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ShowHowToCiteCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowHowToCiteCommand.java
/* * ShowHowToCiteCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICommand; import jloda.swing.util.Message; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import javax.swing.*; import java.awt.event.ActionEvent; /** * how to cite * Daniel Huson, 6.2010 */ public class ShowHowToCiteCommand extends CommandBase implements ICommand { public String getSyntax() { return "show window=howToCite;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); Message.show(getViewer().getFrame(), "Please cite:\n" + "D.H. Huson et al (2016) MEGAN Community Edition - Interactive exploration and 2 analysis of large-scale microbiome sequencing data,\n" + "PLoS Computational Biology 12(6): e1004957. doi:10.1371/journal. pcbi.1004957\n"); } public void actionPerformed(ActionEvent event) { executeImmediately(getSyntax()); } public boolean isApplicable() { return true; } public String getName() { return "How to Cite..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Help16.gif"); } public String getDescription() { return "Show how to cite the program"; } public boolean isCritical() { return false; } public KeyStroke getAcceleratorKey() { return null; } }
2,303
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowPropertiesCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowPropertiesCommand.java
/* * ShowPropertiesCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.viewer.PropertiesWindow; import javax.swing.*; import java.awt.event.ActionEvent; public class ShowPropertiesCommand extends CommandBase implements ICommand { public String getSyntax() { return "show window=properties;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); new PropertiesWindow(getViewer().getFrame(), getDoc()); } public void actionPerformed(ActionEvent event) { executeImmediately(getSyntax()); } public boolean isApplicable() { return true; } public String getName() { return "Properties..."; } public String getDescription() { return "Show document properties"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Properties16.gif"); } public boolean isCritical() { return false; } }
1,924
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowInspectorCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowInspectorCommand.java
/* * ShowInspectorCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.core.Director; import megan.inspector.InspectorWindow; import megan.util.WindowUtilities; import javax.swing.*; import java.awt.event.ActionEvent; public class ShowInspectorCommand extends CommandBase implements ICommand { public String getSyntax() { return "show window=inspector;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); final Director dir = getDir(); InspectorWindow inspectorWindow = (InspectorWindow) dir.getViewerByClass(InspectorWindow.class); if (inspectorWindow == null) { inspectorWindow = (InspectorWindow) dir.addViewer(new InspectorWindow(dir)); } WindowUtilities.toFront(inspectorWindow.getFrame()); } public void actionPerformed(ActionEvent event) { executeImmediately(getSyntax()); } public boolean isApplicable() { return getDoc().getMeganFile().hasDataConnector(); } public String getName() { return "Inspector Window..."; } public String getDescription() { return "Open inspector window"; } public ImageIcon getIcon() { return ResourceManager.getIcon("Inspector16.gif"); } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return null; } }
2,372
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowSamplesViewerCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowSamplesViewerCommand.java
/* * ShowSamplesViewerCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.samplesviewer.SamplesViewer; import megan.util.WindowUtilities; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; public class ShowSamplesViewerCommand extends megan.commands.CommandBase implements ICommand { public String getSyntax() { return "show window=samplesViewer;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); SamplesViewer samplesViewer = (SamplesViewer) getDir().getViewerByClass(SamplesViewer.class); if (samplesViewer == null) { samplesViewer = new SamplesViewer(getDir()); getDir().addViewer(samplesViewer); } WindowUtilities.toFront(samplesViewer.getFrame()); } public void actionPerformed(ActionEvent event) { SamplesViewer samplesViewer = (SamplesViewer) getDir().getViewerByClass(SamplesViewer.class); if (samplesViewer == null) execute(getSyntax()); else // already exists, just need to bring to the front executeImmediately(getSyntax()); } public boolean isApplicable() { return getDir().getDocument().getNumberOfSamples() > 0; } public static final String NAME = "Samples Viewer..."; public String getName() { return NAME; } public ImageIcon getIcon() { return ResourceManager.getIcon("Table16.gif"); } public String getDescription() { return "Opens the Samples Viewer"; } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()); } }
