar = new JProgressBar(); progressBar.setStringPainted(true); progressBar.setString(langpack.getString("InstallPanel.begin")); buildConstraints(gbConstraints, 0, 2, 2, 1, 1.0, 0.0); layout.addLayoutComponent(progressBar, gbConstraints); contentPane.add(progressBar); destroyButton = ButtonFactory.createButton(langpack.getString("uninstaller.uninstall"), icons.getImageIcon("delete"), buttonsHColor); destroyButton.addActionListener(handler); buildConstraints(gbConstraints, 0, 3, 1, 1, 0.5, 0.0); gbConstraints.fill = GridBagConstraints.NONE; gbConstraints.anchor = GridBagConstraints.WEST; layout.addLayoutComponent(destroyButton, gbConstraints); contentPane.add(destroyButton); quitButton = ButtonFactory.createButton(langpack.getString("installer.quit"), icons.getImageIcon("stop"), buttonsHColor); quitButton.addActionListener(handler); buildConstraints(gbConstraints, 1, 3, 1, 1, 0.5, 0.0); gbConstraints.anchor = GridBagConstraints.EAST; layout.addLayoutComponent(quitButton, gbConstraints); contentPane.add(quitButton); }

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private void buildGUI() { // We initialize our layout JPanel contentPane = (JPanel) getContentPane(); layout = new GridBagLayout(); contentPane.setLayout(layout); gbConstraints = new GridBagConstraints(); gbConstraints.insets = new Insets(5, 5, 5, 5); // We prepare our action handler ActionsHandler handler = new ActionsHandler(); // Prepares the glass pane to block gui interaction when needed JPanel glassPane = (JPanel) getGlassPane(); glassPane.addMouseListener( new MouseAdapter() { }); glassPane.addMouseMotionListener( new MouseMotionAdapter() { }); glassPane.addKeyListener( new KeyAdapter() { }); // We set-up the buttons factory ButtonFactory.useButtonIcons(); ButtonFactory.useHighlightButtons(); // We put our components warningLabel = new JLabel(langpack.getString("uninstaller.warning"), icons.getImageIcon("warning"), JLabel.TRAILING); buildConstraints(gbConstraints, 0, 0, 2, 1, 1.0, 0.0); gbConstraints.anchor = GridBagConstraints.WEST; gbConstraints.fill = GridBagConstraints.NONE; layout.addLayoutComponent(warningLabel, gbConstraints); contentPane.add(warningLabel); targetDestroyCheckbox = new JCheckBox(langpack.getString("uninstaller.destroytarget") + installPath, false); buildConstraints(gbConstraints, 0, 1, 2, 1, 1.0, 0.0); layout.addLayoutComponent(targetDestroyCheckbox, gbConstraints); contentPane.add(targetDestroyCheckbox); gbConstraints.fill = GridBagConstraints.HORIZONTAL; progressBar = new JProgressBar(); progressBar.setStringPainted(true); progressBar.setString(langpack.getString("InstallPanel.begin")); buildConstraints(gbConstraints, 0, 2, 2, 1, 1.0, 0.0); layout.addLayoutComponent(progressBar, gbConstraints); contentPane.add(progressBar); destroyButton = ButtonFactory.createButton(langpack.getString("uninstaller.uninstall"), icons.getImageIcon("delete"), buttonsHColor); destroyButton.addActionListener(handler); buildConstraints(gbConstraints, 0, 3, 1, 1, 0.5, 0.0); gbConstraints.fill = GridBagConstraints.NONE; gbConstraints.anchor = GridBagConstraints.WEST; layout.addLayoutComponent(destroyButton, gbConstraints); contentPane.add(destroyButton); quitButton = ButtonFactory.createButton(langpack.getString("installer.quit"), icons.getImageIcon("stop"), buttonsHColor); quitButton.addActionListener(handler); buildConstraints(gbConstraints, 1, 3, 1, 1, 0.5, 0.0); gbConstraints.anchor = GridBagConstraints.EAST; layout.addLayoutComponent(quitButton, gbConstraints); contentPane.add(quitButton); }

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private void buildGUI() { // We initialize our layout JPanel contentPane = (JPanel) getContentPane(); layout = new GridBagLayout(); contentPane.setLayout(layout); gbConstraints = new GridBagConstraints(); gbConstraints.insets = new Insets(5, 5, 5, 5); // We prepare our action handler ActionsHandler handler = new ActionsHandler(); // Prepares the glass pane to block gui interaction when needed JPanel glassPane = (JPanel) getGlassPane(); glassPane.addMouseListener( new MouseAdapter() { }); glassPane.addMouseMotionListener( new MouseMotionAdapter() { }); glassPane.addKeyListener( new KeyAdapter() { }); // We set-up the buttons factory ButtonFactory.useButtonIcons(); ButtonFactory.useHighlightButtons(); // We put our components warningLabel = new JLabel(langpack.getString("uninstaller.warning"), icons.getImageIcon("warning"), JLabel.TRAILING); buildConstraints(gbConstraints, 0, 0, 2, 1, 1.0, 0.0); gbConstraints.anchor = GridBagConstraints.WEST; gbConstraints.fill = GridBagConstraints.NONE; layout.addLayoutComponent(warningLabel, gbConstraints); contentPane.add(warningLabel); targetDestroyCheckbox = new JCheckBox(langpack.getString("uninstaller.destroytarget") + installPath, false); buildConstraints(gbConstraints, 0, 1, 2, 1, 1.0, 0.0); layout.addLayoutComponent(targetDestroyCheckbox, gbConstraints); contentPane.add(targetDestroyCheckbox); gbConstraints.fill = GridBagConstraints.HORIZONTAL; progressBar = new JProgressBar(); progressBar.setStringPainted(true); progressBar.setString(langpack.getString("InstallPanel.begin")); buildConstraints(gbConstraints, 0, 2, 2, 1, 1.0, 0.0); layout.addLayoutComponent(progressBar, gbConstraints); contentPane.add(progressBar); destroyButton = ButtonFactory.createButton(langpack.getString("uninstaller.uninstall"), icons.getImageIcon("delete"), buttonsHColor); destroyButton.addActionListener(handler); buildConstraints(gbConstraints, 0, 3, 1, 1, 0.5, 0.0); gbConstraints.fill = GridBagConstraints.NONE; gbConstraints.anchor = GridBagConstraints.WEST; layout.addLayoutComponent(destroyButton, gbConstraints); contentPane.add(destroyButton); quitButton = ButtonFactory.createButton(langpack.getString("installer.quit"), icons.getImageIcon("stop"), buttonsHColor); quitButton.addActionListener(handler); buildConstraints(gbConstraints, 1, 3, 1, 1, 0.5, 0.0); gbConstraints.anchor = GridBagConstraints.EAST; layout.addLayoutComponent(quitButton, gbConstraints); contentPane.add(quitButton); }

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private void buildGUI() { // We initialize our layout JPanel contentPane = (JPanel) getContentPane(); layout = new GridBagLayout(); contentPane.setLayout(layout); gbConstraints = new GridBagConstraints(); gbConstraints.insets = new Insets(5, 5, 5, 5); // We prepare our action handler ActionsHandler handler = new ActionsHandler(); // Prepares the glass pane to block gui interaction when needed JPanel glassPane = (JPanel) getGlassPane(); glassPane.addMouseListener( new MouseAdapter() { }); glassPane.addMouseMotionListener( new MouseMotionAdapter() { }); glassPane.addKeyListener( new KeyAdapter() { }); // We set-up the buttons factory ButtonFactory.useButtonIcons(); ButtonFactory.useHighlightButtons(); // We put our components warningLabel = new JLabel(langpack.getString("uninstaller.warning"), icons.getImageIcon("warning"), JLabel.TRAILING); buildConstraints(gbConstraints, 0, 0, 2, 1, 1.0, 0.0); gbConstraints.anchor = GridBagConstraints.WEST; gbConstraints.fill = GridBagConstraints.NONE; layout.addLayoutComponent(warningLabel, gbConstraints); contentPane.add(warningLabel); targetDestroyCheckbox = new JCheckBox(langpack.getString("uninstaller.destroytarget") + installPath, false); buildConstraints(gbConstraints, 0, 1, 2, 1, 1.0, 0.0); layout.addLayoutComponent(targetDestroyCheckbox, gbConstraints); contentPane.add(targetDestroyCheckbox); gbConstraints.fill = GridBagConstraints.HORIZONTAL; progressBar = new JProgressBar(); progressBar.setStringPainted(true); progressBar.setString(langpack.getString("InstallPanel.begin")); buildConstraints(gbConstraints, 0, 2, 2, 1, 1.0, 0.0); layout.addLayoutComponent(progressBar, gbConstraints); contentPane.add(progressBar); destroyButton = ButtonFactory.createButton(langpack.getString("uninstaller.uninstall"), icons.getImageIcon("delete"), buttonsHColor); destroyButton.addActionListener(handler); buildConstraints(gbConstraints, 0, 3, 1, 1, 0.5, 0.0); gbConstraints.fill = GridBagConstraints.NONE; gbConstraints.anchor = GridBagConstraints.WEST; layout.addLayoutComponent(destroyButton, gbConstraints); contentPane.add(destroyButton); quitButton = ButtonFactory.createButton(langpack.getString("installer.quit"), icons.getImageIcon("stop"), buttonsHColor); quitButton.addActionListener(handler); buildConstraints(gbConstraints, 1, 3, 1, 1, 0.5, 0.0); gbConstraints.anchor = GridBagConstraints.EAST; layout.addLayoutComponent(quitButton, gbConstraints); contentPane.add(quitButton); }

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private void centerFrame(Window frame) { Dimension frameSize = frame.getSize(); Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); frame.setLocation((screenSize.width - frameSize.width) / 2, (screenSize.height - frameSize.height) / 2 - 10); }

private void centerFrame(Window frame) { Dimension frameSize = frame.getSize(); Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); frame.setLocation( (screenSize.width - frameSize.width) / 2, (screenSize.height - frameSize.height) / 2 - 10); }

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private void divideLabel () { int width; int startPos; int currentPos; int lastPos; int endPos; line.clear (); FontMetrics fm = this.getFontMetrics (this.getFont ()); startPos = 0; currentPos = startPos; lastPos = currentPos; endPos = (labelText.length () - 1); while (currentPos < endPos) { width = 0; // ---------------------------------------------------------------- // find the first substring that occupies more than the granted space. // Break at the end of the string or a line break // ---------------------------------------------------------------- while ( (width < maxAllowed) && (currentPos < endPos) && (labelText.charAt (currentPos) != NEW_LINE)) { lastPos = currentPos; currentPos = getPosition (labelText, currentPos, WHITE_SPACE, FOUND); width = fm.stringWidth (labelText.substring (startPos, currentPos)); } // ---------------------------------------------------------------- // if we have a line break we want to copy everything up to currentPos // ---------------------------------------------------------------- if (labelText.charAt (currentPos) == NEW_LINE) { lastPos = currentPos; } // ---------------------------------------------------------------- // if we are at the end of the string we want to copy everything up to // the last character. Since there seems to be a problem to get the last // character if the substring definition ends at the very last character // we have to call a different substring function than normal. // ---------------------------------------------------------------- if (currentPos == endPos) { lastPos = currentPos; String s = labelText.substring (startPos); line.addElement (s); } // ---------------------------------------------------------------- // in all other cases copy the substring that we have found to fit and // add it as a new line of text to the line vector. // ---------------------------------------------------------------- else { // ------------------------------------------------------------ // make sure it's not a single word. If so we must break it at the // proper location. // ------------------------------------------------------------ if (lastPos == startPos) { lastPos = startPos + breakWord (labelText.substring (startPos, currentPos), fm); } String s = labelText.substring (startPos, lastPos); line.addElement (s); } // ---------------------------------------------------------------- // seek for the end of the white space to cut out any unnecessary spaces // and tabs and set the new start condition. // ---------------------------------------------------------------- startPos = getPosition (labelText, lastPos, SPACES, NOT_FOUND); currentPos = startPos; } numLines = line.size (); lineWidth = new int [numLines]; }

private void divideLabel () { int width; int startPos; int currentPos; int lastPos; int endPos; line.clear (); FontMetrics fm = this.getFontMetrics (this.getFont ()); startPos = 0; currentPos = startPos; lastPos = currentPos; endPos = (labelText.length () - 1); while (currentPos < endPos) { width = 0; // ---------------------------------------------------------------- // find the first substring that occupies more than the granted space. // Break at the end of the string or a line break // ---------------------------------------------------------------- while ( (width < maxAllowed) && (currentPos < endPos) && (labelText.charAt (currentPos) != NEW_LINE)) { lastPos = currentPos; currentPos = getPosition (labelText, currentPos, WHITE_SPACE, FOUND); width = fm.stringWidth (labelText.substring (startPos, currentPos)); } // ---------------------------------------------------------------- // if we have a line break we want to copy everything up to currentPos // ---------------------------------------------------------------- if (labelText.charAt (currentPos) == NEW_LINE) { lastPos = currentPos; } // ---------------------------------------------------------------- // if we are at the end of the string we want to copy everything up to // the last character. Since there seems to be a problem to get the last // character if the substring definition ends at the very last character // we have to call a different substring function than normal. // ---------------------------------------------------------------- if (currentPos == endPos && width <= maxAllowed) { lastPos = currentPos; String s = labelText.substring (startPos); line.addElement (s); } // ---------------------------------------------------------------- // in all other cases copy the substring that we have found to fit and // add it as a new line of text to the line vector. // ---------------------------------------------------------------- else { // ------------------------------------------------------------ // make sure it's not a single word. If so we must break it at the // proper location. // ------------------------------------------------------------ if (lastPos == startPos) { lastPos = startPos + breakWord (labelText.substring (startPos, currentPos), fm); } String s = labelText.substring (startPos, lastPos); line.addElement (s); } // ---------------------------------------------------------------- // seek for the end of the white space to cut out any unnecessary spaces // and tabs and set the new start condition. // ---------------------------------------------------------------- startPos = getPosition (labelText, lastPos, SPACES, NOT_FOUND); currentPos = startPos; } numLines = line.size (); lineWidth = new int [numLines]; }

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public InfoPanel(InstallerFrame parent, InstallData idata) { super(parent, idata); // We initialize our layout layout = new GridBagLayout(); gbConstraints = new GridBagConstraints(); setLayout(layout); // We load the text loadInfo(); // We add the components infoLabel = new JLabel(parent.langpack.getString("InfoPanel.info"), parent.icons.getImageIcon("edit"), JLabel.TRAILING); parent.buildConstraints(gbConstraints, 0, 0, 1, 1, 1.0, 0.1); gbConstraints.insets = new Insets(5, 5, 5, 5); gbConstraints.fill = GridBagConstraints.NONE; gbConstraints.anchor = GridBagConstraints.SOUTHWEST; layout.addLayoutComponent(infoLabel, gbConstraints); add(infoLabel); textArea = new JTextArea(info); textArea.setCaretPosition(0); textArea.setEditable(false); scroller = new JScrollPane(textArea); parent.buildConstraints(gbConstraints, 0, 1, 1, 1, 1.0, 0.9); gbConstraints.fill = GridBagConstraints.BOTH; gbConstraints.anchor = GridBagConstraints.CENTER; layout.addLayoutComponent(scroller, gbConstraints); add(scroller); }

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private void loadInfo() { try { String resNamePrifix = "InfoPanel.info"; info = ResourceManager.getInstance().getTextResource(resNamePrifix); } catch (Exception err) { info = "Error : could not load the info text !"; } }

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public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged) { //#[ operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,Temperature,Pressure,boolean) ReactionTime rt = p_beginStatus.getTime(); if (!rt.equals(p_beginTime)) throw new InvalidBeginStatusException(); // set time double tBegin = p_beginTime.getStandardTime(); double tEnd = p_endTime.getStandardTime(); // set reaction set //if (p_initialization || p_reactionChanged || p_conditionChanged) { //generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedList rList = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateAllODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //p_reactionChanged = true; //} // set numbers System.out.println("Total number of reactions to Daspk is "+rList.size()); int nState = p_reactionModel.getSpeciesNumber(); int nParameter = 0; LinkedList initialSpecies = new LinkedList();// if (parameterInfor!=null) nParameter = parameterInfor.length; if (parameterInfor != 0) { nParameter = rList.size(); //svp if (initialStatus == null) System.out.println("initialStatus = null"); Iterator spe_iter = initialStatus.getSpeciesStatus(); while (spe_iter.hasNext()) { SpeciesStatus ss = (SpeciesStatus) spe_iter.next(); String name = ss.getSpecies().getName(); initialSpecies.add(name); nParameter++; } } int neq = nState*(nParameter+1); // set temperature and pressure double T = p_temperature.getK(); double P = p_pressure.getAtm(); // set initial value of y and yprime; double [] y = new double[neq]; double [] yprime = new double[neq]; //double numberOfReactedSpecies=0; // get the present status at t_begin, and set y and y' accordingly System.out.println("Before ODE: " + String.valueOf(tBegin) + "SEC"); System.out.println("End at : " + String.valueOf(tEnd) + "SEC"); for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) { SpeciesStatus ss = (SpeciesStatus)iter.next(); double conc = ss.getConcentration(); double flux = ss.getFlux(); if (ss.isReactedSpecies()) { Species spe = ss.getSpecies(); int id = getRealID(spe); System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getName() + '\t' + String.valueOf(conc) + '\t' + String.valueOf(flux)); y[id-1] = conc; yprime[id-1] = flux; } } if (nParameter != 0){//svp parameterInforArray = new ParameterInfor[nParameter]; for (int i = 1; i <= rList.size(); i++){ parameterInforArray[i-1] = new ParameterInfor("k",i,0.00); } for (int i=rList.size()+1; i<=nParameter;i++){ parameterInforArray[i - 1] = new ParameterInfor("CO", nParameter, 0.00); } if (p_beginTime.getTime() == 0 || p_beginTime.getTime() == 0.00) { LinkedList sensitivityStatus = new LinkedList(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber();// for (int i=0;i<reactionNumber*speciesNumber;i++){ for (int i=0; i<nParameter*speciesNumber;i++){ sensitivityStatus.add(i,null); } p_beginStatus.addSensitivity(sensitivityStatus); double sflux = 1; Iterator species_iter = p_reactionModel.getSpecies(); while (species_iter.hasNext()) { Species spe = (Species) species_iter.next(); int m = getRealID(spe); for (int p=0;p<nParameter;p++){ int k = m + (p+1) * speciesNumber - 1; if (p >= rList.size()){ int speciesNum = p-rList.size(); String name = (String)initialSpecies.get(speciesNum); sflux = 0; SensitivityStatus senStatus; if (name.equalsIgnoreCase(spe.getName())){ senStatus = new SensitivityStatus(1, sflux, m, p + 1); y[k] = 1; } else{ senStatus = new SensitivityStatus(0,sflux,m,p+1); y[k]=0; } sensitivityStatus.add(k - p_reactionModel.getSpeciesNumber(), senStatus); p_beginStatus.putSensitivityStatus(k - speciesNumber, senStatus); yprime[k] = sflux; } else{ Reaction rxn = (Reaction)rList.get(p); if (rxn.containsAsProduct(spe)) { sflux = 1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } if (rxn.containsAsReactant(spe)) { sflux = -1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } else { sflux = 0; } SensitivityStatus senStatus = new SensitivityStatus(0, sflux, m, p+1); sensitivityStatus.add(k-p_reactionModel.getSpeciesNumber(),senStatus); p_beginStatus.putSensitivityStatus(k-speciesNumber,senStatus); y[k] = 0; yprime[k] = sflux; } } } } else { for (int i = p_reactionModel.getSpeciesNumber(); i < y.length; i++) { SensitivityStatus ss = (SensitivityStatus) p_beginStatus. getSensitivityStatus(i-p_reactionModel.getSpeciesNumber()); double sens = ss.getSensitivity(); double sflux = ss.getSFlux(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber(); Iterator species_iter = p_reactionModel.getSpecies(); y[i] = sens; yprime[i] = sflux; } } } //System.out.println("Number of Reacted Species is " + numberOfReactedSpecies); int idid; HashMap speStatus = new HashMap(); LinkedList senStatus = new LinkedList(); double[] tPresent = {tBegin}; int temp = 1; if (nParameter==0) { idid = solveDAE(p_initialization, reactionList, true, thirdBodyReactionList, nState, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid !=1 && idid != 2 && idid != 3) { System.out.println("The idid from DASPK was "+idid + " at time "+tPresent[0]); throw new DynamicSimulatorException("DASPK: SA off."); } System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, 0); } else { idid = solveSEN(p_initialization, reactionList, p_reactionChanged, thirdBodyReactionList, nState, nParameter, this.parameterInforArray, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid != 2 && idid != 3) throw new DynamicSimulatorException("DASPK: SA on."); //speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); senStatus = generateSensitivityStatus(p_reactionModel,y,yprime,nParameter); SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, senStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); sss.setIDTranslator(IDTranslator); sss.setReactionList(rList); return sss; } SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CH4"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO2"), rList, sss, p_temperature); return sss; //#] }

generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); publicgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SystemSnapshotgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); solve(booleangenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_initialization,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ReactionModelgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_reactionModel,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); booleangenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_reactionChanged,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SystemSnapshotgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginStatus,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ReactionTimegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginTime,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ReactionTimegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_endTime,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); TemperaturegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_temperature,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); PressuregenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_pressure,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); booleangenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_conditionChanged)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //#[generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); operationgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,Temperature,Pressure,boolean)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ReactionTimegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); rtgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginStatus.getTime();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (!rt.equals(p_beginTime))generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); throwgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); InvalidBeginStatusException();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); setgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); timegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); doublegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); tBegingenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginTime.getStandardTime();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); doublegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); tEndgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_endTime.getStandardTime();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); setgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); reactiongenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); setgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (p_initializationgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ||generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_reactionChangedgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ||generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_conditionChanged)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateThirdBodyReactionList(p_reactionModel,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginStatus,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_temperature,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_pressure);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedListgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); rListgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generatePDepODEReactionList(p_reactionModel,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginStatus,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_temperature,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_pressure);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateAllODEReactionList(p_reactionModel,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginStatus,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_temperature,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_pressure);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //p_reactionChangedgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); true;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //}generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); setgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); numbers System.out.println("TotalgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); numbergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ofgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); reactionsgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); togenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); DaspkgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); isgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "+rList.size());generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); nStategenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_reactionModel.getSpeciesNumber();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); nParametergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 0;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedListgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); initialSpeciesgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedList();//generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (parameterInfor!=null)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); nParametergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); parameterInfor.length;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (parameterInforgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); !=generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 0)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); nParametergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); rList.size();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //svpgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (initialStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ==generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); null)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); System.out.println("initialStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); null");generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); IteratorgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); spe_itergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); initialStatus.getSpeciesStatus();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); whilegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (spe_iter.hasNext())generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SpeciesStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ssgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (SpeciesStatus)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); spe_iter.next();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); StringgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); namegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ss.getSpecies().getName();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); initialSpecies.add(name);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); nParameter++;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); neqgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); nState*(nParameter+1);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); setgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); temperaturegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); andgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); pressuregenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); doublegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); TgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_temperature.getK();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); doublegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); PgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_pressure.getAtm();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); setgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); initialgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); valuegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ofgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ygenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); andgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); yprime;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); doublegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); []generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ygenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); double[neq];generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); doublegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); []generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); yprimegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); double[neq]; //doublegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); numberOfReactedSpecies=0;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); getgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); thegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); presentgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); statusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); atgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); t_begin,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); andgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); setgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ygenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); andgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); y'generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); accordinglygenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); System.out.println("BeforegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ODE:generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); String.valueOf(tBegin)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "SEC");generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); System.out.println("EndgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); atgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); :generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); String.valueOf(tEnd)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "SEC");generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); forgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (IteratorgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); itergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginStatus.getSpeciesStatus();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); iter.hasNext();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); )generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SpeciesStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ssgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (SpeciesStatus)iter.next();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); doublegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); concgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ss.getConcentration();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); doublegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); fluxgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ss.getFlux();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (ss.isReactedSpecies())generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SpeciesgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); spegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ss.getSpecies();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); idgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); getRealID(spe);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); System.out.println(String.valueOf(spe.getID())generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); '\t'generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); spe.getName()generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); '\t'generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); String.valueOf(conc)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); '\t'generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); String.valueOf(flux));generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); y[id-1]generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); conc;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); yprime[id-1]generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); flux;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (nParametergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); !=generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 0){//svpgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); parameterInforArraygenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ParameterInfor[nParameter];generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); forgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); igenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 1;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); igenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); <=generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); rList.size();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); i++){generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); parameterInforArray[i-1]generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ParameterInfor("k",i,0.00);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); forgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); i=rList.size()+1;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); i<=nParameter;i++){generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); parameterInforArray[igenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); -generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 1]generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ParameterInfor("CO",generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); nParameter,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 0.00);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (p_beginTime.getTime()generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ==generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 0generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ||generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginTime.getTime()generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ==generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 0.00)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedListgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sensitivityStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedList();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); reactionNumbergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); rList.size();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); speciesNumbergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_reactionModel.getSpeciesNumber();//generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); forgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); i=0;i<reactionNumber*speciesNumber;i++){generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); forgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); i=0;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); i<nParameter*speciesNumber;i++){generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sensitivityStatus.add(i,null);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginStatus.addSensitivity(sensitivityStatus);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); doublegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sfluxgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 1;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); IteratorgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); species_itergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_reactionModel.getSpecies();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); whilegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (species_iter.hasNext())generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SpeciesgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); spegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (Species)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); species_iter.next();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); mgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); getRealID(spe);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); forgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p=0;p<nParameter;p++){generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); kgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); mgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (p+1)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); *generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); speciesNumbergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); -generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 1;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (pgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); >=generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); rList.size()){generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); speciesNumgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p-rList.size();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); StringgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); namegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (String)initialSpecies.get(speciesNum);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sfluxgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 0;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SensitivityStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); senStatus;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (name.equalsIgnoreCase(spe.getName())){generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); senStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SensitivityStatus(1,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sflux,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); m,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); pgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 1);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); y[k]generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 1;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); else{generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); senStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SensitivityStatus(0,sflux,m,p+1);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); y[k]=0;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sensitivityStatus.add(kgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); -generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_reactionModel.getSpeciesNumber(),generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); senStatus);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginStatus.putSensitivityStatus(kgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); -generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); speciesNumber,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); senStatus);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); yprime[k]generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sflux;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); else{generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ReactiongenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); rxngenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (Reaction)rList.get(p);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (rxn.containsAsProduct(spe))generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sfluxgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 1;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); IteratorgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); new_itergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); rxn.getReactants();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); whilegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (new_iter.hasNext())generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ChemGraphgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); cggenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (ChemGraph)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); new_iter.next();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SpeciesgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); reactantgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); cg.getSpecies();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SpeciesStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ssgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginStatus.getSpeciesStatus(reactant);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (ssgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); !=generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); null)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sfluxgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); *=generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ss.getConcentration();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); elsegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sfluxgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 0;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (rxn.containsAsReactant(spe))generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sfluxgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); -1;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); IteratorgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); new_itergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); rxn.getReactants();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); whilegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (new_iter.hasNext())generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ChemGraphgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); cggenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (ChemGraph)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); new_iter.next();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SpeciesgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); reactantgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); cg.getSpecies();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SpeciesStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ssgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginStatus.getSpeciesStatus(reactant);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (ssgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); !=generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); null)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 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ss.getConcentration();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); elsegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sfluxgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 0;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); elsegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sfluxgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 0;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SensitivityStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); senStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SensitivityStatus(0,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sflux,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); m,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p+1);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sensitivityStatus.add(k-p_reactionModel.getSpeciesNumber(),senStatus);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginStatus.putSensitivityStatus(k-speciesNumber,senStatus);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); y[k]generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 0;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); yprime[k]generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sflux;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); elsegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); forgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); igenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_reactionModel.getSpeciesNumber();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); igenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); <generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); y.length;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); i++)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SensitivityStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ssgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (SensitivityStatus)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginStatus.generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); getSensitivityStatus(i-p_reactionModel.getSpeciesNumber());generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); doublegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sensgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ss.getSensitivity();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); doublegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sfluxgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ss.getSFlux();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); reactionNumbergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); rList.size();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); speciesNumbergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_reactionModel.getSpeciesNumber();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); IteratorgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); species_itergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_reactionModel.getSpecies();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); y[i]generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sens;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); yprime[i]generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sflux;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); } //System.out.println("NumbergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ofgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ReactedgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SpeciesgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); isgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); numberOfReactedSpecies);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); idid;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); HashMapgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); speStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); HashMap();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedListgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); senStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedList();generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); double[]generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); tPresentgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {tBegin}; intgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); tempgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 1;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (nParameter==0)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ididgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); solveDAE(p_initialization,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); reactionList,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); true,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); thirdBodyReactionList,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); nState,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); y,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); yprime,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); tBegin,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); tEnd,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); this.rtol,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); this.atol,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); T,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); P);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (ididgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); !=1generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); &&generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ididgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); !=generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 2generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); &&generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ididgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); !=generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 3) { System.out.println("ThegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ididgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); fromgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); DASPKgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); wasgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "+ididgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); atgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); timegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "+tPresent[0]); throwgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); DynamicSimulatorException("DASPK:generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SAgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); off.");generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); System.out.println("AftergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ODE:generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); fromgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); String.valueOf(tBegin)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SECgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); togenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); String.valueOf(tEnd)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "SEC");generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); speStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateSpeciesStatus(p_reactionModel,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); y,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); yprime,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 0);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); elsegenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); {generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ididgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); solveSEN(p_initialization,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); reactionList,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_reactionChanged,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); thirdBodyReactionList,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); nState,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); nParameter,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); this.parameterInforArray,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); y,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); yprime,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); tBegin,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); tEnd,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); this.rtol,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); this.atol,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); T,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); P);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ifgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); (ididgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); !=generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 2generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); &&generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ididgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); !=generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); 3)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); throwgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); DynamicSimulatorException("DASPK:generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SAgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); on.");generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //speStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateSpeciesStatus(p_reactionModel,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); y,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); yprime,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); nParameter);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); System.out.println("AftergenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); ODE:generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); fromgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); String.valueOf(tBegin)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SECgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); togenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); String.valueOf(tEnd)generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); +generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); "SEC");generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); speStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateSpeciesStatus(p_reactionModel,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); y,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); yprime,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); nParameter);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); senStatusgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateSensitivityStatus(p_reactionModel,y,yprime,nParameter);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SystemSnapshotgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sssgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SystemSnapshot(p_endTime,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); speStatus,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); senStatus,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginStatus.getTemperature(),generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginStatus.getPressure());generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sss.setIDTranslator(IDTranslator);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sss.setReactionList(rList);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); returngenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sss;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); } SystemSnapshotgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sssgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); =generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); newgenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); SystemSnapshot(p_endTime,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); speStatus,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginStatus.getTemperature(),generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_beginStatus.getPressure()); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CH4"),generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); rList,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sss,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_temperature);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO"),generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); rList,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sss,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_temperature);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO2"),generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); rList,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sss,generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); p_temperature);generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); returngenerateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); sss;generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //#]generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); }

3,240,354

public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged) { //#[ operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,Temperature,Pressure,boolean) ReactionTime rt = p_beginStatus.getTime(); if (!rt.equals(p_beginTime)) throw new InvalidBeginStatusException(); // set time double tBegin = p_beginTime.getStandardTime(); double tEnd = p_endTime.getStandardTime(); // set reaction set //if (p_initialization || p_reactionChanged || p_conditionChanged) { //generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedList rList = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateAllODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //p_reactionChanged = true; //} // set numbers System.out.println("Total number of reactions to Daspk is "+rList.size()); int nState = p_reactionModel.getSpeciesNumber(); int nParameter = 0; LinkedList initialSpecies = new LinkedList();// if (parameterInfor!=null) nParameter = parameterInfor.length; if (parameterInfor != 0) { nParameter = rList.size(); //svp if (initialStatus == null) System.out.println("initialStatus = null"); Iterator spe_iter = initialStatus.getSpeciesStatus(); while (spe_iter.hasNext()) { SpeciesStatus ss = (SpeciesStatus) spe_iter.next(); String name = ss.getSpecies().getName(); initialSpecies.add(name); nParameter++; } } int neq = nState*(nParameter+1); // set temperature and pressure double T = p_temperature.getK(); double P = p_pressure.getAtm(); // set initial value of y and yprime; double [] y = new double[neq]; double [] yprime = new double[neq]; //double numberOfReactedSpecies=0; // get the present status at t_begin, and set y and y' accordingly System.out.println("Before ODE: " + String.valueOf(tBegin) + "SEC"); System.out.println("End at : " + String.valueOf(tEnd) + "SEC"); for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) { SpeciesStatus ss = (SpeciesStatus)iter.next(); double conc = ss.getConcentration(); double flux = ss.getFlux(); if (ss.isReactedSpecies()) { Species spe = ss.getSpecies(); int id = getRealID(spe); System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getName() + '\t' + String.valueOf(conc) + '\t' + String.valueOf(flux)); y[id-1] = conc; yprime[id-1] = flux; } } if (nParameter != 0){//svp parameterInforArray = new ParameterInfor[nParameter]; for (int i = 1; i <= rList.size(); i++){ parameterInforArray[i-1] = new ParameterInfor("k",i,0.00); } for (int i=rList.size()+1; i<=nParameter;i++){ parameterInforArray[i - 1] = new ParameterInfor("CO", nParameter, 0.00); } if (p_beginTime.getTime() == 0 || p_beginTime.getTime() == 0.00) { LinkedList sensitivityStatus = new LinkedList(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber();// for (int i=0;i<reactionNumber*speciesNumber;i++){ for (int i=0; i<nParameter*speciesNumber;i++){ sensitivityStatus.add(i,null); } p_beginStatus.addSensitivity(sensitivityStatus); double sflux = 1; Iterator species_iter = p_reactionModel.getSpecies(); while (species_iter.hasNext()) { Species spe = (Species) species_iter.next(); int m = getRealID(spe); for (int p=0;p<nParameter;p++){ int k = m + (p+1) * speciesNumber - 1; if (p >= rList.size()){ int speciesNum = p-rList.size(); String name = (String)initialSpecies.get(speciesNum); sflux = 0; SensitivityStatus senStatus; if (name.equalsIgnoreCase(spe.getName())){ senStatus = new SensitivityStatus(1, sflux, m, p + 1); y[k] = 1; } else{ senStatus = new SensitivityStatus(0,sflux,m,p+1); y[k]=0; } sensitivityStatus.add(k - p_reactionModel.getSpeciesNumber(), senStatus); p_beginStatus.putSensitivityStatus(k - speciesNumber, senStatus); yprime[k] = sflux; } else{ Reaction rxn = (Reaction)rList.get(p); if (rxn.containsAsProduct(spe)) { sflux = 1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } if (rxn.containsAsReactant(spe)) { sflux = -1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } else { sflux = 0; } SensitivityStatus senStatus = new SensitivityStatus(0, sflux, m, p+1); sensitivityStatus.add(k-p_reactionModel.getSpeciesNumber(),senStatus); p_beginStatus.putSensitivityStatus(k-speciesNumber,senStatus); y[k] = 0; yprime[k] = sflux; } } } } else { for (int i = p_reactionModel.getSpeciesNumber(); i < y.length; i++) { SensitivityStatus ss = (SensitivityStatus) p_beginStatus. getSensitivityStatus(i-p_reactionModel.getSpeciesNumber()); double sens = ss.getSensitivity(); double sflux = ss.getSFlux(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber(); Iterator species_iter = p_reactionModel.getSpecies(); y[i] = sens; yprime[i] = sflux; } } } //System.out.println("Number of Reacted Species is " + numberOfReactedSpecies); int idid; HashMap speStatus = new HashMap(); LinkedList senStatus = new LinkedList(); double[] tPresent = {tBegin}; int temp = 1; if (nParameter==0) { idid = solveDAE(p_initialization, reactionList, true, thirdBodyReactionList, nState, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid !=1 && idid != 2 && idid != 3) { System.out.println("The idid from DASPK was "+idid + " at time "+tPresent[0]); throw new DynamicSimulatorException("DASPK: SA off."); } System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, 0); } else { idid = solveSEN(p_initialization, reactionList, p_reactionChanged, thirdBodyReactionList, nState, nParameter, this.parameterInforArray, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid != 2 && idid != 3) throw new DynamicSimulatorException("DASPK: SA on."); //speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); senStatus = generateSensitivityStatus(p_reactionModel,y,yprime,nParameter); SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, senStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); sss.setIDTranslator(IDTranslator); sss.setReactionList(rList); return sss; } SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CH4"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO2"), rList, sss, p_temperature); return sss; //#] }