2,734
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowCheckForUpdateCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowCheckForUpdateCommand.java
/* * ShowCheckForUpdateCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.director.IDirector; import jloda.swing.director.ProjectManager; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.main.CheckForUpdate; import javax.swing.*; import java.awt.event.ActionEvent; /** * show the message window * Daniel Huson, 6.2010 */ public class ShowCheckForUpdateCommand extends CommandBase implements ICommand { private final static String NAME = "Check For Updates..."; /** * get the name to be used as a menu label * * @return name */ public String getName() { return NAME; } /** * get description to be used as a tooltip * * @return description */ public String getDescription() { return "Check for updates"; } /** * get icon to be used in menu or button * * @return icon */ public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Refresh16.gif"); } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); CheckForUpdate.apply(); } /** * action to be performed * */ public void actionPerformed(ActionEvent ev) { execute(getSyntax()); } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { for (IDirector dir : ProjectManager.getProjects()) { if (dir.getDirty()) return false; } return true; } /** * get command-line usage description * * @return usage */ @Override public String getSyntax() { return "checkForUpdate;"; } /** * gets the command needed to undo this command * * @return undo command */ public String getUndo() { return null; } }
3,339
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
CompareCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/CompareCommand.java
/* * CompareCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICommand; import jloda.swing.director.ProjectManager; import jloda.swing.util.ProgramProperties; import jloda.swing.util.RecursiveFileLister; import jloda.swing.util.ResourceManager; import jloda.util.CanceledException; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import jloda.util.progress.ProgressListener; import megan.commands.CommandBase; import megan.core.Director; import megan.core.Document; import megan.core.MeganFile; import megan.dialogs.compare.CompareWindow; import megan.dialogs.compare.Comparer; import megan.main.MeganProperties; import megan.util.MeganFileFilter; import megan.util.MeganizedDAAFileFilter; import megan.util.RMAFileFilter; import megan.viewer.MainViewer; import megan.viewer.gui.NodeDrawer; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; import java.io.IOException; import java.util.ArrayList; import java.util.LinkedList; public class CompareCommand extends CommandBase implements ICommand { public String getSyntax() { return "compare mode={" + StringUtils.toString(Comparer.COMPARISON_MODE.values(), "|") + "}" + " readAssignmentMode={" + StringUtils.toString(Document.ReadAssignmentMode.values(), "|") + "}" + " [keep1={false|true}] [ignoreUnassigned={false|true}] [pid=<number> ...] [meganFile=<filename> ...];"; } public void apply(NexusStreamParser np) throws Exception { final Director dir = getDir(); final Document doc = dir.getDocument(); final ProgressListener progress = doc.getProgressListener(); if (!doc.neverOpenedReads) throw new Exception("Internal error: document already used"); doc.neverOpenedReads = false; np.matchIgnoreCase("compare"); final Comparer comparer = new Comparer(); if (np.peekMatchIgnoreCase("mode")) { np.matchIgnoreCase("mode="); comparer.setMode(np.getWordMatchesIgnoringCase(StringUtils.toString(Comparer.COMPARISON_MODE.values(), " "))); } Document.ReadAssignmentMode readAssignmentMode = Document.ReadAssignmentMode.readCount; if (np.peekMatchIgnoreCase("readAssignmentMode")) { np.matchIgnoreCase("readAssignmentMode="); readAssignmentMode = Document.ReadAssignmentMode.valueOfIgnoreCase(np.getWordMatchesIgnoringCase(StringUtils.toString(Document.ReadAssignmentMode.values(), " "))); } if (np.peekMatchIgnoreCase("keep1")) { np.matchIgnoreCase("keep1="); comparer.setKeep1(np.getBoolean()); } if (np.peekMatchIgnoreCase("ignoreUnassigned")) { np.matchIgnoreCase("ignoreUnassigned="); comparer.setIgnoreUnassigned(np.getBoolean()); } final java.util.List<Director> toDelete = new LinkedList<>(); try { if (np.peekMatchIgnoreCase("pid")) { np.matchIgnoreCase("pid="); do { int pid = np.getInt(); Director newDir = (Director) ProjectManager.getProject(pid); if (newDir == null) throw new IOException("No such project id: " + pid); if (newDir.getDocument().getNumberOfReads() == 0) throw new IOException("No reads found in file: '" + newDir.getDocument().getMeganFile().getFileName() + "' (id=" + pid + ")"); comparer.addDirector(newDir); if (np.peekMatchIgnoreCase(",")) // for backward compatibility np.matchAnyTokenIgnoreCase(","); } while (!np.peekMatchAnyTokenIgnoreCase("; meganFile")); } if (np.peekMatchIgnoreCase("meganFile")) { np.matchIgnoreCase("meganFile="); final ArrayList<String> files = new ArrayList<>(); do { String fileName = np.getWordRespectCase(); if (fileName.contains("::")) { files.add(fileName); } else { files.addAll(RecursiveFileLister.apply(fileName, new MeganFileFilter(), new RMAFileFilter(), MeganizedDAAFileFilter.getInstance())); } if (np.peekMatchIgnoreCase(",")) np.matchAnyTokenIgnoreCase(","); // for backward compatibility } while (!np.peekMatchIgnoreCase(";")); np.matchIgnoreCase(";"); progress.setProgress(0); progress.setMaximum(files.size()); for (String fileName : files) { progress.setTasks("Comparison", "Loading files"); final Director newDir = Director.newProject(false, true); newDir.executeImmediately("open file='" + fileName + "' readOnly=true;update;", newDir.getMainViewer().getCommandManager()); if (newDir.getDocument().getNumberOfReads() == 0) { throw new IOException("No reads found in file: '" + fileName + "'"); } comparer.addDirector(newDir); toDelete.add(newDir); progress.incrementProgress(); } } doc.getMeganFile().setFileName(ProjectManager.getUniqueName("Comparison.megan")); doc.clearReads(); doc.setReadAssignmentMode(readAssignmentMode); comparer.computeComparison(doc.getSampleAttributeTable(), doc.getDataTable(), progress); doc.setNumberReads(doc.getDataTable().getTotalReads()); doc.processReadHits(); doc.setTopPercent(100); doc.setMinScore(0); doc.setMinSupportPercent(0); doc.setMinSupport(1); doc.setMaxExpected(10000); doc.getActiveViewers().addAll(doc.getDataTable().getClassification2Class2Counts().keySet()); doc.setDirty(true); doc.getMeganFile().setFileType(MeganFile.Type.MEGAN_SUMMARY_FILE); final MainViewer mainViewer = dir.getMainViewer(); if (mainViewer != null) { if (mainViewer.isVisible()) { mainViewer.getNodeDrawer().setStyle(ProgramProperties.get(MeganProperties.COMPARISON_STYLE, ""), NodeDrawer.Style.BarChart); mainViewer.collapseToDefault(); mainViewer.setDoReInduce(true); mainViewer.setDoReset(true); mainViewer.setVisible(true); doc.loadColorTableFromDataTable(); } } } finally { for (Director aDir : toDelete) { aDir.close(); } } } /** * display the dialog and then execute the command entered, if any * */ public void actionPerformed(ActionEvent event) { final Director newDir = Director.newProject(); boolean ok = false; final CompareWindow compareWindow = new CompareWindow(newDir.getMainViewer().getFrame(), newDir, null); if (!compareWindow.isCanceled()) { final String command = compareWindow.getCommand(); if (command != null) { newDir.execute(command, newDir.getCommandManager()); ok = true; } } if (!ok) { try { newDir.close(); } catch (CanceledException e) { e.printStackTrace(); } ProjectManager.removeProject(newDir); } } public boolean isApplicable() { return true; } public String getName() { return "Compare..."; } public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_M, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()); } public String getDescription() { return "Open compare dialog to produce a comparison of multiple datasets"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/New16.gif"); } public boolean isCritical() { return true; } }
9,041
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowTimeSeriesViewerCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowTimeSeriesViewerCommand.java
/* * ShowTimeSeriesViewerCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.Basic; import jloda.util.parse.NexusStreamParser; import megan.core.Director; import megan.timeseriesviewer.TimeSeriesViewer; import megan.util.WindowUtilities; import megan.viewer.ClassificationViewer; import javax.swing.*; import java.awt.event.ActionEvent; public class ShowTimeSeriesViewerCommand extends megan.commands.CommandBase implements ICommand { public String getSyntax() { return "show window=timeSeriesViewer;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); TimeSeriesViewer viewer = (TimeSeriesViewer) getDir().getViewerByClass(TimeSeriesViewer.class); if (viewer == null) { try { viewer = new TimeSeriesViewer(getViewer().getFrame(), getDir()); getDir().addViewer(viewer); WindowUtilities.toFront(viewer.getFrame()); } catch (Exception e) { Basic.caught(e); } } else { viewer.updateView(Director.ALL); WindowUtilities.toFront(viewer.getFrame()); } } public void actionPerformed(ActionEvent event) { execute(getSyntax()); } public boolean isApplicable() { return getDir().getDocument().getNumberOfSamples() > 0 && getViewer() instanceof ClassificationViewer; } public String getName() { return "Time Series Viewer..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("TimeSeries16.gif"); } public String getDescription() { return "Opens the Time Series Viewer"; } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return null; } }
2,704
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowLRInspectorCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowLRInspectorCommand.java
/* * ShowLRInspectorCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.Pair; import jloda.util.parse.NexusStreamParser; import megan.core.Director; import megan.dialogs.lrinspector.LRInspectorViewer; import megan.util.WindowUtilities; import megan.viewer.ClassificationViewer; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; import java.util.Collection; import java.util.HashMap; import java.util.Map; /** * show long read inspector command * Daniel Huson, 2.2107 */ public class ShowLRInspectorCommand extends CommandBase implements ICommand { private static final Map<Pair<String, Integer>, LRInspectorViewer> classification2viewer = new HashMap<>(); /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("show window=longReadInspector"); final boolean alwaysNew; if (np.peekMatchIgnoreCase("alwaysNew")) { np.matchIgnoreCase("alwaysNew="); alwaysNew = np.getBoolean(); } else alwaysNew = false; np.matchIgnoreCase(";"); if (getViewer() instanceof ClassificationViewer) { final Director dir = (Director) getDir(); final ClassificationViewer parentViewer = (ClassificationViewer) getViewer(); final String classification = parentViewer.getClassName(); final Collection<Integer> classIds = parentViewer.getSelectedNodeIds(); if (classIds.size() > 0) { if (classIds.size() >= 5 && JOptionPane.showConfirmDialog(parentViewer.getFrame(), "Do you really want to open " + classIds.size() + " windows?", "Confirmation - MEGAN", JOptionPane.YES_NO_CANCEL_OPTION) != JOptionPane.YES_OPTION) return; for (Integer classId : classIds) { final Pair<String, Integer> pair = new Pair<>(dir.getID() + "." + classification, classId); LRInspectorViewer viewer = classification2viewer.get(pair); if (viewer != null) { if (dir.getViewers().contains(viewer)) { WindowUtilities.toFront(viewer); } else { classification2viewer.remove(pair); viewer = null; } } if (alwaysNew || viewer == null) { viewer = new LRInspectorViewer(parentViewer.getFrame(), parentViewer, classId); viewer.setRunOnDestroy(() -> classification2viewer.keySet().remove(pair)); classification2viewer.put(pair, viewer); dir.addViewer(viewer); } } } } } /** * get command-line usage description * * @return usage */ @Override public String getSyntax() { return "show window=longReadInspector [alwaysNew={false|true}];"; } /** * action to be performed * */ @Override public void actionPerformed(ActionEvent ev) { executeImmediately("show window=longReadInspector" + ((ev.getModifiers() & ActionEvent.SHIFT_MASK) == 0 ? ";" : " alwaysNew=false;")); } private static final String NAME = "Inspect Long Reads..."; public String getName() { return NAME; } /** * get description to be used as a tooltip * * @return description */ public String getDescription() { return "Show visual long read inspector"; } /** * get icon to be used in menu or button * * @return icon */ public ImageIcon getIcon() { return ResourceManager.getIcon("Inspector16.gif"); } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx() | java.awt.event.InputEvent.SHIFT_DOWN_MASK); } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return getViewer() instanceof ClassificationViewer && ((ClassificationViewer) getViewer()).getDocument().getMeganFile().hasDataConnector() && ((ClassificationViewer) getViewer()).getSelectedNodes().size() > 0; } }
5,758
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowLegendCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowLegendCommand.java
/* * ShowLegendCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICheckBoxCommand; import jloda.swing.director.IDirector; import jloda.swing.director.IViewerWithLegend; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; /** * show legend * Daniel Huson, 3.2013 */ public class ShowLegendCommand extends CommandBase implements ICheckBoxCommand { public boolean isSelected() { return getViewer() instanceof IViewerWithLegend && (((IViewerWithLegend) getViewer()).getShowLegend().equals("horizontal") || ((IViewerWithLegend) getViewer()).getShowLegend().equals("vertical")); } public String getSyntax() { return "show legend={horizontal|vertical|none};"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("show legend="); String which = np.getWordMatchesIgnoringCase("horizontal vertical none"); np.matchIgnoreCase(";"); if (getViewer() instanceof IViewerWithLegend) { IViewerWithLegend viewer = (IViewerWithLegend) getViewer(); viewer.setShowLegend(which); if (getViewer() != null) { getViewer().updateView(IDirector.ENABLE_STATE); } } } public void actionPerformed(ActionEvent event) { if (getViewer() instanceof IViewerWithLegend) { String legend = ((IViewerWithLegend) getViewer()).getShowLegend(); switch (legend) { case "none" -> executeImmediately("show legend=horizontal;"); case "horizontal" -> executeImmediately("show legend=vertical;"); case "vertical" -> executeImmediately("show legend=none;"); } } } public boolean isApplicable() { return getDir().getDocument().getNumberOfSamples() > 1 && getViewer() instanceof IViewerWithLegend; } public String getName() { return "Show Legend"; } public ImageIcon getIcon() { return ResourceManager.getIcon("Legend16.gif"); } public String getDescription() { return "Show horizontal or vertical legend, or hide"; } public boolean isCritical() { return false; } public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_J, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx() | java.awt.event.InputEvent.SHIFT_DOWN_MASK); } }