public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged) { //#[ operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,Temperature,Pressure,boolean) ReactionTime rt = p_beginStatus.getTime(); if (!rt.equals(p_beginTime)) throw new InvalidBeginStatusException(); // set time double tBegin = p_beginTime.getStandardTime(); double tEnd = p_endTime.getStandardTime(); // set reaction set //if (p_initialization || p_reactionChanged || p_conditionChanged) { //generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedList rList = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateAllODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //p_reactionChanged = true; //} // set numbers System.out.println("Total number of reactions to Daspk is "+rList.size()); int nState = p_reactionModel.getSpeciesNumber(); int nParameter = 0; LinkedList initialSpecies = new LinkedList();// if (parameterInfor!=null) nParameter = parameterInfor.length; if (parameterInfor != 0) { nParameter = rList.size()+thirdBodyReactionList.length; //svp if (initialStatus == null) System.out.println("initialStatus = null"); Iterator spe_iter = initialStatus.getSpeciesStatus(); while (spe_iter.hasNext()) { SpeciesStatus ss = (SpeciesStatus) spe_iter.next(); String name = ss.getSpecies().getName(); initialSpecies.add(name); nParameter++; } } int neq = nState*(nParameter+1); // set temperature and pressure double T = p_temperature.getK(); double P = p_pressure.getAtm(); // set initial value of y and yprime; double [] y = new double[neq]; double [] yprime = new double[neq]; //double numberOfReactedSpecies=0; // get the present status at t_begin, and set y and y' accordingly System.out.println("Before ODE: " + String.valueOf(tBegin) + "SEC"); System.out.println("End at : " + String.valueOf(tEnd) + "SEC"); for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) { SpeciesStatus ss = (SpeciesStatus)iter.next(); double conc = ss.getConcentration(); double flux = ss.getFlux(); if (ss.isReactedSpecies()) { Species spe = ss.getSpecies(); int id = getRealID(spe); System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getName() + '\t' + String.valueOf(conc) + '\t' + String.valueOf(flux)); y[id-1] = conc; yprime[id-1] = flux; } } if (nParameter != 0){//svp parameterInforArray = new ParameterInfor[nParameter]; for (int i = 1; i <= rList.size(); i++){ parameterInforArray[i-1] = new ParameterInfor("k",i,0.00); } for (int i=rList.size()+1; i<=nParameter;i++){ parameterInforArray[i - 1] = new ParameterInfor("CO", nParameter, 0.00); } if (p_beginTime.getTime() == 0 || p_beginTime.getTime() == 0.00) { LinkedList sensitivityStatus = new LinkedList(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber();// for (int i=0;i<reactionNumber*speciesNumber;i++){ for (int i=0; i<nParameter*speciesNumber;i++){ sensitivityStatus.add(i,null); } p_beginStatus.addSensitivity(sensitivityStatus); double sflux = 1; Iterator species_iter = p_reactionModel.getSpecies(); while (species_iter.hasNext()) { Species spe = (Species) species_iter.next(); int m = getRealID(spe); for (int p=0;p<nParameter;p++){ int k = m + (p+1) * speciesNumber - 1; if (p >= rList.size()){ int speciesNum = p-rList.size(); String name = (String)initialSpecies.get(speciesNum); sflux = 0; SensitivityStatus senStatus; if (name.equalsIgnoreCase(spe.getName())){ senStatus = new SensitivityStatus(1, sflux, m, p + 1); y[k] = 1; } else{ senStatus = new SensitivityStatus(0,sflux,m,p+1); y[k]=0; } sensitivityStatus.add(k - p_reactionModel.getSpeciesNumber(), senStatus); p_beginStatus.putSensitivityStatus(k - speciesNumber, senStatus); yprime[k] = sflux; } else{ Reaction rxn = (Reaction)rList.get(p); if (rxn.containsAsProduct(spe)) { sflux = 1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } if (rxn.containsAsReactant(spe)) { sflux = -1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } else { sflux = 0; } SensitivityStatus senStatus = new SensitivityStatus(0, sflux, m, p+1); sensitivityStatus.add(k-p_reactionModel.getSpeciesNumber(),senStatus); p_beginStatus.putSensitivityStatus(k-speciesNumber,senStatus); y[k] = 0; yprime[k] = sflux; } } } } else { for (int i = p_reactionModel.getSpeciesNumber(); i < y.length; i++) { SensitivityStatus ss = (SensitivityStatus) p_beginStatus. getSensitivityStatus(i-p_reactionModel.getSpeciesNumber()); double sens = ss.getSensitivity(); double sflux = ss.getSFlux(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber(); Iterator species_iter = p_reactionModel.getSpecies(); y[i] = sens; yprime[i] = sflux; } } } //System.out.println("Number of Reacted Species is " + numberOfReactedSpecies); int idid; HashMap speStatus = new HashMap(); LinkedList senStatus = new LinkedList(); double[] tPresent = {tBegin}; int temp = 1; if (nParameter==0) { idid = solveDAE(p_initialization, reactionList, true, thirdBodyReactionList, nState, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid !=1 && idid != 2 && idid != 3) { System.out.println("The idid from DASPK was "+idid + " at time "+tPresent[0]); throw new DynamicSimulatorException("DASPK: SA off."); } System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, 0); } else { idid = solveSEN(p_initialization, reactionList, p_reactionChanged, thirdBodyReactionList, nState, nParameter, this.parameterInforArray, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid != 2 && idid != 3) throw new DynamicSimulatorException("DASPK: SA on."); //speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); senStatus = generateSensitivityStatus(p_reactionModel,y,yprime,nParameter); SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, senStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); sss.setIDTranslator(IDTranslator); sss.setReactionList(rList); return sss; } SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CH4"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO2"), rList, sss, p_temperature); return sss; //#] }

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public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged) { //#[ operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,Temperature,Pressure,boolean) ReactionTime rt = p_beginStatus.getTime(); if (!rt.equals(p_beginTime)) throw new InvalidBeginStatusException(); // set time double tBegin = p_beginTime.getStandardTime(); double tEnd = p_endTime.getStandardTime(); // set reaction set //if (p_initialization || p_reactionChanged || p_conditionChanged) { //generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedList rList = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateAllODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //p_reactionChanged = true; //} // set numbers System.out.println("Total number of reactions to Daspk is "+rList.size()); int nState = p_reactionModel.getSpeciesNumber(); int nParameter = 0; LinkedList initialSpecies = new LinkedList();// if (parameterInfor!=null) nParameter = parameterInfor.length; if (parameterInfor != 0) { nParameter = rList.size(); //svp if (initialStatus == null) System.out.println("initialStatus = null"); Iterator spe_iter = initialStatus.getSpeciesStatus(); while (spe_iter.hasNext()) { SpeciesStatus ss = (SpeciesStatus) spe_iter.next(); String name = ss.getSpecies().getName(); initialSpecies.add(name); nParameter++; } } int neq = nState*(nParameter+1); // set temperature and pressure double T = p_temperature.getK(); double P = p_pressure.getAtm(); // set initial value of y and yprime; double [] y = new double[neq]; double [] yprime = new double[neq]; //double numberOfReactedSpecies=0; // get the present status at t_begin, and set y and y' accordingly System.out.println("Before ODE: " + String.valueOf(tBegin) + "SEC"); System.out.println("End at : " + String.valueOf(tEnd) + "SEC"); for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) { SpeciesStatus ss = (SpeciesStatus)iter.next(); double conc = ss.getConcentration(); double flux = ss.getFlux(); if (ss.isReactedSpecies()) { Species spe = ss.getSpecies(); int id = getRealID(spe); System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getName() + '\t' + String.valueOf(conc) + '\t' + String.valueOf(flux)); y[id-1] = conc; yprime[id-1] = flux; } } if (nParameter != 0){//svp parameterInforArray = new ParameterInfor[nParameter]; for (int i = 1; i <= rList.size(); i++){ parameterInforArray[i-1] = new ParameterInfor("k",i,0.00); } for (int i=rList.size()+1; i<=nParameter;i++){ parameterInforArray[i - 1] = new ParameterInfor("CO", nParameter, 0.00); } if (p_beginTime.getTime() == 0 || p_beginTime.getTime() == 0.00) { LinkedList sensitivityStatus = new LinkedList(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber();// for (int i=0;i<reactionNumber*speciesNumber;i++){ for (int i=0; i<nParameter*speciesNumber;i++){ sensitivityStatus.add(i,null); } p_beginStatus.addSensitivity(sensitivityStatus); double sflux = 1; Iterator species_iter = p_reactionModel.getSpecies(); while (species_iter.hasNext()) { Species spe = (Species) species_iter.next(); int m = getRealID(spe); for (int p=0;p<nParameter;p++){ int k = m + (p+1) * speciesNumber - 1; if (p >= rList.size()){ int speciesNum = p-rList.size(); String name = (String)initialSpecies.get(speciesNum); sflux = 0; SensitivityStatus senStatus; if (name.equalsIgnoreCase(spe.getName())){ senStatus = new SensitivityStatus(1, sflux, m, p + 1); y[k] = 1; } else{ senStatus = new SensitivityStatus(0,sflux,m,p+1); y[k]=0; } sensitivityStatus.add(k - p_reactionModel.getSpeciesNumber(), senStatus); p_beginStatus.putSensitivityStatus(k - speciesNumber, senStatus); yprime[k] = sflux; } else{ Reaction rxn = (Reaction)rList.get(p); if (rxn.containsAsProduct(spe)) { sflux = 1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } if (rxn.containsAsReactant(spe)) { sflux = -1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } else { sflux = 0; } SensitivityStatus senStatus = new SensitivityStatus(0, sflux, m, p+1); sensitivityStatus.add(k-p_reactionModel.getSpeciesNumber(),senStatus); p_beginStatus.putSensitivityStatus(k-speciesNumber,senStatus); y[k] = 0; yprime[k] = sflux; } } } } else { for (int i = p_reactionModel.getSpeciesNumber(); i < y.length; i++) { SensitivityStatus ss = (SensitivityStatus) p_beginStatus. getSensitivityStatus(i-p_reactionModel.getSpeciesNumber()); double sens = ss.getSensitivity(); double sflux = ss.getSFlux(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber(); Iterator species_iter = p_reactionModel.getSpecies(); y[i] = sens; yprime[i] = sflux; } } } //System.out.println("Number of Reacted Species is " + numberOfReactedSpecies); int idid; HashMap speStatus = new HashMap(); LinkedList senStatus = new LinkedList(); double[] tPresent = {tBegin}; int temp = 1; if (nParameter==0) { idid = solveDAE(p_initialization, reactionList, true, thirdBodyReactionList, nState, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid !=1 && idid != 2 && idid != 3) { System.out.println("The idid from DASPK was "+idid + " at time "+tPresent[0]); throw new DynamicSimulatorException("DASPK: SA off."); } System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, 0); } else { idid = solveSEN(p_initialization, reactionList, p_reactionChanged, thirdBodyReactionList, nState, nParameter, this.parameterInforArray, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid != 2 && idid != 3) throw new DynamicSimulatorException("DASPK: SA on."); //speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); senStatus = generateSensitivityStatus(p_reactionModel,y,yprime,nParameter); SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, senStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); sss.setIDTranslator(IDTranslator); sss.setReactionList(rList); return sss; } SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CH4"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO2"), rList, sss, p_temperature); return sss; //#] }

public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged) { //#[ operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,Temperature,Pressure,boolean) ReactionTime rt = p_beginStatus.getTime(); if (!rt.equals(p_beginTime)) throw new InvalidBeginStatusException(); // set time double tBegin = p_beginTime.getStandardTime(); double tEnd = p_endTime.getStandardTime(); // set reaction set //if (p_initialization || p_reactionChanged || p_conditionChanged) { //generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedList rList = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateAllODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //p_reactionChanged = true; //} // set numbers System.out.println("Total number of reactions to Daspk is "+rList.size()); int nState = p_reactionModel.getSpeciesNumber(); int nParameter = 0; LinkedList initialSpecies = new LinkedList();// if (parameterInfor!=null) nParameter = parameterInfor.length; if (parameterInfor != 0) { nParameter = rList.size(); //svp if (initialStatus == null) System.out.println("initialStatus = null"); Iterator spe_iter = initialStatus.getSpeciesStatus(); while (spe_iter.hasNext()) { SpeciesStatus ss = (SpeciesStatus) spe_iter.next(); String name = ss.getSpecies().getName(); initialSpecies.add(name); nParameter++; } } int neq = nState*(nParameter+1); // set temperature and pressure double T = p_temperature.getK(); double P = p_pressure.getAtm(); // set initial value of y and yprime; double [] y = new double[neq]; double [] yprime = new double[neq]; //double numberOfReactedSpecies=0; // get the present status at t_begin, and set y and y' accordingly System.out.println("Before ODE: " + String.valueOf(tBegin) + "SEC"); System.out.println("End at : " + String.valueOf(tEnd) + "SEC"); for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) { SpeciesStatus ss = (SpeciesStatus)iter.next(); double conc = ss.getConcentration(); double flux = ss.getFlux(); if (ss.isReactedSpecies()) { Species spe = ss.getSpecies(); int id = getRealID(spe); System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getName() + '\t' + String.valueOf(conc) + '\t' + String.valueOf(flux)); y[id-1] = conc; yprime[id-1] = flux; } } if (nParameter != 0){//svp parameterInforArray = new ParameterInfor[nParameter]; for (int i = 1; i <= rList.size()+thirdBodyReactionList.length; i++){ parameterInforArray[i-1] = new ParameterInfor("k",i,0.00); } for (int i=rList.size()+1; i<=nParameter;i++){ parameterInforArray[i - 1] = new ParameterInfor("CO", nParameter, 0.00); } if (p_beginTime.getTime() == 0 || p_beginTime.getTime() == 0.00) { LinkedList sensitivityStatus = new LinkedList(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber();// for (int i=0;i<reactionNumber*speciesNumber;i++){ for (int i=0; i<nParameter*speciesNumber;i++){ sensitivityStatus.add(i,null); } p_beginStatus.addSensitivity(sensitivityStatus); double sflux = 1; Iterator species_iter = p_reactionModel.getSpecies(); while (species_iter.hasNext()) { Species spe = (Species) species_iter.next(); int m = getRealID(spe); for (int p=0;p<nParameter;p++){ int k = m + (p+1) * speciesNumber - 1; if (p >= rList.size()){ int speciesNum = p-rList.size(); String name = (String)initialSpecies.get(speciesNum); sflux = 0; SensitivityStatus senStatus; if (name.equalsIgnoreCase(spe.getName())){ senStatus = new SensitivityStatus(1, sflux, m, p + 1); y[k] = 1; } else{ senStatus = new SensitivityStatus(0,sflux,m,p+1); y[k]=0; } sensitivityStatus.add(k - p_reactionModel.getSpeciesNumber(), senStatus); p_beginStatus.putSensitivityStatus(k - speciesNumber, senStatus); yprime[k] = sflux; } else{ Reaction rxn = (Reaction)rList.get(p); if (rxn.containsAsProduct(spe)) { sflux = 1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } if (rxn.containsAsReactant(spe)) { sflux = -1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } else { sflux = 0; } SensitivityStatus senStatus = new SensitivityStatus(0, sflux, m, p+1); sensitivityStatus.add(k-p_reactionModel.getSpeciesNumber(),senStatus); p_beginStatus.putSensitivityStatus(k-speciesNumber,senStatus); y[k] = 0; yprime[k] = sflux; } } } } else { for (int i = p_reactionModel.getSpeciesNumber(); i < y.length; i++) { SensitivityStatus ss = (SensitivityStatus) p_beginStatus. getSensitivityStatus(i-p_reactionModel.getSpeciesNumber()); double sens = ss.getSensitivity(); double sflux = ss.getSFlux(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber(); Iterator species_iter = p_reactionModel.getSpecies(); y[i] = sens; yprime[i] = sflux; } } } //System.out.println("Number of Reacted Species is " + numberOfReactedSpecies); int idid; HashMap speStatus = new HashMap(); LinkedList senStatus = new LinkedList(); double[] tPresent = {tBegin}; int temp = 1; if (nParameter==0) { idid = solveDAE(p_initialization, reactionList, true, thirdBodyReactionList, nState, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid !=1 && idid != 2 && idid != 3) { System.out.println("The idid from DASPK was "+idid + " at time "+tPresent[0]); throw new DynamicSimulatorException("DASPK: SA off."); } System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, 0); } else { idid = solveSEN(p_initialization, reactionList, p_reactionChanged, thirdBodyReactionList, nState, nParameter, this.parameterInforArray, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid != 2 && idid != 3) throw new DynamicSimulatorException("DASPK: SA on."); //speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); senStatus = generateSensitivityStatus(p_reactionModel,y,yprime,nParameter); SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, senStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); sss.setIDTranslator(IDTranslator); sss.setReactionList(rList); return sss; } SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CH4"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO2"), rList, sss, p_temperature); return sss; //#] }

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public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged) { //#[ operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,Temperature,Pressure,boolean) ReactionTime rt = p_beginStatus.getTime(); if (!rt.equals(p_beginTime)) throw new InvalidBeginStatusException(); // set time double tBegin = p_beginTime.getStandardTime(); double tEnd = p_endTime.getStandardTime(); // set reaction set //if (p_initialization || p_reactionChanged || p_conditionChanged) { //generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedList rList = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateAllODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //p_reactionChanged = true; //} // set numbers System.out.println("Total number of reactions to Daspk is "+rList.size()); int nState = p_reactionModel.getSpeciesNumber(); int nParameter = 0; LinkedList initialSpecies = new LinkedList();// if (parameterInfor!=null) nParameter = parameterInfor.length; if (parameterInfor != 0) { nParameter = rList.size(); //svp if (initialStatus == null) System.out.println("initialStatus = null"); Iterator spe_iter = initialStatus.getSpeciesStatus(); while (spe_iter.hasNext()) { SpeciesStatus ss = (SpeciesStatus) spe_iter.next(); String name = ss.getSpecies().getName(); initialSpecies.add(name); nParameter++; } } int neq = nState*(nParameter+1); // set temperature and pressure double T = p_temperature.getK(); double P = p_pressure.getAtm(); // set initial value of y and yprime; double [] y = new double[neq]; double [] yprime = new double[neq]; //double numberOfReactedSpecies=0; // get the present status at t_begin, and set y and y' accordingly System.out.println("Before ODE: " + String.valueOf(tBegin) + "SEC"); System.out.println("End at : " + String.valueOf(tEnd) + "SEC"); for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) { SpeciesStatus ss = (SpeciesStatus)iter.next(); double conc = ss.getConcentration(); double flux = ss.getFlux(); if (ss.isReactedSpecies()) { Species spe = ss.getSpecies(); int id = getRealID(spe); System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getName() + '\t' + String.valueOf(conc) + '\t' + String.valueOf(flux)); y[id-1] = conc; yprime[id-1] = flux; } } if (nParameter != 0){//svp parameterInforArray = new ParameterInfor[nParameter]; for (int i = 1; i <= rList.size(); i++){ parameterInforArray[i-1] = new ParameterInfor("k",i,0.00); } for (int i=rList.size()+1; i<=nParameter;i++){ parameterInforArray[i - 1] = new ParameterInfor("CO", nParameter, 0.00); } if (p_beginTime.getTime() == 0 || p_beginTime.getTime() == 0.00) { LinkedList sensitivityStatus = new LinkedList(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber();// for (int i=0;i<reactionNumber*speciesNumber;i++){ for (int i=0; i<nParameter*speciesNumber;i++){ sensitivityStatus.add(i,null); } p_beginStatus.addSensitivity(sensitivityStatus); double sflux = 1; Iterator species_iter = p_reactionModel.getSpecies(); while (species_iter.hasNext()) { Species spe = (Species) species_iter.next(); int m = getRealID(spe); for (int p=0;p<nParameter;p++){ int k = m + (p+1) * speciesNumber - 1; if (p >= rList.size()){ int speciesNum = p-rList.size(); String name = (String)initialSpecies.get(speciesNum); sflux = 0; SensitivityStatus senStatus; if (name.equalsIgnoreCase(spe.getName())){ senStatus = new SensitivityStatus(1, sflux, m, p + 1); y[k] = 1; } else{ senStatus = new SensitivityStatus(0,sflux,m,p+1); y[k]=0; } sensitivityStatus.add(k - p_reactionModel.getSpeciesNumber(), senStatus); p_beginStatus.putSensitivityStatus(k - speciesNumber, senStatus); yprime[k] = sflux; } else{ Reaction rxn = (Reaction)rList.get(p); if (rxn.containsAsProduct(spe)) { sflux = 1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } if (rxn.containsAsReactant(spe)) { sflux = -1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } else { sflux = 0; } SensitivityStatus senStatus = new SensitivityStatus(0, sflux, m, p+1); sensitivityStatus.add(k-p_reactionModel.getSpeciesNumber(),senStatus); p_beginStatus.putSensitivityStatus(k-speciesNumber,senStatus); y[k] = 0; yprime[k] = sflux; } } } } else { for (int i = p_reactionModel.getSpeciesNumber(); i < y.length; i++) { SensitivityStatus ss = (SensitivityStatus) p_beginStatus. getSensitivityStatus(i-p_reactionModel.getSpeciesNumber()); double sens = ss.getSensitivity(); double sflux = ss.getSFlux(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber(); Iterator species_iter = p_reactionModel.getSpecies(); y[i] = sens; yprime[i] = sflux; } } } //System.out.println("Number of Reacted Species is " + numberOfReactedSpecies); int idid; HashMap speStatus = new HashMap(); LinkedList senStatus = new LinkedList(); double[] tPresent = {tBegin}; int temp = 1; if (nParameter==0) { idid = solveDAE(p_initialization, reactionList, true, thirdBodyReactionList, nState, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid !=1 && idid != 2 && idid != 3) { System.out.println("The idid from DASPK was "+idid + " at time "+tPresent[0]); throw new DynamicSimulatorException("DASPK: SA off."); } System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, 0); } else { idid = solveSEN(p_initialization, reactionList, p_reactionChanged, thirdBodyReactionList, nState, nParameter, this.parameterInforArray, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid != 2 && idid != 3) throw new DynamicSimulatorException("DASPK: SA on."); //speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); senStatus = generateSensitivityStatus(p_reactionModel,y,yprime,nParameter); SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, senStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); sss.setIDTranslator(IDTranslator); sss.setReactionList(rList); return sss; } SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CH4"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO2"), rList, sss, p_temperature); return sss; //#] }

public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged) { //#[ operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,Temperature,Pressure,boolean) ReactionTime rt = p_beginStatus.getTime(); if (!rt.equals(p_beginTime)) throw new InvalidBeginStatusException(); // set time double tBegin = p_beginTime.getStandardTime(); double tEnd = p_endTime.getStandardTime(); // set reaction set //if (p_initialization || p_reactionChanged || p_conditionChanged) { //generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedList rList = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateAllODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //p_reactionChanged = true; //} // set numbers System.out.println("Total number of reactions to Daspk is "+rList.size()); int nState = p_reactionModel.getSpeciesNumber(); int nParameter = 0; LinkedList initialSpecies = new LinkedList();// if (parameterInfor!=null) nParameter = parameterInfor.length; if (parameterInfor != 0) { nParameter = rList.size(); //svp if (initialStatus == null) System.out.println("initialStatus = null"); Iterator spe_iter = initialStatus.getSpeciesStatus(); while (spe_iter.hasNext()) { SpeciesStatus ss = (SpeciesStatus) spe_iter.next(); String name = ss.getSpecies().getName(); initialSpecies.add(name); nParameter++; } } int neq = nState*(nParameter+1); // set temperature and pressure double T = p_temperature.getK(); double P = p_pressure.getAtm(); // set initial value of y and yprime; double [] y = new double[neq]; double [] yprime = new double[neq]; //double numberOfReactedSpecies=0; // get the present status at t_begin, and set y and y' accordingly System.out.println("Before ODE: " + String.valueOf(tBegin) + "SEC"); System.out.println("End at : " + String.valueOf(tEnd) + "SEC"); for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) { SpeciesStatus ss = (SpeciesStatus)iter.next(); double conc = ss.getConcentration(); double flux = ss.getFlux(); if (ss.isReactedSpecies()) { Species spe = ss.getSpecies(); int id = getRealID(spe); System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getName() + '\t' + String.valueOf(conc) + '\t' + String.valueOf(flux)); y[id-1] = conc; yprime[id-1] = flux; } } if (nParameter != 0){//svp parameterInforArray = new ParameterInfor[nParameter]; for (int i = 1; i <= rList.size(); i++){ parameterInforArray[i-1] = new ParameterInfor("k",i,0.00); } for (int i=rList.size()+1+thirdBodyReactionList.length; i<=nParameter;i++){ parameterInforArray[i - 1] = new ParameterInfor("CO", nParameter, 0.00); } if (p_beginTime.getTime() == 0 || p_beginTime.getTime() == 0.00) { LinkedList sensitivityStatus = new LinkedList(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber();// for (int i=0;i<reactionNumber*speciesNumber;i++){ for (int i=0; i<nParameter*speciesNumber;i++){ sensitivityStatus.add(i,null); } p_beginStatus.addSensitivity(sensitivityStatus); double sflux = 1; Iterator species_iter = p_reactionModel.getSpecies(); while (species_iter.hasNext()) { Species spe = (Species) species_iter.next(); int m = getRealID(spe); for (int p=0;p<nParameter;p++){ int k = m + (p+1) * speciesNumber - 1; if (p >= rList.size()){ int speciesNum = p-rList.size(); String name = (String)initialSpecies.get(speciesNum); sflux = 0; SensitivityStatus senStatus; if (name.equalsIgnoreCase(spe.getName())){ senStatus = new SensitivityStatus(1, sflux, m, p + 1); y[k] = 1; } else{ senStatus = new SensitivityStatus(0,sflux,m,p+1); y[k]=0; } sensitivityStatus.add(k - p_reactionModel.getSpeciesNumber(), senStatus); p_beginStatus.putSensitivityStatus(k - speciesNumber, senStatus); yprime[k] = sflux; } else{ Reaction rxn = (Reaction)rList.get(p); if (rxn.containsAsProduct(spe)) { sflux = 1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } if (rxn.containsAsReactant(spe)) { sflux = -1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } else { sflux = 0; } SensitivityStatus senStatus = new SensitivityStatus(0, sflux, m, p+1); sensitivityStatus.add(k-p_reactionModel.getSpeciesNumber(),senStatus); p_beginStatus.putSensitivityStatus(k-speciesNumber,senStatus); y[k] = 0; yprime[k] = sflux; } } } } else { for (int i = p_reactionModel.getSpeciesNumber(); i < y.length; i++) { SensitivityStatus ss = (SensitivityStatus) p_beginStatus. getSensitivityStatus(i-p_reactionModel.getSpeciesNumber()); double sens = ss.getSensitivity(); double sflux = ss.getSFlux(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber(); Iterator species_iter = p_reactionModel.getSpecies(); y[i] = sens; yprime[i] = sflux; } } } //System.out.println("Number of Reacted Species is " + numberOfReactedSpecies); int idid; HashMap speStatus = new HashMap(); LinkedList senStatus = new LinkedList(); double[] tPresent = {tBegin}; int temp = 1; if (nParameter==0) { idid = solveDAE(p_initialization, reactionList, true, thirdBodyReactionList, nState, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid !=1 && idid != 2 && idid != 3) { System.out.println("The idid from DASPK was "+idid + " at time "+tPresent[0]); throw new DynamicSimulatorException("DASPK: SA off."); } System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, 0); } else { idid = solveSEN(p_initialization, reactionList, p_reactionChanged, thirdBodyReactionList, nState, nParameter, this.parameterInforArray, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid != 2 && idid != 3) throw new DynamicSimulatorException("DASPK: SA on."); //speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); senStatus = generateSensitivityStatus(p_reactionModel,y,yprime,nParameter); SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, senStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); sss.setIDTranslator(IDTranslator); sss.setReactionList(rList); return sss; } SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CH4"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO2"), rList, sss, p_temperature); return sss; //#] }

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public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged) { //#[ operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,Temperature,Pressure,boolean) ReactionTime rt = p_beginStatus.getTime(); if (!rt.equals(p_beginTime)) throw new InvalidBeginStatusException(); // set time double tBegin = p_beginTime.getStandardTime(); double tEnd = p_endTime.getStandardTime(); // set reaction set //if (p_initialization || p_reactionChanged || p_conditionChanged) { //generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedList rList = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateAllODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //p_reactionChanged = true; //} // set numbers System.out.println("Total number of reactions to Daspk is "+rList.size()); int nState = p_reactionModel.getSpeciesNumber(); int nParameter = 0; LinkedList initialSpecies = new LinkedList();// if (parameterInfor!=null) nParameter = parameterInfor.length; if (parameterInfor != 0) { nParameter = rList.size(); //svp if (initialStatus == null) System.out.println("initialStatus = null"); Iterator spe_iter = initialStatus.getSpeciesStatus(); while (spe_iter.hasNext()) { SpeciesStatus ss = (SpeciesStatus) spe_iter.next(); String name = ss.getSpecies().getName(); initialSpecies.add(name); nParameter++; } } int neq = nState*(nParameter+1); // set temperature and pressure double T = p_temperature.getK(); double P = p_pressure.getAtm(); // set initial value of y and yprime; double [] y = new double[neq]; double [] yprime = new double[neq]; //double numberOfReactedSpecies=0; // get the present status at t_begin, and set y and y' accordingly System.out.println("Before ODE: " + String.valueOf(tBegin) + "SEC"); System.out.println("End at : " + String.valueOf(tEnd) + "SEC"); for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) { SpeciesStatus ss = (SpeciesStatus)iter.next(); double conc = ss.getConcentration(); double flux = ss.getFlux(); if (ss.isReactedSpecies()) { Species spe = ss.getSpecies(); int id = getRealID(spe); System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getName() + '\t' + String.valueOf(conc) + '\t' + String.valueOf(flux)); y[id-1] = conc; yprime[id-1] = flux; } } if (nParameter != 0){//svp parameterInforArray = new ParameterInfor[nParameter]; for (int i = 1; i <= rList.size(); i++){ parameterInforArray[i-1] = new ParameterInfor("k",i,0.00); } for (int i=rList.size()+1; i<=nParameter;i++){ parameterInforArray[i - 1] = new ParameterInfor("CO", nParameter, 0.00); } if (p_beginTime.getTime() == 0 || p_beginTime.getTime() == 0.00) { LinkedList sensitivityStatus = new LinkedList(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber();// for (int i=0;i<reactionNumber*speciesNumber;i++){ for (int i=0; i<nParameter*speciesNumber;i++){ sensitivityStatus.add(i,null); } p_beginStatus.addSensitivity(sensitivityStatus); double sflux = 1; Iterator species_iter = p_reactionModel.getSpecies(); while (species_iter.hasNext()) { Species spe = (Species) species_iter.next(); int m = getRealID(spe); for (int p=0;p<nParameter;p++){ int k = m + (p+1) * speciesNumber - 1; if (p >= rList.size()){ int speciesNum = p-rList.size(); String name = (String)initialSpecies.get(speciesNum); sflux = 0; SensitivityStatus senStatus; if (name.equalsIgnoreCase(spe.getName())){ senStatus = new SensitivityStatus(1, sflux, m, p + 1); y[k] = 1; } else{ senStatus = new SensitivityStatus(0,sflux,m,p+1); y[k]=0; } sensitivityStatus.add(k - p_reactionModel.getSpeciesNumber(), senStatus); p_beginStatus.putSensitivityStatus(k - speciesNumber, senStatus); yprime[k] = sflux; } else{ Reaction rxn = (Reaction)rList.get(p); if (rxn.containsAsProduct(spe)) { sflux = 1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } if (rxn.containsAsReactant(spe)) { sflux = -1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } else { sflux = 0; } SensitivityStatus senStatus = new SensitivityStatus(0, sflux, m, p+1); sensitivityStatus.add(k-p_reactionModel.getSpeciesNumber(),senStatus); p_beginStatus.putSensitivityStatus(k-speciesNumber,senStatus); y[k] = 0; yprime[k] = sflux; } } } } else { for (int i = p_reactionModel.getSpeciesNumber(); i < y.length; i++) { SensitivityStatus ss = (SensitivityStatus) p_beginStatus. getSensitivityStatus(i-p_reactionModel.getSpeciesNumber()); double sens = ss.getSensitivity(); double sflux = ss.getSFlux(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber(); Iterator species_iter = p_reactionModel.getSpecies(); y[i] = sens; yprime[i] = sflux; } } } //System.out.println("Number of Reacted Species is " + numberOfReactedSpecies); int idid; HashMap speStatus = new HashMap(); LinkedList senStatus = new LinkedList(); double[] tPresent = {tBegin}; int temp = 1; if (nParameter==0) { idid = solveDAE(p_initialization, reactionList, true, thirdBodyReactionList, nState, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid !=1 && idid != 2 && idid != 3) { System.out.println("The idid from DASPK was "+idid + " at time "+tPresent[0]); throw new DynamicSimulatorException("DASPK: SA off."); } System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, 0); } else { idid = solveSEN(p_initialization, reactionList, p_reactionChanged, thirdBodyReactionList, nState, nParameter, this.parameterInforArray, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid != 2 && idid != 3) throw new DynamicSimulatorException("DASPK: SA on."); //speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); senStatus = generateSensitivityStatus(p_reactionModel,y,yprime,nParameter); SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, senStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); sss.setIDTranslator(IDTranslator); sss.setReactionList(rList); return sss; } SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CH4"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO2"), rList, sss, p_temperature); return sss; //#] }

public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged) { //#[ operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,Temperature,Pressure,boolean) ReactionTime rt = p_beginStatus.getTime(); if (!rt.equals(p_beginTime)) throw new InvalidBeginStatusException(); // set time double tBegin = p_beginTime.getStandardTime(); double tEnd = p_endTime.getStandardTime(); // set reaction set //if (p_initialization || p_reactionChanged || p_conditionChanged) { //generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedList rList = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateAllODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //p_reactionChanged = true; //} // set numbers System.out.println("Total number of reactions to Daspk is "+rList.size()); int nState = p_reactionModel.getSpeciesNumber(); int nParameter = 0; LinkedList initialSpecies = new LinkedList();// if (parameterInfor!=null) nParameter = parameterInfor.length; if (parameterInfor != 0) { nParameter = rList.size(); //svp if (initialStatus == null) System.out.println("initialStatus = null"); Iterator spe_iter = initialStatus.getSpeciesStatus(); while (spe_iter.hasNext()) { SpeciesStatus ss = (SpeciesStatus) spe_iter.next(); String name = ss.getSpecies().getName(); initialSpecies.add(name); nParameter++; } } int neq = nState*(nParameter+1); // set temperature and pressure double T = p_temperature.getK(); double P = p_pressure.getAtm(); // set initial value of y and yprime; double [] y = new double[neq]; double [] yprime = new double[neq]; //double numberOfReactedSpecies=0; // get the present status at t_begin, and set y and y' accordingly System.out.println("Before ODE: " + String.valueOf(tBegin) + "SEC"); System.out.println("End at : " + String.valueOf(tEnd) + "SEC"); for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) { SpeciesStatus ss = (SpeciesStatus)iter.next(); double conc = ss.getConcentration(); double flux = ss.getFlux(); if (ss.isReactedSpecies()) { Species spe = ss.getSpecies(); int id = getRealID(spe); System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getName() + '\t' + String.valueOf(conc) + '\t' + String.valueOf(flux)); y[id-1] = conc; yprime[id-1] = flux; } } if (nParameter != 0){//svp parameterInforArray = new ParameterInfor[nParameter]; for (int i = 1; i <= rList.size(); i++){ parameterInforArray[i-1] = new ParameterInfor("k",i,0.00); } for (int i=rList.size()+1; i<=nParameter;i++){ parameterInforArray[i - 1] = new ParameterInfor("CO", nParameter, 0.00); } if (p_beginTime.getTime() == 0 || p_beginTime.getTime() == 0.00) { LinkedList sensitivityStatus = new LinkedList(); int reactionNumber = rList.size()+thirdBodyReactionList.length; int speciesNumber = p_reactionModel.getSpeciesNumber();// for (int i=0;i<reactionNumber*speciesNumber;i++){ for (int i=0; i<nParameter*speciesNumber;i++){ sensitivityStatus.add(i,null); } p_beginStatus.addSensitivity(sensitivityStatus); double sflux = 1; Iterator species_iter = p_reactionModel.getSpecies(); while (species_iter.hasNext()) { Species spe = (Species) species_iter.next(); int m = getRealID(spe); for (int p=0;p<nParameter;p++){ int k = m + (p+1) * speciesNumber - 1; if (p >= rList.size()){ int speciesNum = p-rList.size(); String name = (String)initialSpecies.get(speciesNum); sflux = 0; SensitivityStatus senStatus; if (name.equalsIgnoreCase(spe.getName())){ senStatus = new SensitivityStatus(1, sflux, m, p + 1); y[k] = 1; } else{ senStatus = new SensitivityStatus(0,sflux,m,p+1); y[k]=0; } sensitivityStatus.add(k - p_reactionModel.getSpeciesNumber(), senStatus); p_beginStatus.putSensitivityStatus(k - speciesNumber, senStatus); yprime[k] = sflux; } else{ Reaction rxn = (Reaction)rList.get(p); if (rxn.containsAsProduct(spe)) { sflux = 1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } if (rxn.containsAsReactant(spe)) { sflux = -1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } else { sflux = 0; } SensitivityStatus senStatus = new SensitivityStatus(0, sflux, m, p+1); sensitivityStatus.add(k-p_reactionModel.getSpeciesNumber(),senStatus); p_beginStatus.putSensitivityStatus(k-speciesNumber,senStatus); y[k] = 0; yprime[k] = sflux; } } } } else { for (int i = p_reactionModel.getSpeciesNumber(); i < y.length; i++) { SensitivityStatus ss = (SensitivityStatus) p_beginStatus. getSensitivityStatus(i-p_reactionModel.getSpeciesNumber()); double sens = ss.getSensitivity(); double sflux = ss.getSFlux(); int reactionNumber = rList.size()+thirdBodyReactionList.length; int speciesNumber = p_reactionModel.getSpeciesNumber(); Iterator species_iter = p_reactionModel.getSpecies(); y[i] = sens; yprime[i] = sflux; } } } //System.out.println("Number of Reacted Species is " + numberOfReactedSpecies); int idid; HashMap speStatus = new HashMap(); LinkedList senStatus = new LinkedList(); double[] tPresent = {tBegin}; int temp = 1; if (nParameter==0) { idid = solveDAE(p_initialization, reactionList, true, thirdBodyReactionList, nState, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid !=1 && idid != 2 && idid != 3) { System.out.println("The idid from DASPK was "+idid + " at time "+tPresent[0]); throw new DynamicSimulatorException("DASPK: SA off."); } System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, 0); } else { idid = solveSEN(p_initialization, reactionList, p_reactionChanged, thirdBodyReactionList, nState, nParameter, this.parameterInforArray, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid != 2 && idid != 3) throw new DynamicSimulatorException("DASPK: SA on."); //speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); senStatus = generateSensitivityStatus(p_reactionModel,y,yprime,nParameter); SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, senStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); sss.setIDTranslator(IDTranslator); sss.setReactionList(rList); return sss; } SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CH4"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO2"), rList, sss, p_temperature); return sss; //#] }