3,414
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowReanalyzeDialogCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowReanalyzeDialogCommand.java
/* * ShowReanalyzeDialogCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.CommandBase; import jloda.swing.commands.CommandManager; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.core.Director; import megan.dialogs.reanalyze.ReanalyzeDialog; import javax.swing.*; import java.awt.event.ActionEvent; /** * meganize DAA files command * Daniel Huson, 3.2016 */ public class ShowReanalyzeDialogCommand extends CommandBase implements ICommand { public ShowReanalyzeDialogCommand() { } public ShowReanalyzeDialogCommand(CommandManager commandManager) { super(commandManager); } /** * get command-line usage description * * @return usage */ @Override public String getSyntax() { return "show window=Reanalyze;"; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); final ReanalyzeDialog dialog = new ReanalyzeDialog(getViewer().getFrame(), (Director) getDir()); final String command = dialog.showAndGetCommand(); if (command != null) execute(command); } /** * action to be performed * */ @Override public void actionPerformed(ActionEvent ev) { executeImmediately(getSyntax()); } public static final String NAME = "Reanalyze Files..."; /** * get the name to be used as a menu label * * @return name */ public String getName() { return NAME; } /** * get description to be used as a tooltip * * @return description */ public String getDescription() { return "Show the 'renalyze files' dialog"; } /** * get icon to be used in menu or button * * @return icon */ public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Refresh16.gif"); } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return ((Director) getDir()).getDocument().neverOpenedReads; } }
3,494
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowExtractReadsDialogCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowExtractReadsDialogCommand.java
/* * ShowExtractReadsDialogCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICommand; import jloda.swing.director.IDirectableViewer; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.core.ClassificationType; import megan.core.Director; import megan.dialogs.extractor.ExtractReadsViewer; import megan.util.WindowUtilities; import megan.viewer.ClassificationViewer; import megan.viewer.MainViewer; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.IOException; public class ShowExtractReadsDialogCommand extends CommandBase implements ICommand { public String getSyntax() { return "show window=ExtractReads;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); final Director dir = getDir(); ExtractReadsViewer extractReadsViewer = (ExtractReadsViewer) dir.getViewerByClass(ExtractReadsViewer.class); final IDirectableViewer viewer = getViewer(); if (extractReadsViewer == null) extractReadsViewer = (ExtractReadsViewer) dir.addViewer(new ExtractReadsViewer(viewer.getFrame(), dir)); if (viewer instanceof MainViewer) extractReadsViewer.setMode(ClassificationType.Taxonomy.toString()); else if (viewer instanceof ClassificationViewer) extractReadsViewer.setMode(getViewer().getClassName()); else { throw new IOException("Invalid viewer"); } WindowUtilities.toFront(extractReadsViewer); } public void actionPerformed(ActionEvent event) { execute(getSyntax()); } public boolean isApplicable() { return getViewer() != null && getViewer() instanceof ClassificationViewer && getDir().getDocument().getMeganFile().hasDataConnector(); } private final static String NAME = "Extract Reads..."; public String getName() { return NAME; } public String getDescription() { return "Extract reads for the selected nodes"; } public ImageIcon getIcon() { return ResourceManager.getIcon("Extractor16.gif"); } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return null; } }
3,143
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowMainViewerCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowMainViewerCommand.java
/* * ShowMainViewerCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICommand; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.util.WindowUtilities; import megan.viewer.MainViewer; import javax.swing.*; import java.awt.event.ActionEvent; public class ShowMainViewerCommand extends megan.commands.CommandBase implements ICommand { public String getSyntax() { return "show window=mainViewer;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); if (ProgramProperties.isUseGUI()) { final MainViewer viewer = (MainViewer) getDir().getViewerByClass(MainViewer.class); WindowUtilities.toFront(viewer.getFrame()); } } public void actionPerformed(ActionEvent event) { executeImmediately(getSyntax()); } public boolean isApplicable() { return true; } public String getName() { return "Main Viewer..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("TaxonomyViewer16.gif"); } public String getDescription() { return "Brings the main viewer to the front"; } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return null; } }