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public SystemSnapshot solve(boolean p_initialization, ReactionModel p_reactionModel, boolean p_reactionChanged, SystemSnapshot p_beginStatus, ReactionTime p_beginTime, ReactionTime p_endTime, Temperature p_temperature, Pressure p_pressure, boolean p_conditionChanged) { //#[ operation solve(boolean,ReactionModel,boolean,SystemSnapshot,ReactionTime,ReactionTime,Temperature,Pressure,boolean) ReactionTime rt = p_beginStatus.getTime(); if (!rt.equals(p_beginTime)) throw new InvalidBeginStatusException(); // set time double tBegin = p_beginTime.getStandardTime(); double tEnd = p_endTime.getStandardTime(); // set reaction set //if (p_initialization || p_reactionChanged || p_conditionChanged) { //generateThirdBodyReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); LinkedList rList = generatePDepODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //generateAllODEReactionList(p_reactionModel, p_beginStatus, p_temperature, p_pressure); //p_reactionChanged = true; //} // set numbers System.out.println("Total number of reactions to Daspk is "+rList.size()); int nState = p_reactionModel.getSpeciesNumber(); int nParameter = 0; LinkedList initialSpecies = new LinkedList();// if (parameterInfor!=null) nParameter = parameterInfor.length; if (parameterInfor != 0) { nParameter = rList.size(); //svp if (initialStatus == null) System.out.println("initialStatus = null"); Iterator spe_iter = initialStatus.getSpeciesStatus(); while (spe_iter.hasNext()) { SpeciesStatus ss = (SpeciesStatus) spe_iter.next(); String name = ss.getSpecies().getName(); initialSpecies.add(name); nParameter++; } } int neq = nState*(nParameter+1); // set temperature and pressure double T = p_temperature.getK(); double P = p_pressure.getAtm(); // set initial value of y and yprime; double [] y = new double[neq]; double [] yprime = new double[neq]; //double numberOfReactedSpecies=0; // get the present status at t_begin, and set y and y' accordingly System.out.println("Before ODE: " + String.valueOf(tBegin) + "SEC"); System.out.println("End at : " + String.valueOf(tEnd) + "SEC"); for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) { SpeciesStatus ss = (SpeciesStatus)iter.next(); double conc = ss.getConcentration(); double flux = ss.getFlux(); if (ss.isReactedSpecies()) { Species spe = ss.getSpecies(); int id = getRealID(spe); System.out.println(String.valueOf(spe.getID()) + '\t' + spe.getName() + '\t' + String.valueOf(conc) + '\t' + String.valueOf(flux)); y[id-1] = conc; yprime[id-1] = flux; } } if (nParameter != 0){//svp parameterInforArray = new ParameterInfor[nParameter]; for (int i = 1; i <= rList.size(); i++){ parameterInforArray[i-1] = new ParameterInfor("k",i,0.00); } for (int i=rList.size()+1; i<=nParameter;i++){ parameterInforArray[i - 1] = new ParameterInfor("CO", nParameter, 0.00); } if (p_beginTime.getTime() == 0 || p_beginTime.getTime() == 0.00) { LinkedList sensitivityStatus = new LinkedList(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber();// for (int i=0;i<reactionNumber*speciesNumber;i++){ for (int i=0; i<nParameter*speciesNumber;i++){ sensitivityStatus.add(i,null); } p_beginStatus.addSensitivity(sensitivityStatus); double sflux = 1; Iterator species_iter = p_reactionModel.getSpecies(); while (species_iter.hasNext()) { Species spe = (Species) species_iter.next(); int m = getRealID(spe); for (int p=0;p<nParameter;p++){ int k = m + (p+1) * speciesNumber - 1; if (p >= rList.size()){ int speciesNum = p-rList.size(); String name = (String)initialSpecies.get(speciesNum); sflux = 0; SensitivityStatus senStatus; if (name.equalsIgnoreCase(spe.getName())){ senStatus = new SensitivityStatus(1, sflux, m, p + 1); y[k] = 1; } else{ senStatus = new SensitivityStatus(0,sflux,m,p+1); y[k]=0; } sensitivityStatus.add(k - p_reactionModel.getSpeciesNumber(), senStatus); p_beginStatus.putSensitivityStatus(k - speciesNumber, senStatus); yprime[k] = sflux; } else{ Reaction rxn = (Reaction)rList.get(p); if (rxn.containsAsProduct(spe)) { sflux = 1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } if (rxn.containsAsReactant(spe)) { sflux = -1; Iterator new_iter = rxn.getReactants(); while (new_iter.hasNext()) { ChemGraph cg = (ChemGraph) new_iter.next(); Species reactant = cg.getSpecies(); SpeciesStatus ss = p_beginStatus.getSpeciesStatus(reactant); if (ss != null) { sflux *= ss.getConcentration(); } else { sflux = 0; } } } else { sflux = 0; } SensitivityStatus senStatus = new SensitivityStatus(0, sflux, m, p+1); sensitivityStatus.add(k-p_reactionModel.getSpeciesNumber(),senStatus); p_beginStatus.putSensitivityStatus(k-speciesNumber,senStatus); y[k] = 0; yprime[k] = sflux; } } } } else { for (int i = p_reactionModel.getSpeciesNumber(); i < y.length; i++) { SensitivityStatus ss = (SensitivityStatus) p_beginStatus. getSensitivityStatus(i-p_reactionModel.getSpeciesNumber()); double sens = ss.getSensitivity(); double sflux = ss.getSFlux(); int reactionNumber = rList.size(); int speciesNumber = p_reactionModel.getSpeciesNumber(); Iterator species_iter = p_reactionModel.getSpecies(); y[i] = sens; yprime[i] = sflux; } } } //System.out.println("Number of Reacted Species is " + numberOfReactedSpecies); int idid; HashMap speStatus = new HashMap(); LinkedList senStatus = new LinkedList(); double[] tPresent = {tBegin}; int temp = 1; if (nParameter==0) { idid = solveDAE(p_initialization, reactionList, true, thirdBodyReactionList, nState, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid !=1 && idid != 2 && idid != 3) { System.out.println("The idid from DASPK was "+idid + " at time "+tPresent[0]); throw new DynamicSimulatorException("DASPK: SA off."); } System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, 0); } else { idid = solveSEN(p_initialization, reactionList, p_reactionChanged, thirdBodyReactionList, nState, nParameter, this.parameterInforArray, y, yprime, tBegin, tEnd, this.rtol, this.atol, T, P); if (idid != 2 && idid != 3) throw new DynamicSimulatorException("DASPK: SA on."); //speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); System.out.println("After ODE: from " + String.valueOf(tBegin) + " SEC to " + String.valueOf(tEnd) + "SEC"); speStatus = generateSpeciesStatus(p_reactionModel, y, yprime, nParameter); senStatus = generateSensitivityStatus(p_reactionModel,y,yprime,nParameter); SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, senStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); sss.setIDTranslator(IDTranslator); sss.setReactionList(rList); return sss; } SystemSnapshot sss = new SystemSnapshot(p_endTime, speStatus, p_beginStatus.getTemperature(), p_beginStatus.getPressure()); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CH4"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO"), rList, sss, p_temperature); //ReactionSystem.outputAllPathways(SpeciesDictionary.getSpeciesFromName("CO2"), rList, sss, p_temperature); return sss; //#] }

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private boolean pathMatches (String path) { //System.out.println ("checking path " + path); File file = null; if ((this.filename == null) && (this.searchType == TYPE_DIRECTORY)) { file = new File (path); } else { file = new File (path, this.filename); } if (file.exists ()) { if ((this.searchType == TYPE_DIRECTORY) && (file.isDirectory())) return true; if ((this.searchType == TYPE_FILE) && (file.isFile ())) return true; } //System.out.println (path + " did not match"); return false; }

private boolean pathMatches (String path) { //System.out.println ("checking path " + path); File file = null; if ((this.filename == null) || (this.searchType == TYPE_DIRECTORY)) { file = new File (path); } else { file = new File (path, this.filename); } if (file.exists ()) { if ((this.searchType == TYPE_DIRECTORY) && (file.isDirectory())) return true; if ((this.searchType == TYPE_FILE) && (file.isFile ())) return true; } //System.out.println (path + " did not match"); return false; }

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private boolean pathMatches (String path) { //System.out.println ("checking path " + path); File file = null; if ((this.filename == null) && (this.searchType == TYPE_DIRECTORY)) { file = new File (path); } else { file = new File (path, this.filename); } if (file.exists ()) { if ((this.searchType == TYPE_DIRECTORY) && (file.isDirectory())) return true; if ((this.searchType == TYPE_FILE) && (file.isFile ())) return true; } //System.out.println (path + " did not match"); return false; }

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private void addSearch (XMLElement spec) { Vector forPacks = spec.getChildrenNamed (PACKS); XMLElement element = spec.getFirstChildNamed (SPEC); String variable = spec.getAttribute (VARIABLE); String filename = null; int search_type = 0; int result_type = 0; JComboBox combobox = new JComboBox (); JLabel label = null; //System.out.println ("adding search combobox, variable "+variable); // allow the user to enter something combobox.setEditable (true); // ---------------------------------------------------- // extract the specification details // ---------------------------------------------------- if (element != null) { label = new JLabel (getText (element)); // search type is optional (default: file) search_type = SearchField.TYPE_FILE; String search_type_str = element.getAttribute (SEARCH_TYPE); if (search_type_str != null) { if (search_type_str.equals (SEARCH_FILE)) { search_type = SearchField.TYPE_FILE; } else if (search_type_str.equals (SEARCH_DIRECTORY)) { search_type = SearchField.TYPE_DIRECTORY; } } // result type is mandatory too String result_type_str = element.getAttribute (SEARCH_RESULT); if (result_type_str == null) { return; } else if (result_type_str.equals (SEARCH_FILE)) { result_type = SearchField.RESULT_FILE; } else if (result_type_str.equals (SEARCH_DIRECTORY)) { result_type = SearchField.RESULT_DIRECTORY; } else if (result_type_str.equals (SEARCH_PARENTDIR)) { result_type = SearchField.RESULT_PARENTDIR; } else { return; } // might be missing - null is okay filename = element.getAttribute (SEARCH_FILENAME); Vector choices = element.getChildrenNamed (SEARCH_CHOICE); if (choices == null) { return; } for (int i = 0; i < choices.size (); i++) { String value = ((XMLElement)choices.elementAt (i)).getAttribute (SEARCH_VALUE); combobox.addItem (value); String set = ((XMLElement)choices.elementAt (i)).getAttribute (SET); if (set != null) { if (set.equals (TRUE)) { combobox.setSelectedIndex (i); } } } } // ---------------------------------------------------- // if there is no specification element, return without // doing anything. // ---------------------------------------------------- else { return; } // ---------------------------------------------------- // get the description and add it to the list of UI // elements if it exists. // ---------------------------------------------------- element = spec.getFirstChildNamed (DESCRIPTION); addDescription (element, forPacks); TwoColumnConstraints westconstraint1 = new TwoColumnConstraints (); westconstraint1.position = TwoColumnConstraints.WEST; uiElements.add (new Object [] {null, FIELD_LABEL, null, westconstraint1, label, forPacks}); TwoColumnConstraints eastconstraint1 = new TwoColumnConstraints (); eastconstraint1.position = TwoColumnConstraints.EAST; combobox.setToolTipText (parent.langpack.getString ("UserInputPanel.search.location") + filename); uiElements.add (new Object [] {null, SEARCH_FIELD, variable, eastconstraint1, combobox, forPacks}); JPanel buttonPanel = new JPanel (); buttonPanel.setLayout (new com.izforge.izpack.gui.FlowLayout (com.izforge.izpack.gui.FlowLayout.LEADING)); JButton autodetectButton = ButtonFactory.createButton (parent.langpack.getString ("UserInputPanel.search.autodetect"), idata.buttonsHColor); autodetectButton.setToolTipText (parent.langpack.getString ("UserInputPanel.search.autodetect.tooltip")); buttonPanel.add (autodetectButton); JButton browseButton = ButtonFactory.createButton (parent.langpack.getString ("UserInputPanel.search.browse"), idata.buttonsHColor); buttonPanel.add (browseButton); TwoColumnConstraints eastonlyconstraint = new TwoColumnConstraints (); eastonlyconstraint.position = TwoColumnConstraints.EASTONLY; uiElements.add (new Object [] {null, SEARCH_BUTTON_FIELD, null, eastonlyconstraint, buttonPanel, forPacks}); searchFields.add (new SearchField (filename, parent, combobox, autodetectButton, browseButton, search_type, result_type)); }

private void addSearch (XMLElement spec) { Vector forPacks = spec.getChildrenNamed (PACKS); XMLElement element = spec.getFirstChildNamed (SPEC); String variable = spec.getAttribute (VARIABLE); String filename = null; int search_type = 0; int result_type = 0; JComboBox combobox = new JComboBox (); JLabel label = null; //System.out.println ("adding search combobox, variable "+variable); // allow the user to enter something combobox.setEditable (true); // ---------------------------------------------------- // extract the specification details // ---------------------------------------------------- if (element != null) { label = new JLabel (getText (element)); // search type is optional (default: file) search_type = SearchField.TYPE_FILE; String search_type_str = element.getAttribute (SEARCH_TYPE); if (search_type_str != null) { if (search_type_str.equals (SEARCH_FILE)) { search_type = SearchField.TYPE_FILE; } else if (search_type_str.equals (SEARCH_DIRECTORY)) { search_type = SearchField.TYPE_DIRECTORY; } } // result type is mandatory too String result_type_str = element.getAttribute (SEARCH_RESULT); if (result_type_str == null) { return; } else if (result_type_str.equals (SEARCH_FILE)) { result_type = SearchField.RESULT_FILE; } else if (result_type_str.equals (SEARCH_DIRECTORY)) { result_type = SearchField.RESULT_DIRECTORY; } else if (result_type_str.equals (SEARCH_PARENTDIR)) { result_type = SearchField.RESULT_PARENTDIR; } else { return; } // might be missing - null is okay filename = element.getAttribute (SEARCH_FILENAME); Vector choices = element.getChildrenNamed (SEARCH_CHOICE); if (choices == null) { return; } for (int i = 0; i < choices.size (); i++) { XMLElement choice_el = (XMLElement)choices.elementAt (i); if (! OsConstraint.oneMatchesCurrentSystem(element)) continue; String value = choice_el.getAttribute (SEARCH_VALUE); combobox.addItem (value); String set = ((XMLElement)choices.elementAt (i)).getAttribute (SET); if (set != null) { if (set.equals (TRUE)) { combobox.setSelectedIndex (i); } } } } // ---------------------------------------------------- // if there is no specification element, return without // doing anything. // ---------------------------------------------------- else { return; } // ---------------------------------------------------- // get the description and add it to the list of UI // elements if it exists. // ---------------------------------------------------- element = spec.getFirstChildNamed (DESCRIPTION); addDescription (element, forPacks); TwoColumnConstraints westconstraint1 = new TwoColumnConstraints (); westconstraint1.position = TwoColumnConstraints.WEST; uiElements.add (new Object [] {null, FIELD_LABEL, null, westconstraint1, label, forPacks}); TwoColumnConstraints eastconstraint1 = new TwoColumnConstraints (); eastconstraint1.position = TwoColumnConstraints.EAST; combobox.setToolTipText (parent.langpack.getString ("UserInputPanel.search.location") + filename); uiElements.add (new Object [] {null, SEARCH_FIELD, variable, eastconstraint1, combobox, forPacks}); JPanel buttonPanel = new JPanel (); buttonPanel.setLayout (new com.izforge.izpack.gui.FlowLayout (com.izforge.izpack.gui.FlowLayout.LEADING)); JButton autodetectButton = ButtonFactory.createButton (parent.langpack.getString ("UserInputPanel.search.autodetect"), idata.buttonsHColor); autodetectButton.setToolTipText (parent.langpack.getString ("UserInputPanel.search.autodetect.tooltip")); buttonPanel.add (autodetectButton); JButton browseButton = ButtonFactory.createButton (parent.langpack.getString ("UserInputPanel.search.browse"), idata.buttonsHColor); buttonPanel.add (browseButton); TwoColumnConstraints eastonlyconstraint = new TwoColumnConstraints (); eastonlyconstraint.position = TwoColumnConstraints.EASTONLY; uiElements.add (new Object [] {null, SEARCH_BUTTON_FIELD, null, eastonlyconstraint, buttonPanel, forPacks}); searchFields.add (new SearchField (filename, parent, combobox, autodetectButton, browseButton, search_type, result_type)); }

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public HelloPanel(InstallerFrame parent, InstallData idata) { super(parent, idata); // The 'super' layout GridBagLayout superLayout = new GridBagLayout(); setLayout(superLayout); GridBagConstraints gbConstraints = new GridBagConstraints(); gbConstraints.insets = new Insets(0, 0, 0, 0); gbConstraints.fill = GridBagConstraints.NONE; gbConstraints.anchor = GridBagConstraints.CENTER; // We initialize our 'real' layout JPanel centerPanel = new JPanel(); layout = new BoxLayout(centerPanel, BoxLayout.Y_AXIS); centerPanel.setLayout(layout); superLayout.addLayoutComponent(centerPanel, gbConstraints); add(centerPanel); // We create and put the labels String str; centerPanel.add(Box.createVerticalStrut(10)); str = parent.langpack.getString("HelloPanel.welcome1") + idata.info.getAppName() + " " + idata.info.getAppVersion() + parent.langpack.getString("HelloPanel.welcome2"); welcomeLabel = LabelFactory.create(str, parent.icons.getImageIcon("host"), JLabel.TRAILING); centerPanel.add(welcomeLabel); centerPanel.add(Box.createVerticalStrut(20)); ArrayList authors = idata.info.getAuthors(); int size = authors.size(); if (size > 0) { str = parent.langpack.getString("HelloPanel.authors"); appAuthorsLabel = LabelFactory.create(str, parent.icons.getImageIcon("information"), JLabel.TRAILING); centerPanel.add(appAuthorsLabel); JLabel label; for (int i = 0; i < size; i++) { Info.Author a = (Info.Author) authors.get(i); String email = (a.getEmail() != null) ? (" <" + a.getEmail() + ">") : ""; label = LabelFactory.create(" - " + a.getName() + email, parent.icons .getImageIcon("empty"), JLabel.TRAILING); centerPanel.add(label); } centerPanel.add(Box.createVerticalStrut(20)); } if (idata.info.getAppURL() != null) { str = parent.langpack.getString("HelloPanel.url") + idata.info.getAppURL(); appURLLabel = LabelFactory.create(str, parent.icons.getImageIcon("bookmark"), JLabel.TRAILING); centerPanel.add(appURLLabel); } }

public HelloPanel(InstallerFrame parent, InstallData idata) { super(parent, idata); // The 'super' layout GridBagLayout superLayout = new GridBagLayout(); setLayout(superLayout); GridBagConstraints gbConstraints = new GridBagConstraints(); gbConstraints.insets = new Insets(0, 0, 0, 0); gbConstraints.fill = GridBagConstraints.NONE; gbConstraints.anchor = GridBagConstraints.CENTER; // We initialize our 'real' layout JPanel centerPanel = new JPanel(); layout = new BoxLayout(centerPanel, BoxLayout.Y_AXIS); centerPanel.setLayout(layout); superLayout.addLayoutComponent(centerPanel, gbConstraints); add(centerPanel); // We create and put the labels String str; centerPanel.add(Box.createVerticalStrut(10)); str = parent.langpack.getString("HelloPanel.welcome1") + idata.info.getAppName() + " " + idata.info.getAppVersion() + parent.langpack.getString("HelloPanel.welcome2"); welcomeLabel = LabelFactory.create(str, parent.icons.getImageIcon("host"), JLabel.TRAILING); centerPanel.add(welcomeLabel); centerPanel.add(Box.createVerticalStrut(20)); ArrayList authors = idata.info.getAuthors(); int size = authors.size(); if (size > 0) { str = parent.langpack.getString("HelloPanel.authors"); appAuthorsLabel = LabelFactory.create(str, parent.icons.getImageIcon("information"), JLabel.TRAILING); centerPanel.add(appAuthorsLabel); JLabel label; for (int i = 0; i < size; i++) { Info.Author a = (Info.Author) authors.get(i); String email = (a.getEmail() != null && a.getEmail().length() > 0) ? (" <" + a.getEmail() + ">") : ""; label = LabelFactory.create(" - " + a.getName() + email, parent.icons .getImageIcon("empty"), JLabel.TRAILING); centerPanel.add(label); } centerPanel.add(Box.createVerticalStrut(20)); } if (idata.info.getAppURL() != null) { str = parent.langpack.getString("HelloPanel.url") + idata.info.getAppURL(); appURLLabel = LabelFactory.create(str, parent.icons.getImageIcon("bookmark"), JLabel.TRAILING); centerPanel.add(appURLLabel); } }

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public static void loadDefaultInstallDir(InstallerFrame parentFrame, InstallData idata) { // Load only once ... if (getDefaultInstallDir() != null) return; BufferedReader br = null; try { InputStream in = null; if (OsVersion.IS_WINDOWS) in = parentFrame.getResource("TargetPanel.dir.windows"); else if (OsVersion.IS_OSX) in = parentFrame.getResource("TargetPanel.dir.macosx"); else { String os = System.getProperty("os.name"); // first try to look up by specific os name os = os.replace(' ', '_'); // avoid spaces in file names os = os.toLowerCase(); // for consistency among TargetPanel res // files try { in = parentFrame.getResource("TargetPanel.dir.".concat(os)); } catch (ResourceNotFoundException rnfe) {} // if not specific os, try getting generic 'unix' resource file if (in == null) in = parentFrame.getResource("TargetPanel.dir.unix"); // if all those failed, try to look up a generic dir file if (in == null) { try { in = parentFrame.getResource("TargetPanel.dir.unix"); } catch (ResourceNotFoundException eee) {} } } // if all above tests failed, there is no resource file, // so use system default if (in == null) { try { in = parentFrame.getResource("TargetPanel.dir"); } catch (ResourceNotFoundException eee) {} } // now read the file, once we've identified which one to read InputStreamReader isr = new InputStreamReader(in); br = new BufferedReader(isr); String line; while ((line = br.readLine()) != null) { line = line.trim(); // use the first non-blank line if (!line.equals("")) break; } defaultInstallDir = line; VariableSubstitutor vs = new VariableSubstitutor(idata.getVariables()); defaultInstallDir = vs.substitute(defaultInstallDir, null); } catch (Exception e) { defaultInstallDir = null; // leave unset to take the system default set by Installer class } finally { try { if (br != null) br.close(); } catch (IOException ignored) {} } }

public static void loadDefaultInstallDir(InstallerFrame parentFrame, InstallData idata) { // Load only once ... if (getDefaultInstallDir() != null) return; BufferedReader br = null; try { InputStream in = null; if (OsVersion.IS_WINDOWS) in = parentFrame.getResource("TargetPanel.dir.windows"); else if (OsVersion.IS_OSX) in = parentFrame.getResource("TargetPanel.dir.macosx"); else { String os = System.getProperty("os.name"); // first try to look up by specific os name os = os.replace(' ', '_'); // avoid spaces in file names os = os.toLowerCase(); // for consistency among TargetPanel res // files try { in = parentFrame.getResource("TargetPanel.dir.".concat(os)); } catch (ResourceNotFoundException rnfe) {} // if not specific os, try getting generic 'unix' resource file if (in == null) in = parentFrame.getResource("TargetPanel.dir.unix"); // if all those failed, try to look up a generic dir file if (in == null) { try { in = parentFrame.getResource("TargetPanel.dir.unix"); } catch (ResourceNotFoundException eee) {} } } // if all above tests failed, there is no resource file, // so use system default if (in == null) { try { in = parentFrame.getResource("TargetPanel.dir"); } catch (ResourceNotFoundException eee) {} } // now read the file, once we've identified which one to read InputStreamReader isr = new InputStreamReader(in); br = new BufferedReader(isr); String line; while ((line = br.readLine()) != null) { line = line.trim(); // use the first non-blank line if (!"".equals(line)) break; } defaultInstallDir = line; VariableSubstitutor vs = new VariableSubstitutor(idata.getVariables()); defaultInstallDir = vs.substitute(defaultInstallDir, null); } catch (Exception e) { defaultInstallDir = null; // leave unset to take the system default set by Installer class } finally { try { if (br != null) br.close(); } catch (IOException ignored) {} } }

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public boolean emitWarning (String title, String message) { return (JOptionPane.showConfirmDialog(this, message, title, JOptionPane.WARNING_MESSAGE, JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION); }

public boolean emitWarning(String title, String message) { return (JOptionPane.showConfirmDialog(this, message, title, JOptionPane.WARNING_MESSAGE, JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION); }

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public boolean emitWarning (String title, String message) { return (JOptionPane.showConfirmDialog(this, message, title, JOptionPane.WARNING_MESSAGE, JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION); }

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private boolean readRadioButton (Object [] field) { String variable = null; String value = null; JRadioButton button = null; try { button = (JRadioButton)field [POS_FIELD]; if (!button.isSelected ()) { return (true); } variable = (String)field [POS_VARIABLE]; value = (String)field [POS_TRUE]; } catch (Throwable exception) { return (true); } if ((variable == null) || (value == null)) { } idata.getVariableValueMap ().setVariable (variable, value); entries.add (new TextValuePair (variable, value)); return (true); }

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private void addCustomListeners(XMLElement data) throws Exception { compilerListeners = new ArrayList(); // We get the listeners XMLElement root = data.getFirstChildNamed("listeners"); if (root == null) return; Iterator iter = root.getChildrenNamed("listener").iterator(); while (iter.hasNext()) { XMLElement xmlAction = (XMLElement) iter.next(); Object[] listener = getCompilerListenerInstance(xmlAction); if (listener != null) addCompilerListener((CompilerListener) listener[0]); String[] typeNames = new String[] { "installer", "uninstaller"}; int[] types = new int[] { CustomData.INSTALLER_LISTENER, CustomData.UNINSTALLER_LISTENER}; for (int i = 0; i < typeNames.length; ++i) { String className = xmlAction.getAttribute(typeNames[i]); if (className != null) { String jarPath = "bin/customActions/" + className + ".jar"; URL url = findIzPackResource(jarPath, "CustomAction jar file", xmlAction); CustomData ca = new CustomData(getFullClassName(url, className), getContainedFilePaths(url), OsConstraint.getOsList(xmlAction), types[i]); packager.addCustomJar(ca, url); } } } }

private void addCustomListeners(XMLElement data) throws Exception { compilerListeners = new ArrayList(); // We get the listeners XMLElement root = data.getFirstChildNamed("listeners"); if (root == null) return; Iterator iter = root.getChildrenNamed("listener").iterator(); while (iter.hasNext()) { XMLElement xmlAction = (XMLElement) iter.next(); Object[] listener = getCompilerListenerInstance(xmlAction); if (listener != null) addCompilerListener((CompilerListener) listener[0]); String[] typeNames = new String[] { "installer", "uninstaller"}; int[] types = new int[] { CustomData.INSTALLER_LISTENER, CustomData.UNINSTALLER_LISTENER}; for (int i = 0; i < typeNames.length; ++i) { String className = xmlAction.getAttribute(typeNames[i]); if (className != null) { String jarPath = xmlAction.getAttribute("jar"); if( jarPath == null ) jarPath = "bin/customActions/" + className + ".jar"; URL url = findIzPackResource(jarPath, "CustomAction jar file", xmlAction); CustomData ca = new CustomData(getFullClassName(url, className), getContainedFilePaths(url), OsConstraint.getOsList(xmlAction), types[i]); packager.addCustomJar(ca, url); } } } }

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public FinishPanel(InstallerFrame parent, InstallData idata) { super(parent, idata); vs = new VariableSubstitutor(idata.getVariables()); // The 'super' layout GridBagLayout superLayout = new GridBagLayout(); setLayout(superLayout); GridBagConstraints gbConstraints = new GridBagConstraints(); gbConstraints.insets = new Insets(0, 0, 0, 0); gbConstraints.fill = GridBagConstraints.NONE; gbConstraints.anchor = GridBagConstraints.CENTER; // We initialize our 'real' layout centerPanel = new JPanel(); layout = new BoxLayout(centerPanel, BoxLayout.Y_AXIS); centerPanel.setLayout(layout); superLayout.addLayoutComponent(centerPanel, gbConstraints); add(centerPanel); }

public FinishPanel(InstallerFrame parent, InstallData idata) { super(parent, idata); vs = new VariableSubstitutor(idata.getVariables()); // The 'super' layout GridBagLayout superLayout = new GridBagLayout(); setLayout(superLayout); GridBagConstraints gbConstraints = new GridBagConstraints(); gbConstraints.insets = new Insets(0, 0, 0, 0); gbConstraints.fill = GridBagConstraints.NONE; gbConstraints.anchor = GridBagConstraints.CENTER; // We initialize our 'real' layout centerPanel = new JPanel(); BoxLayout layout = new BoxLayout(centerPanel, BoxLayout.Y_AXIS); centerPanel.setLayout(layout); superLayout.addLayoutComponent(centerPanel, gbConstraints); add(centerPanel); }

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public InputStream getResource(String res) throws Exception { InputStream result; String basePath = ""; ResourceManager rm = null; try { rm = ResourceManager.getInstance(); basePath = rm.resourceBasePath; } catch(Exception e) { e.printStackTrace(); } result = this.getClass().getResourceAsStream( basePath+res ); if( result == null ) { throw new ResourceNotFoundException( "Warning: Resource not found: " + res ); } return result; }

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public InputStream getResource(String res) throws Exception { InputStream result; String basePath = ""; ResourceManager rm = null; try { rm = ResourceManager.getInstance(); basePath = rm.resourceBasePath; } catch(Exception e) { e.printStackTrace(); } result = this.getClass().getResourceAsStream( basePath+res ); if( result == null ) { throw new ResourceNotFoundException( "Warning: Resource not found: " + res ); } return result; }

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protected void switchPanel(int last) { if (installdata.curPanelNumber<last) { isBack = true; } panelsContainer.setVisible(false); IzPanel panel = (IzPanel) installdata.panels.get(installdata.curPanelNumber); IzPanel l_panel = (IzPanel) installdata.panels.get(last); l_panel.makeXMLData(installdata.xmlData.getChildAtIndex(last)); panelsContainer.remove(l_panel); panelsContainer.add(panel); if (installdata.curPanelNumber == 0) { prevButton.setVisible(false); lockPrevButton(); unlockNextButton(); // if we push the button back at the license panel } else if (installdata.curPanelNumber == installdata.panels.size() - 1) { prevButton.setVisible(false); nextButton.setVisible(false); lockNextButton(); // Set the default button to the only visible button. getRootPane().setDefaultButton(quitButton); } else { prevButton.setVisible(true); nextButton.setVisible(true); unlockPrevButton(); unlockNextButton(); } l_panel.panelDeactivate(); if( panel.getInitialFocus() != null ) { // Give a hint for the initial focus to the system. Component inFoc = panel.getInitialFocus(); if( JAVA_SPECIFICATION_VERSION < 1.4) inFoc.requestFocus(); else inFoc.requestFocusInWindow(); // Call the IzPanel specific method. panel.panelActivate(); // On editable text components positionite the caret to the end // of the cust existent text. if( inFoc instanceof JTextComponent ) { JTextComponent inText = (JTextComponent) inFoc; if( inText.isEditable() && inText.getDocument() != null) { inText.setCaretPosition( inText.getDocument().getLength()); } } } else panel.panelActivate(); panelsContainer.setVisible(true); loadImage(installdata.curPanelNumber); isBack = false; }

protected void switchPanel(int last) { try { if (installdata.curPanelNumber < last) { isBack = true; } panelsContainer.setVisible(false); IzPanel panel = (IzPanel) installdata.panels.get(installdata.curPanelNumber); IzPanel l_panel = (IzPanel) installdata.panels.get(last); l_panel.makeXMLData(installdata.xmlData.getChildAtIndex(last)); panelsContainer.remove(l_panel); panelsContainer.add(panel); if (installdata.curPanelNumber == 0) { prevButton.setVisible(false); lockPrevButton(); unlockNextButton(); // if we push the button back at the license panel } else if (installdata.curPanelNumber == installdata.panels.size() - 1) { prevButton.setVisible(false); nextButton.setVisible(false); lockNextButton(); // Set the default button to the only visible button. getRootPane().setDefaultButton(quitButton); } else { prevButton.setVisible(true); nextButton.setVisible(true); unlockPrevButton(); unlockNextButton(); } l_panel.panelDeactivate(); if( panel.getInitialFocus() != null ) { // Give a hint for the initial focus to the system. Component inFoc = panel.getInitialFocus(); if( JAVA_SPECIFICATION_VERSION < 1.4) inFoc.requestFocus(); else inFoc.requestFocusInWindow(); // Call the IzPanel specific method. panel.panelActivate(); // On editable text components positionite the caret to the end // of the cust existent text. if( inFoc instanceof JTextComponent ) { JTextComponent inText = (JTextComponent) inFoc; if( inText.isEditable() && inText.getDocument() != null) { inText.setCaretPosition( inText.getDocument().getLength()); } } } else panel.panelActivate(); panelsContainer.setVisible(true); loadImage(installdata.curPanelNumber); isBack = false; }

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protected void switchPanel(int last) { if (installdata.curPanelNumber<last) { isBack = true; } panelsContainer.setVisible(false); IzPanel panel = (IzPanel) installdata.panels.get(installdata.curPanelNumber); IzPanel l_panel = (IzPanel) installdata.panels.get(last); l_panel.makeXMLData(installdata.xmlData.getChildAtIndex(last)); panelsContainer.remove(l_panel); panelsContainer.add(panel); if (installdata.curPanelNumber == 0) { prevButton.setVisible(false); lockPrevButton(); unlockNextButton(); // if we push the button back at the license panel } else if (installdata.curPanelNumber == installdata.panels.size() - 1) { prevButton.setVisible(false); nextButton.setVisible(false); lockNextButton(); // Set the default button to the only visible button. getRootPane().setDefaultButton(quitButton); } else { prevButton.setVisible(true); nextButton.setVisible(true); unlockPrevButton(); unlockNextButton(); } l_panel.panelDeactivate(); if( panel.getInitialFocus() != null ) { // Give a hint for the initial focus to the system. Component inFoc = panel.getInitialFocus(); if( JAVA_SPECIFICATION_VERSION < 1.4) inFoc.requestFocus(); else inFoc.requestFocusInWindow(); // Call the IzPanel specific method. panel.panelActivate(); // On editable text components positionite the caret to the end // of the cust existent text. if( inFoc instanceof JTextComponent ) { JTextComponent inText = (JTextComponent) inFoc; if( inText.isEditable() && inText.getDocument() != null) { inText.setCaretPosition( inText.getDocument().getLength()); } } } else panel.panelActivate(); panelsContainer.setVisible(true); loadImage(installdata.curPanelNumber); isBack = false; }