2,202
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowMatchesHistogramCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowMatchesHistogramCommand.java
/* * ShowMatchesHistogramCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICommand; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.core.ClassificationType; import megan.core.Document; import megan.data.IConnector; import megan.data.IMatchBlock; import megan.data.IReadBlock; import megan.data.IReadBlockIterator; import megan.viewer.MainViewer; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.IOException; import java.util.Arrays; import java.util.HashMap; import java.util.Map; /** * shows the histogram of matches for a given node * Daniel Huson, 11.2010 */ public class ShowMatchesHistogramCommand extends CommandBase implements ICommand { /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("show histogram taxonId="); int taxId = np.getInt(); np.matchIgnoreCase(";"); Document doc = getDir().getDocument(); int[] values = computeHistogram(taxId, doc); System.err.println("Histogram for taxonId=" + taxId + ":"); for (int value : values) { System.err.println(value); } } /** * get command-line usage description * * @return usage */ @Override public String getSyntax() { return "show histogram taxonId=<num>;"; } /** * action to be performed * */ @Override public void actionPerformed(ActionEvent ev) { int taxId = ((MainViewer) getViewer()).getSelectedNodeIds().iterator().next(); String command = "show histogram taxonId=" + taxId + ";"; execute(command); } /** * compute the histogram associated with a given class * * @return histogram of counts of matches to different sequences */ private int[] computeHistogram(int classId, Document doc) throws IOException { IConnector connector = doc.getConnector(); Map<String, Integer> matched2count = new HashMap<>(); try (IReadBlockIterator it = connector.getReadsIterator(ClassificationType.Taxonomy.toString(), classId, doc.getMinScore(), doc.getMaxExpected(), false, true)) { while (it.hasNext()) { final IReadBlock readBlock = it.next(); for (int i = 0; i < readBlock.getNumberOfAvailableMatchBlocks(); i++) { IMatchBlock matchBlock = readBlock.getMatchBlock(i); if (matchBlock.getBitScore() >= doc.getMinScore() && matchBlock.getExpected() <= doc.getMaxExpected() && (matchBlock.getPercentIdentity() == 0 || matchBlock.getPercentIdentity() >= doc.getMinPercentIdentity())) { String firstLine = matchBlock.getText().split("\n")[0]; matched2count.merge(firstLine, 1, Integer::sum); } } } } int[] values = new int[matched2count.size()]; int i = 0; for (Integer count : matched2count.values()) { values[i++] = count; } Arrays.sort(values); return values; } /** * get the name to be used as a menu label * * @return name */ public String getName() { return "Show Matches Histogram"; } /** * get description to be used as a tooltip * * @return description */ public String getDescription() { return "Shows the distribution of matches for a given taxon"; } /** * get icon to be used in menu or button * * @return icon */ public ImageIcon getIcon() { return null; } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return ((MainViewer) getViewer()).getSelectedNodeIds().size() == 1; } }
5,199
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowChartCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowChartCommand.java
/* * ShowChartCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICommand; import jloda.swing.util.PopupMenu; import jloda.swing.util.ResourceManager; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.chart.AttributesChart; import megan.chart.FViewerChart; import megan.chart.MetadataChart; import megan.chart.TaxaChart; import megan.chart.data.ChartCommandHelper; import megan.chart.drawers.BarChartDrawer; import megan.chart.drawers.DrawerManager; import megan.chart.gui.ChartViewer; import megan.classification.Classification; import megan.classification.ClassificationManager; import megan.commands.CommandBase; import megan.core.Director; import megan.util.WindowUtilities; import megan.viewer.ClassificationViewer; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.io.IOException; /** * show chart command * Daniel Huson, 6.2012 */ public class ShowChartCommand extends CommandBase implements ICommand { public String getSyntax() { return "show chart drawer={" + StringUtils.toString(DrawerManager.getAllSupportedChartDrawers(), ",") + "} data={" + StringUtils.toString(ClassificationManager.getAllSupportedClassifications(), "|") + "|attributes|metadata};"; } public void apply(NexusStreamParser np) throws Exception { final Director dir = getDir(); np.matchIgnoreCase("show chart drawer="); final String drawerType = np.getWordMatchesRespectingCase(StringUtils.toString(DrawerManager.getAllSupportedChartDrawers(), " ")); np.matchIgnoreCase("data="); final String data = np.getWordMatchesRespectingCase(StringUtils.toString(ClassificationManager.getAllSupportedClassifications(), " ") + " attributes metadata"); np.matchIgnoreCase(";"); ChartViewer chartViewer = null; if (data.equalsIgnoreCase(Classification.Taxonomy) || data.equalsIgnoreCase("taxa")) // taxa for legacy { chartViewer = (TaxaChart) dir.getViewerByClass(TaxaChart.class); if (chartViewer == null) { chartViewer = new TaxaChart(dir); getDir().addViewer(chartViewer); if (drawerType.equals(BarChartDrawer.NAME) && getDir().getDocument().getNumberOfSamples() > 1) chartViewer.setTranspose(true); chartViewer.chooseDrawer(drawerType); } else { chartViewer.sync(); chartViewer.chooseDrawer(drawerType); chartViewer.updateView(Director.ALL); } } else if (data.equalsIgnoreCase("attributes")) { chartViewer = (AttributesChart) dir.getViewerByClass(AttributesChart.class); if (chartViewer == null) { chartViewer = new AttributesChart(dir); getDir().addViewer(chartViewer); chartViewer.chooseDrawer(drawerType); } else { chartViewer.sync(); chartViewer.chooseDrawer(drawerType); chartViewer.updateView(Director.ALL); } } else if (data.equalsIgnoreCase("metadata")) { chartViewer = (MetadataChart) dir.getViewerByClass(AttributesChart.class); if (chartViewer == null) { chartViewer = new MetadataChart(dir, dir.getMainViewer()); getDir().addViewer(chartViewer); chartViewer.chooseDrawer(drawerType); } else { chartViewer.sync(); chartViewer.chooseDrawer(drawerType); chartViewer.updateView(Director.ALL); } } else if (ClassificationManager.getAllSupportedClassifications().contains(data.toUpperCase())) { chartViewer = (FViewerChart) dir.getViewerByClassName(FViewerChart.getClassName(data)); if (chartViewer == null) { ClassificationViewer classificationViewer = (ClassificationViewer) dir.getViewerByClassName(ClassificationViewer.getClassName(data)); if (classificationViewer == null) throw new IOException(data + " viewer must be open for " + data + " chart to operate"); chartViewer = new FViewerChart(dir, classificationViewer); getDir().addViewer(chartViewer); if (getDir().getDocument().getNumberOfSamples() == 1) chartViewer.setTranspose(true); chartViewer.chooseDrawer(drawerType); } else { chartViewer.sync(); chartViewer.chooseDrawer(drawerType); chartViewer.updateView(Director.ALL); } } WindowUtilities.toFront(chartViewer); } public boolean isCritical() { return true; } public void actionPerformed(ActionEvent event) { final JPopupMenu popupMenu = new PopupMenu(this, ChartCommandHelper.getOpenChartMenuString(), getCommandManager()); final Point location = MouseInfo.getPointerInfo().getLocation(); SwingUtilities.convertPointFromScreen(location, getViewer().getFrame()); popupMenu.show(getViewer().getFrame(), location.x, location.y); } public boolean isApplicable() { return getDir().getDocument().getNumberOfReads() > 0 && getViewer() instanceof ClassificationViewer; } public String getName() { return "Chart..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("BarChart16.gif"); } public String getDescription() { return "Show chart"; } }
6,390
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowRemoteBrowserCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowRemoteBrowserCommand.java
/* * ShowRemoteBrowserCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.ms.clientdialog.RemoteServiceBrowser; import megan.ms.clientdialog.service.RemoteServiceManager; import megan.util.WindowUtilities; import megan.viewer.MainViewer; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.InputEvent; import java.awt.event.KeyEvent; public class ShowRemoteBrowserCommand extends CommandBase implements ICommand { private static RemoteServiceBrowser remoteServiceBrowser; public String getSyntax() { return "show window=RemoteBrowser;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); if (remoteServiceBrowser == null) { RemoteServiceManager.ensureCredentialsHaveBeenLoadedFromProperties(); RemoteServiceManager.ensureDefaultService(); remoteServiceBrowser = new RemoteServiceBrowser(MainViewer.getLastActiveFrame()); } WindowUtilities.toFront(remoteServiceBrowser.getFrame()); } public void actionPerformed(ActionEvent event) { executeImmediately(getSyntax()); } public boolean isApplicable() { return true; } private final static String NAME = "Open From Server..."; public String getName() { return NAME; } public String getDescription() { return "Open browser for remote files"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Open16.gif"); } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_O, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx() | InputEvent.SHIFT_DOWN_MASK); } }