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protected void switchPanel(int last) { if (installdata.curPanelNumber<last) { isBack = true; } panelsContainer.setVisible(false); IzPanel panel = (IzPanel) installdata.panels.get(installdata.curPanelNumber); IzPanel l_panel = (IzPanel) installdata.panels.get(last); l_panel.makeXMLData(installdata.xmlData.getChildAtIndex(last)); panelsContainer.remove(l_panel); panelsContainer.add(panel); if (installdata.curPanelNumber == 0) { prevButton.setVisible(false); lockPrevButton(); unlockNextButton(); // if we push the button back at the license panel } else if (installdata.curPanelNumber == installdata.panels.size() - 1) { prevButton.setVisible(false); nextButton.setVisible(false); lockNextButton(); // Set the default button to the only visible button. getRootPane().setDefaultButton(quitButton); } else { prevButton.setVisible(true); nextButton.setVisible(true); unlockPrevButton(); unlockNextButton(); } l_panel.panelDeactivate(); if( panel.getInitialFocus() != null ) { // Give a hint for the initial focus to the system. Component inFoc = panel.getInitialFocus(); if( JAVA_SPECIFICATION_VERSION < 1.4) inFoc.requestFocus(); else inFoc.requestFocusInWindow(); // Call the IzPanel specific method. panel.panelActivate(); // On editable text components positionite the caret to the end // of the cust existent text. if( inFoc instanceof JTextComponent ) { JTextComponent inText = (JTextComponent) inFoc; if( inText.isEditable() && inText.getDocument() != null) { inText.setCaretPosition( inText.getDocument().getLength()); } } } else panel.panelActivate(); panelsContainer.setVisible(true); loadImage(installdata.curPanelNumber); isBack = false; }

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protected void switchPanel(int last) { if (installdata.curPanelNumber<last) { isBack = true; } panelsContainer.setVisible(false); IzPanel panel = (IzPanel) installdata.panels.get(installdata.curPanelNumber); IzPanel l_panel = (IzPanel) installdata.panels.get(last); l_panel.makeXMLData(installdata.xmlData.getChildAtIndex(last)); panelsContainer.remove(l_panel); panelsContainer.add(panel); if (installdata.curPanelNumber == 0) { prevButton.setVisible(false); lockPrevButton(); unlockNextButton(); // if we push the button back at the license panel } else if (installdata.curPanelNumber == installdata.panels.size() - 1) { prevButton.setVisible(false); nextButton.setVisible(false); lockNextButton(); // Set the default button to the only visible button. getRootPane().setDefaultButton(quitButton); } else { prevButton.setVisible(true); nextButton.setVisible(true); unlockPrevButton(); unlockNextButton(); } l_panel.panelDeactivate(); if( panel.getInitialFocus() != null ) { // Give a hint for the initial focus to the system. Component inFoc = panel.getInitialFocus(); if( JAVA_SPECIFICATION_VERSION < 1.4) inFoc.requestFocus(); else inFoc.requestFocusInWindow(); // Call the IzPanel specific method. panel.panelActivate(); // On editable text components positionite the caret to the end // of the cust existent text. if( inFoc instanceof JTextComponent ) { JTextComponent inText = (JTextComponent) inFoc; if( inText.isEditable() && inText.getDocument() != null) { inText.setCaretPosition( inText.getDocument().getLength()); } } } else panel.panelActivate(); panelsContainer.setVisible(true); loadImage(installdata.curPanelNumber); isBack = false; }

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protected void switchPanel(int last) { if (installdata.curPanelNumber<last) { isBack = true; } panelsContainer.setVisible(false); IzPanel panel = (IzPanel) installdata.panels.get(installdata.curPanelNumber); IzPanel l_panel = (IzPanel) installdata.panels.get(last); l_panel.makeXMLData(installdata.xmlData.getChildAtIndex(last)); panelsContainer.remove(l_panel); panelsContainer.add(panel); if (installdata.curPanelNumber == 0) { prevButton.setVisible(false); lockPrevButton(); unlockNextButton(); // if we push the button back at the license panel } else if (installdata.curPanelNumber == installdata.panels.size() - 1) { prevButton.setVisible(false); nextButton.setVisible(false); lockNextButton(); // Set the default button to the only visible button. getRootPane().setDefaultButton(quitButton); } else { prevButton.setVisible(true); nextButton.setVisible(true); unlockPrevButton(); unlockNextButton(); } l_panel.panelDeactivate(); if( panel.getInitialFocus() != null ) { // Give a hint for the initial focus to the system. Component inFoc = panel.getInitialFocus(); if( JAVA_SPECIFICATION_VERSION < 1.4) inFoc.requestFocus(); else inFoc.requestFocusInWindow(); // Call the IzPanel specific method. panel.panelActivate(); // On editable text components positionite the caret to the end // of the cust existent text. if( inFoc instanceof JTextComponent ) { JTextComponent inText = (JTextComponent) inFoc; if( inText.isEditable() && inText.getDocument() != null) { inText.setCaretPosition( inText.getDocument().getLength()); } } } else panel.panelActivate(); panelsContainer.setVisible(true); loadImage(installdata.curPanelNumber); isBack = false; }

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private void writeUninstallData() { try { // We get the data UninstallData udata = UninstallData.getInstance(); List files = udata.getFilesList(); ZipOutputStream outJar = installdata.uninstallOutJar; if (outJar == null) return; // We write the files log outJar.putNextEntry(new ZipEntry("install.log")); BufferedWriter logWriter = new BufferedWriter(new OutputStreamWriter(outJar)); logWriter.write(installdata.getInstallPath()); logWriter.newLine(); Iterator iter = files.iterator(); while (iter.hasNext()) { logWriter.write((String) iter.next()); if (iter.hasNext()) logWriter.newLine(); } logWriter.flush(); outJar.closeEntry(); // We write the uninstaller jar file log outJar.putNextEntry(new ZipEntry("jarlocation.log")); logWriter = new BufferedWriter(new OutputStreamWriter(outJar)); logWriter.write(udata.getUninstallerJarFilename()); logWriter.newLine(); logWriter.write(udata.getUninstallerPath()); logWriter.flush(); outJar.closeEntry(); // Write out executables to execute on uninstall outJar.putNextEntry(new ZipEntry("executables")); ObjectOutputStream execStream = new ObjectOutputStream(outJar); iter = udata.getExecutablesList().iterator(); execStream.writeInt(udata.getExecutablesList().size()); while (iter.hasNext()) { ExecutableFile file = (ExecutableFile) iter.next(); execStream.writeObject(file); } execStream.flush(); outJar.closeEntry(); // Write out additional uninstall data // Do not "kill" the installation if there is a problem // with custom uninstall data. Therefore log it to Debug, // but do not throw. Map additionalData = udata.getAdditionalData(); if( additionalData != null && ! additionalData.isEmpty()) { Iterator keys = additionalData.keySet().iterator(); HashSet exist = new HashSet(); while( keys != null && keys.hasNext()) { String key = (String) keys.next(); Object contents = additionalData.get(key); if( key.equals("__uninstallLibs__")) { Iterator nativeLibIter = ((List) contents).iterator(); while( nativeLibIter != null && nativeLibIter.hasNext() ) { String nativeLibName = (String) ((List) nativeLibIter.next()).get(0); byte[] buffer = new byte[5120]; long bytesCopied = 0; int bytesInBuffer; outJar.putNextEntry(new ZipEntry( "native/" + nativeLibName)); InputStream in = getClass().getResourceAsStream("/native/" + nativeLibName); while ((bytesInBuffer = in.read(buffer)) != -1) { outJar.write(buffer, 0, bytesInBuffer); bytesCopied += bytesInBuffer; } outJar.closeEntry(); } } else if( key.equals("uninstallerListeners") || key.equals("uninstallerJars")) { // It is a ArrayList of ArrayLists which contains the full // package paths of all needed class files. // First we create a new ArrayList which contains only // the full paths for the uninstall listener self; thats // the first entry of each sub ArrayList. ArrayList subContents = new ArrayList(); // Secound put the class into uninstaller.jar Iterator listenerIter = ((List) contents).iterator(); while( listenerIter.hasNext() ) { byte[] buffer = new byte[5120]; long bytesCopied = 0; int bytesInBuffer; CustomData customData = (CustomData) listenerIter.next(); // First element of the list contains the listener class path; // remind it for later. if(customData.listenerName != null ) subContents.add(customData.listenerName); Iterator liClaIter = customData.contents.iterator(); while( liClaIter.hasNext() ) { String contentPath = (String) liClaIter.next(); if( exist.contains(contentPath )) continue; exist.add(contentPath); try { outJar.putNextEntry(new ZipEntry( contentPath)); } catch(ZipException ze ) { // Ignore, or ignore not ?? May be it is a exception because // a doubled entry was tried, then we should ignore ... Debug.trace("ZipException in writing custom data: " + ze.getMessage() ); continue; } InputStream in = getClass().getResourceAsStream("/" + contentPath); if( in != null ) { while ((bytesInBuffer = in.read(buffer)) != -1) { outJar.write(buffer, 0, bytesInBuffer); bytesCopied += bytesInBuffer; } } else Debug.trace("custom data not found: " + contentPath ); outJar.closeEntry(); } } // Third we write the list into the // uninstaller.jar outJar.putNextEntry(new ZipEntry(key)); ObjectOutputStream objOut = new ObjectOutputStream(outJar); objOut.writeObject(subContents); objOut.flush(); outJar.closeEntry(); } else { outJar.putNextEntry(new ZipEntry(key)); if( contents instanceof ByteArrayOutputStream ) { ((ByteArrayOutputStream) contents).writeTo(outJar); } else { ObjectOutputStream objOut = new ObjectOutputStream(outJar); objOut.writeObject(contents); objOut.flush(); } outJar.closeEntry(); } } } // Cleanup outJar.flush(); outJar.close(); } catch (Exception err) { err.printStackTrace(); } }

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private void writeUninstallData() { try { // We get the data UninstallData udata = UninstallData.getInstance(); List files = udata.getFilesList(); ZipOutputStream outJar = installdata.uninstallOutJar; if (outJar == null) return; // We write the files log outJar.putNextEntry(new ZipEntry("install.log")); BufferedWriter logWriter = new BufferedWriter(new OutputStreamWriter(outJar)); logWriter.write(installdata.getInstallPath()); logWriter.newLine(); Iterator iter = files.iterator(); while (iter.hasNext()) { logWriter.write((String) iter.next()); if (iter.hasNext()) logWriter.newLine(); } logWriter.flush(); outJar.closeEntry(); // We write the uninstaller jar file log outJar.putNextEntry(new ZipEntry("jarlocation.log")); logWriter = new BufferedWriter(new OutputStreamWriter(outJar)); logWriter.write(udata.getUninstallerJarFilename()); logWriter.newLine(); logWriter.write(udata.getUninstallerPath()); logWriter.flush(); outJar.closeEntry(); // Write out executables to execute on uninstall outJar.putNextEntry(new ZipEntry("executables")); ObjectOutputStream execStream = new ObjectOutputStream(outJar); iter = udata.getExecutablesList().iterator(); execStream.writeInt(udata.getExecutablesList().size()); while (iter.hasNext()) { ExecutableFile file = (ExecutableFile) iter.next(); execStream.writeObject(file); } execStream.flush(); outJar.closeEntry(); // Write out additional uninstall data // Do not "kill" the installation if there is a problem // with custom uninstall data. Therefore log it to Debug, // but do not throw. Map additionalData = udata.getAdditionalData(); if( additionalData != null && ! additionalData.isEmpty()) { Iterator keys = additionalData.keySet().iterator(); HashSet exist = new HashSet(); while( keys != null && keys.hasNext()) { String key = (String) keys.next(); Object contents = additionalData.get(key); if( key.equals("__uninstallLibs__")) { Iterator nativeLibIter = ((List) contents).iterator(); while( nativeLibIter != null && nativeLibIter.hasNext() ) { String nativeLibName = (String) ((List) nativeLibIter.next()).get(0); byte[] buffer = new byte[5120]; long bytesCopied = 0; int bytesInBuffer; outJar.putNextEntry(new ZipEntry( "native/" + nativeLibName)); InputStream in = getClass().getResourceAsStream("/native/" + nativeLibName); while ((bytesInBuffer = in.read(buffer)) != -1) { outJar.write(buffer, 0, bytesInBuffer); bytesCopied += bytesInBuffer; } outJar.closeEntry(); } } else if( key.equals("uninstallerListeners") || key.equals("uninstallerJars")) { // It is a ArrayList of ArrayLists which contains the full // package paths of all needed class files. // First we create a new ArrayList which contains only // the full paths for the uninstall listener self; thats // the first entry of each sub ArrayList. ArrayList subContents = new ArrayList(); // Secound put the class into uninstaller.jar Iterator listenerIter = ((List) contents).iterator(); while( listenerIter.hasNext() ) { byte[] buffer = new byte[5120]; long bytesCopied = 0; int bytesInBuffer; CustomData customData = (CustomData) listenerIter.next(); // First element of the list contains the listener class path; // remind it for later. if(customData.listenerName != null ) subContents.add(customData.listenerName); Iterator liClaIter = customData.contents.iterator(); while( liClaIter.hasNext() ) { String contentPath = (String) liClaIter.next(); if( exist.contains(contentPath )) continue; exist.add(contentPath); try { outJar.putNextEntry(new ZipEntry( contentPath)); } catch(ZipException ze ) { // Ignore, or ignore not ?? May be it is a exception because // a doubled entry was tried, then we should ignore ... Debug.trace("ZipException in writing custom data: " + ze.getMessage() ); continue; } InputStream in = getClass().getResourceAsStream("/" + contentPath); if( in != null ) { while ((bytesInBuffer = in.read(buffer)) != -1) { outJar.write(buffer, 0, bytesInBuffer); bytesCopied += bytesInBuffer; } } else Debug.trace("custom data not found: " + contentPath ); outJar.closeEntry(); } } // Third we write the list into the // uninstaller.jar outJar.putNextEntry(new ZipEntry(key)); ObjectOutputStream objOut = new ObjectOutputStream(outJar); objOut.writeObject(subContents); objOut.flush(); outJar.closeEntry(); } else { outJar.putNextEntry(new ZipEntry(key)); if( contents instanceof ByteArrayOutputStream ) { ((ByteArrayOutputStream) contents).writeTo(outJar); } else { ObjectOutputStream objOut = new ObjectOutputStream(outJar); objOut.writeObject(contents); objOut.flush(); } outJar.closeEntry(); } } } // Cleanup outJar.flush(); outJar.close(); } catch (Exception err) { err.printStackTrace(); } }

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private void writeUninstallData() { try { // We get the data UninstallData udata = UninstallData.getInstance(); List files = udata.getFilesList(); ZipOutputStream outJar = installdata.uninstallOutJar; if (outJar == null) return; // We write the files log outJar.putNextEntry(new ZipEntry("install.log")); BufferedWriter logWriter = new BufferedWriter(new OutputStreamWriter(outJar)); logWriter.write(installdata.getInstallPath()); logWriter.newLine(); Iterator iter = files.iterator(); while (iter.hasNext()) { logWriter.write((String) iter.next()); if (iter.hasNext()) logWriter.newLine(); } logWriter.flush(); outJar.closeEntry(); // We write the uninstaller jar file log outJar.putNextEntry(new ZipEntry("jarlocation.log")); logWriter = new BufferedWriter(new OutputStreamWriter(outJar)); logWriter.write(udata.getUninstallerJarFilename()); logWriter.newLine(); logWriter.write(udata.getUninstallerPath()); logWriter.flush(); outJar.closeEntry(); // Write out executables to execute on uninstall outJar.putNextEntry(new ZipEntry("executables")); ObjectOutputStream execStream = new ObjectOutputStream(outJar); iter = udata.getExecutablesList().iterator(); execStream.writeInt(udata.getExecutablesList().size()); while (iter.hasNext()) { ExecutableFile file = (ExecutableFile) iter.next(); execStream.writeObject(file); } execStream.flush(); outJar.closeEntry(); // Write out additional uninstall data // Do not "kill" the installation if there is a problem // with custom uninstall data. Therefore log it to Debug, // but do not throw. Map additionalData = udata.getAdditionalData(); if( additionalData != null && ! additionalData.isEmpty()) { Iterator keys = additionalData.keySet().iterator(); HashSet exist = new HashSet(); while( keys != null && keys.hasNext()) { String key = (String) keys.next(); Object contents = additionalData.get(key); if( key.equals("__uninstallLibs__")) { Iterator nativeLibIter = ((List) contents).iterator(); while( nativeLibIter != null && nativeLibIter.hasNext() ) { String nativeLibName = (String) ((List) nativeLibIter.next()).get(0); byte[] buffer = new byte[5120]; long bytesCopied = 0; int bytesInBuffer; outJar.putNextEntry(new ZipEntry( "native/" + nativeLibName)); InputStream in = getClass().getResourceAsStream("/native/" + nativeLibName); while ((bytesInBuffer = in.read(buffer)) != -1) { outJar.write(buffer, 0, bytesInBuffer); bytesCopied += bytesInBuffer; } outJar.closeEntry(); } } else if( key.equals("uninstallerListeners") || key.equals("uninstallerJars")) { // It is a ArrayList of ArrayLists which contains the full // package paths of all needed class files. // First we create a new ArrayList which contains only // the full paths for the uninstall listener self; thats // the first entry of each sub ArrayList. ArrayList subContents = new ArrayList(); // Secound put the class into uninstaller.jar Iterator listenerIter = ((List) contents).iterator(); while( listenerIter.hasNext() ) { byte[] buffer = new byte[5120]; long bytesCopied = 0; int bytesInBuffer; CustomData customData = (CustomData) listenerIter.next(); // First element of the list contains the listener class path; // remind it for later. if(customData.listenerName != null ) subContents.add(customData.listenerName); Iterator liClaIter = customData.contents.iterator(); while( liClaIter.hasNext() ) { String contentPath = (String) liClaIter.next(); if( exist.contains(contentPath )) continue; exist.add(contentPath); try { outJar.putNextEntry(new ZipEntry( contentPath)); } catch(ZipException ze ) { // Ignore, or ignore not ?? May be it is a exception because // a doubled entry was tried, then we should ignore ... Debug.trace("ZipException in writing custom data: " + ze.getMessage() ); continue; } InputStream in = getClass().getResourceAsStream("/" + contentPath); if( in != null ) { while ((bytesInBuffer = in.read(buffer)) != -1) { outJar.write(buffer, 0, bytesInBuffer); bytesCopied += bytesInBuffer; } } else Debug.trace("custom data not found: " + contentPath ); outJar.closeEntry(); } } // Third we write the list into the // uninstaller.jar outJar.putNextEntry(new ZipEntry(key)); ObjectOutputStream objOut = new ObjectOutputStream(outJar); objOut.writeObject(subContents); objOut.flush(); outJar.closeEntry(); } else { outJar.putNextEntry(new ZipEntry(key)); if( contents instanceof ByteArrayOutputStream ) { ((ByteArrayOutputStream) contents).writeTo(outJar); } else { ObjectOutputStream objOut = new ObjectOutputStream(outJar); objOut.writeObject(contents); objOut.flush(); } outJar.closeEntry(); } } } // Cleanup outJar.flush(); outJar.close(); } catch (Exception err) { err.printStackTrace(); } }

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private void writeUninstallData() { try { // We get the data UninstallData udata = UninstallData.getInstance(); List files = udata.getFilesList(); ZipOutputStream outJar = installdata.uninstallOutJar; if (outJar == null) return; // We write the files log outJar.putNextEntry(new ZipEntry("install.log")); BufferedWriter logWriter = new BufferedWriter(new OutputStreamWriter(outJar)); logWriter.write(installdata.getInstallPath()); logWriter.newLine(); Iterator iter = files.iterator(); while (iter.hasNext()) { logWriter.write((String) iter.next()); if (iter.hasNext()) logWriter.newLine(); } logWriter.flush(); outJar.closeEntry(); // We write the uninstaller jar file log outJar.putNextEntry(new ZipEntry("jarlocation.log")); logWriter = new BufferedWriter(new OutputStreamWriter(outJar)); logWriter.write(udata.getUninstallerJarFilename()); logWriter.newLine(); logWriter.write(udata.getUninstallerPath()); logWriter.flush(); outJar.closeEntry(); // Write out executables to execute on uninstall outJar.putNextEntry(new ZipEntry("executables")); ObjectOutputStream execStream = new ObjectOutputStream(outJar); iter = udata.getExecutablesList().iterator(); execStream.writeInt(udata.getExecutablesList().size()); while (iter.hasNext()) { ExecutableFile file = (ExecutableFile) iter.next(); execStream.writeObject(file); } execStream.flush(); outJar.closeEntry(); // Write out additional uninstall data // Do not "kill" the installation if there is a problem // with custom uninstall data. Therefore log it to Debug, // but do not throw. Map additionalData = udata.getAdditionalData(); if( additionalData != null && ! additionalData.isEmpty()) { Iterator keys = additionalData.keySet().iterator(); HashSet exist = new HashSet(); while( keys != null && keys.hasNext()) { String key = (String) keys.next(); Object contents = additionalData.get(key); if( key.equals("__uninstallLibs__")) { Iterator nativeLibIter = ((List) contents).iterator(); while( nativeLibIter != null && nativeLibIter.hasNext() ) { String nativeLibName = (String) ((List) nativeLibIter.next()).get(0); byte[] buffer = new byte[5120]; long bytesCopied = 0; int bytesInBuffer; outJar.putNextEntry(new ZipEntry( "native/" + nativeLibName)); InputStream in = getClass().getResourceAsStream("/native/" + nativeLibName); while ((bytesInBuffer = in.read(buffer)) != -1) { outJar.write(buffer, 0, bytesInBuffer); bytesCopied += bytesInBuffer; } outJar.closeEntry(); } } else if( key.equals("uninstallerListeners") || key.equals("uninstallerJars")) { // It is a ArrayList of ArrayLists which contains the full // package paths of all needed class files. // First we create a new ArrayList which contains only // the full paths for the uninstall listener self; thats // the first entry of each sub ArrayList. ArrayList subContents = new ArrayList(); // Secound put the class into uninstaller.jar Iterator listenerIter = ((List) contents).iterator(); while( listenerIter.hasNext() ) { byte[] buffer = new byte[5120]; long bytesCopied = 0; int bytesInBuffer; CustomData customData = (CustomData) listenerIter.next(); // First element of the list contains the listener class path; // remind it for later. if(customData.listenerName != null ) subContents.add(customData.listenerName); Iterator liClaIter = customData.contents.iterator(); while( liClaIter.hasNext() ) { String contentPath = (String) liClaIter.next(); if( exist.contains(contentPath )) continue; exist.add(contentPath); try { outJar.putNextEntry(new ZipEntry( contentPath)); } catch(ZipException ze ) { // Ignore, or ignore not ?? May be it is a exception because // a doubled entry was tried, then we should ignore ... Debug.trace("ZipException in writing custom data: " + ze.getMessage() ); continue; } InputStream in = getClass().getResourceAsStream("/" + contentPath); if( in != null ) { while ((bytesInBuffer = in.read(buffer)) != -1) { outJar.write(buffer, 0, bytesInBuffer); bytesCopied += bytesInBuffer; } } else Debug.trace("custom data not found: " + contentPath ); outJar.closeEntry(); } } // Third we write the list into the // uninstaller.jar outJar.putNextEntry(new ZipEntry(key)); ObjectOutputStream objOut = new ObjectOutputStream(outJar); objOut.writeObject(subContents); objOut.flush(); outJar.closeEntry(); } else { outJar.putNextEntry(new ZipEntry(key)); if( contents instanceof ByteArrayOutputStream ) { ((ByteArrayOutputStream) contents).writeTo(outJar); } else { ObjectOutputStream objOut = new ObjectOutputStream(outJar); objOut.writeObject(contents); objOut.flush(); } outJar.closeEntry(); } } } // Cleanup outJar.flush(); outJar.close(); } catch (Exception err) { err.printStackTrace(); } }

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public void actionPerformed(ActionEvent e) { // We get the source Object source = e.getSource(); // We act depending of the source if (source == addPackButton) { // We make the new pack element XMLElement pack = new XMLElement("pack"); pack.setAttribute("required", "yes"); String inputValue; inputValue = JOptionPane.showInputDialog(langpack.getString("tabs.packs.pack_name")); if (inputValue == null) return; else pack.setAttribute("name", inputValue); XMLElement desc = new XMLElement("description"); inputValue = JOptionPane.showInputDialog(langpack.getString("tabs.packs.pack_desc")); if (inputValue == null) return; else desc.setContent(inputValue); // We add it pack.addChild(desc); installation.getFirstChildNamed("packs").addChild(pack); // We select it curPack = installation.getFirstChildNamed("packs").getChildrenNamed("pack").size() - 1; curFile = -1; } else if (source == delPackButton) { // We get the selected pack index int index = packsList.getSelectedIndex(); if (index == -1) return; // We remove the element installation.getFirstChildNamed("packs").removeChildAtIndex(index); // We try to keep something selected curPack = (index < packsList.getModel().getSize() - 2) ? index : packsList.getModel().getSize() - 2; curFile = -1; } else if (source == requiredCheckBox) { // We get the selected pack index int index = packsList.getSelectedIndex(); if (index == -1) return; // We update the element XMLElement el = installation.getFirstChildNamed("packs").getChildAtIndex(index); el.setAttribute("required", (requiredCheckBox.isSelected() ? "yes" : "no")); } else if (source == addFileButton) { // We get the selected pack index int index = packsList.getSelectedIndex(); if (index == -1) return; // We make a new element for the file XMLElement file = new XMLElement("file"); JFileChooser fileChooser = new JFileChooser(Frontend.lastDir); fileChooser.addChoosableFileFilter(fileChooser.getAcceptAllFileFilter()); fileChooser.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES); if (fileChooser.showOpenDialog(this) == JFileChooser.APPROVE_OPTION) { Frontend.lastDir = fileChooser.getSelectedFile().getParentFile().getAbsolutePath(); file.setAttribute("src", fileChooser.getSelectedFile().getAbsolutePath()); String inputValue; inputValue = JOptionPane.showInputDialog(langpack.getString("tabs.packs.target")); if (inputValue == null) return; else file.setAttribute("targetdir", inputValue); installation.getFirstChildNamed("packs").getChildAtIndex(index).addChild(file); // We select it curFile = filesList.getModel().getSize(); curPack = index; } } else if (source == delFileButton) { // We get the selected items indices int pindex = packsList.getSelectedIndex(); int findex = filesList.getSelectedIndex(); if ( (findex == -1) || (pindex == -1) ) return; // We remove it XMLElement root = installation.getFirstChildNamed("packs").getChildAtIndex(pindex); Vector v = root.getChildrenNamed("file"); XMLElement file = (XMLElement) v.get(findex); root.removeChild(file); // We try to keep something selected curFile = (findex < filesList.getModel().getSize() - 2) ? findex : filesList.getModel().getSize() - 2; curPack = pindex; } else if (source == parsableCheckBox) { // We get the selected items indices int pindex = packsList.getSelectedIndex(); int findex = filesList.getSelectedIndex(); if ( (findex == -1) || (pindex == -1) ) return; // We look for the file attributes XMLElement root = installation.getFirstChildNamed("packs").getChildAtIndex(pindex); Vector v = root.getChildrenNamed("file"); XMLElement file = (XMLElement) v.get(findex); File destFile = new File(file.getAttribute("src")); String destName = file.getAttribute("targetdir") + "/" + destFile.getName(); // We add or remove the parsable tag if (parsableCheckBox.isSelected()) { // Add it XMLElement p = new XMLElement("parsable"); p.setAttribute("targetfile", destName); root.addChild(p); } else { // Remove it Vector pv = root.getChildrenNamed("parsable"); int size = pv.size(); XMLElement toRemove = null; for (int i = 0; (i < size) && (toRemove == null); i++) { XMLElement el = (XMLElement) pv.get(i); if (el.getAttribute("targetfile").equalsIgnoreCase(destName)) toRemove = el; } root.removeChild(toRemove); } } else if (source == scriptPropsButton) { // We get the selected items indices int pindex = packsList.getSelectedIndex(); int findex = filesList.getSelectedIndex(); if ( (findex == -1) || (pindex == -1) ) return; // We look for the file attributes XMLElement root = installation.getFirstChildNamed("packs").getChildAtIndex(pindex); Vector v = root.getChildrenNamed("file"); XMLElement file = (XMLElement) v.get(findex); File destFile = new File(file.getAttribute("src")); String destName = file.getAttribute("targetdir") + "/" + destFile.getName(); // We find the tag Vector pv = root.getChildrenNamed("parsable"); int size = pv.size(); XMLElement toEdit = null; for (int i = 0; (i < size) && (toEdit == null); i++) { XMLElement el = (XMLElement) pv.get(i); if (el.getAttribute("targetfile").equalsIgnoreCase(destName)) toEdit = el; } // We ask for the extended attributes String inputValue; inputValue = JOptionPane.showInputDialog(langpack.getString("tabs.packs.f_type")); if (inputValue == null) return; else if (inputValue.length() != 0) toEdit.setAttribute("type", inputValue); else toEdit.removeAttribute("type"); inputValue = JOptionPane.showInputDialog(langpack.getString("tabs.packs.f_enc")); if (inputValue == null) return; else if (inputValue.length() != 0) toEdit.setAttribute("encoding", inputValue); else toEdit.removeAttribute("encoding"); } updateComponents(); }

public void actionPerformed(ActionEvent e) { // We get the source Object source = e.getSource(); // We act depending of the source if (source == addPackButton) { // We make the new pack element XMLElement pack = new XMLElement("pack"); pack.setAttribute("required", "yes"); String inputValue; inputValue = JOptionPane.showInputDialog(langpack.getString("tabs.packs.pack_name")); if (inputValue == null) return; else pack.setAttribute("name", inputValue); XMLElement desc = new XMLElement("description"); inputValue = JOptionPane.showInputDialog(langpack.getString("tabs.packs.pack_desc")); if (inputValue == null) return; else desc.setContent(inputValue); // We add it pack.addChild(desc); installation.getFirstChildNamed("packs").addChild(pack); // We select it curPack = installation.getFirstChildNamed("packs").getChildrenNamed("pack").size() - 1; curFile = -1; } else if (source == delPackButton) { // We get the selected pack index int index = packsList.getSelectedIndex(); if (index == -1) return; // We remove the element installation.getFirstChildNamed("packs").removeChildAtIndex(index); // We try to keep something selected curPack = (index < packsList.getModel().getSize() - 2) ? index : packsList.getModel().getSize() - 2; curFile = -1; } else if (source == requiredCheckBox) { // We get the selected pack index int index = packsList.getSelectedIndex(); if (index == -1) return; // We update the element XMLElement el = installation.getFirstChildNamed("packs").getChildAtIndex(index); el.setAttribute("required", (requiredCheckBox.isSelected() ? "yes" : "no")); } else if (source == addFileButton) { // We get the selected pack index int index = packsList.getSelectedIndex(); if (index == -1) return; // We make a new element for the file XMLElement file = new XMLElement("file"); JFileChooser fileChooser = new JFileChooser(Frontend.lastDir); fileChooser.addChoosableFileFilter(fileChooser.getAcceptAllFileFilter()); fileChooser.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES); if (fileChooser.showOpenDialog(this) == JFileChooser.APPROVE_OPTION) { Frontend.lastDir = fileChooser.getSelectedFile().getParentFile().getAbsolutePath(); file.setAttribute("src", fileChooser.getSelectedFile().getAbsolutePath()); String inputValue; inputValue = JOptionPane.showInputDialog(langpack.getString("tabs.packs.target")); if (inputValue == null) return; else file.setAttribute("targetdir", inputValue); installation.getFirstChildNamed("packs").getChildAtIndex(index).addChild(file); // We select it curFile = filesList.getModel().getSize(); curPack = index; } } else if (source == delFileButton) { // We get the selected items indices int pindex = packsList.getSelectedIndex(); int findex = filesList.getSelectedIndex(); if ( (findex == -1) || (pindex == -1) ) return; // We remove it XMLElement root = installation.getFirstChildNamed("packs").getChildAtIndex(pindex); Vector v = root.getChildrenNamed("file"); XMLElement file = (XMLElement) v.get(findex); root.removeChild(file); // We try to keep something selected curFile = (findex < filesList.getModel().getSize() - 2) ? findex : filesList.getModel().getSize() - 2; curPack = pindex; } else if (source == parsableCheckBox) { // We get the selected items indices int pindex = packsList.getSelectedIndex(); int findex = filesList.getSelectedIndex(); if ( (findex == -1) || (pindex == -1) ) return; // We look for the file attributes XMLElement root = installation.getFirstChildNamed("packs").getChildAtIndex(pindex); Vector v = root.getChildrenNamed("file"); XMLElement file = (XMLElement) v.get(findex); File destFile = new File(file.getAttribute("src")); String destName = file.getAttribute("targetdir") + "/" + destFile.getName(); // We add or remove the parsable tag if (parsableCheckBox.isSelected()) { // Add it XMLElement p = new XMLElement("parsable"); p.setAttribute("targetfile", destName); root.addChild(p); } else { // Remove it Vector pv = root.getChildrenNamed("parsable"); int size = pv.size(); XMLElement toRemove = null; for (int i = 0; (i < size) && (toRemove == null); i++) { XMLElement el = (XMLElement) pv.get(i); if (el.getAttribute("targetfile").equalsIgnoreCase(destName)) toRemove = el; } root.removeChild(toRemove); } } else if (source == scriptPropsButton) { // We get the selected items indices int pindex = packsList.getSelectedIndex(); int findex = filesList.getSelectedIndex(); if ( (findex == -1) || (pindex == -1) ) return; // We look for the file attributes XMLElement root = installation.getFirstChildNamed("packs").getChildAtIndex(pindex); Vector v = root.getChildrenNamed("file"); XMLElement file = (XMLElement) v.get(findex); File destFile = new File(file.getAttribute("src")); String destName = file.getAttribute("targetdir") + "/" + destFile.getName(); // We find the tag Vector pv = root.getChildrenNamed("parsable"); int size = pv.size(); XMLElement toEdit = null; for (int i = 0; (i < size) && (toEdit == null); i++) { XMLElement el = (XMLElement) pv.get(i); if (el.getAttribute("targetfile").equalsIgnoreCase(destName)) toEdit = el; } // We ask for the extended attributes String inputValue; inputValue = JOptionPane.showInputDialog(langpack.getString("tabs.packs.f_type")); if (inputValue == null) return; else if (inputValue.length() != 0) toEdit.setAttribute("type", inputValue); else toEdit.removeAttribute("type"); inputValue = JOptionPane.showInputDialog(langpack.getString("tabs.packs.f_enc")); if (inputValue == null) return; else if (inputValue.length() != 0) toEdit.setAttribute("encoding", inputValue); else toEdit.removeAttribute("encoding"); } }

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public void addObject() throws Exception { Object obj = _factory.makeObject(); synchronized(this) { _numActive++; // A little slimy - must do this because returnObject decrements it. this.returnObject(obj); } }

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public void returnObject(Object obj) throws Exception { assertOpen(); boolean success = true; if(_testOnReturn && !(_factory.validateObject(obj))) { success = false; } else { try { _factory.passivateObject(obj); } catch(Exception e) { success = false; } } boolean shouldDestroy = !success; synchronized(this) { _numActive--; if((_maxIdle >= 0) && (_pool.size() >= _maxIdle)) { shouldDestroy = true; } else if(success) { _pool.addFirst(new ObjectTimestampPair(obj)); } notifyAll(); // _numActive has changed } if(shouldDestroy) { try { _factory.destroyObject(obj); } catch(Exception e) { // ignored } } }

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public void setVariable(String var, String val) { setProperty(var, val); }

public void setVariable(String var, String val) { if (var != null && val != null) { setProperty(var, val); } }

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private int dfs(int[] status) { for (int i = 0; i < packs.size(); i++) { Pack pack = (Pack) packs.get(i); int check = checkValues[getPos(pack.name)]; boolean wipe = false; if(Math.abs(check) !=1) { wipe = true; } if(pack.color == Pack.WHITE) { if(dfsVisit(pack,status,wipe)!=0) return -1; } } return 0; }

private int dfs(int[] status) { for (int i = 0; i < packs.size(); i++) { Pack pack = (Pack) packs.get(i); boolean wipe = false; if(Math.abs(check) !=1) { wipe = true; } if(pack.color == Pack.WHITE) { if(dfsVisit(pack,status,wipe)!=0) return -1; } } return 0; }

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private int dfs(int[] status) { for (int i = 0; i < packs.size(); i++) { Pack pack = (Pack) packs.get(i); int check = checkValues[getPos(pack.name)]; boolean wipe = false; if(Math.abs(check) !=1) { wipe = true; } if(pack.color == Pack.WHITE) { if(dfsVisit(pack,status,wipe)!=0) return -1; } } return 0; }

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private int dfsVisit(Pack u,int[] status,boolean wipe) { u.color = Pack.GREY; List deps = u.revDependencies; if (deps != null) { for (int i = 0; i < deps.size(); i++) { String name = (String) deps.get(i); Pack v = (Pack)namesObj.get(name); if(wipe) { status[getPos(v.name)] =1; } int check = checkValues[getPos(v.name)]; if(Math.abs(check) !=1) { wipe = true; } if(v.color == Pack.WHITE) { final int result = dfsVisit(v,status,wipe); if(result != 0) return result; } } } u.color = Pack.BLACK; return 0; }

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