2,750
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowReadLengthDistributionCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowReadLengthDistributionCommand.java
/* * ShowReadLengthDistributionCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICommand; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.dialogs.reads.ReadLengthDistribution; import megan.viewer.ClassificationViewer; import javax.swing.*; import java.awt.event.ActionEvent; public class ShowReadLengthDistributionCommand extends CommandBase implements ICommand { public String getSyntax() { return "show window=readLengthDistribution;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); ClassificationViewer viewer = (ClassificationViewer) getViewer(); if (viewer.getSelectedNodes().size() > 0) { final int classId = viewer.getSelectedNodeIds().iterator().next(); ReadLengthDistribution readLengthDistribution = new ReadLengthDistribution(viewer, classId); readLengthDistribution.show(); } } public void actionPerformed(ActionEvent event) { execute(getSyntax()); } public boolean isApplicable() { return getViewer() != null && getViewer() instanceof ClassificationViewer && ((ClassificationViewer) getViewer()).getSelectedNodes().size() == 1; } private final static String NAME = "Show Read Length Distribution..."; public String getName() { return NAME; } public String getDescription() { return "Show read length distribution"; } public ImageIcon getIcon() { return null; } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return null; } }
2,512
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowMessageWindowCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowMessageWindowCommand.java
/* * ShowMessageWindowCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.core.Director; import javax.swing.*; import java.awt.event.ActionEvent; /** * show the message window * Daniel Huson, 6.2010 */ public class ShowMessageWindowCommand extends CommandBase implements ICommand { private final static String NAME = "Message Window..."; /** * get the name to be used as a menu label * * @return name */ public String getName() { return NAME; } /** * get description to be used as a tooltip * * @return description */ public String getDescription() { return "Open the message window"; } /** * get icon to be used in menu or button * * @return icon */ public ImageIcon getIcon() { return ResourceManager.getIcon("sun/History16.gif"); } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); Director.showMessageWindow(); } /** * action to be performed * */ public void actionPerformed(ActionEvent ev) { executeImmediately(getSyntax()); } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return false; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return true; } /** * get command-line usage description * * @return usage */ @Override public String getSyntax() { return "show window=message;"; } /** * gets the command needed to undo this command * * @return undo command */ public String getUndo() { return null; } }
3,134
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowClusterWindowCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowClusterWindowCommand.java
/* * ShowClusterWindowCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.clusteranalysis.ClusterViewer; import megan.clusteranalysis.TaxonomyClusterViewer; import megan.commands.CommandBase; import megan.core.Director; import megan.viewer.ClassificationViewer; import megan.viewer.MainViewer; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.event.ActionEvent; public class ShowClusterWindowCommand extends CommandBase implements ICommand { public String getSyntax() { return "show window=clusterViewer;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); final Director dir = getDir(); if (getViewer() instanceof MainViewer) { ClusterViewer viewer = (ClusterViewer) dir.getViewerByClass(TaxonomyClusterViewer.class); if (viewer == null) { viewer = new TaxonomyClusterViewer((MainViewer) getViewer()); if (ClusterViewer.clusterViewerAddOn != null) ClusterViewer.clusterViewerAddOn.accept(viewer); dir.addViewer(viewer); } viewer.getFrame().toFront(); } else if (getViewer() instanceof ClassificationViewer) { final String name = getViewer().getClassName().toUpperCase() + "ClusterViewer"; ClusterViewer viewer = (ClusterViewer) dir.getViewerByClassName(name); if (viewer == null) { viewer = new ClusterViewer(dir, (ClassificationViewer) getViewer(), getViewer().getClassName()); if (ClusterViewer.clusterViewerAddOn != null) ClusterViewer.clusterViewerAddOn.accept(viewer); dir.addViewer(viewer); } viewer.toFront(); } } public void actionPerformed(ActionEvent event) { if (getViewer() instanceof ViewerBase && ((ViewerBase) getViewer()).getSelectedNodes().size() == 0) executeImmediately("select nodes=leaves;"); executeImmediately(getSyntax()); } public boolean isApplicable() { return getDir().getDocument().getNumberOfSamples() >= 4 && getViewer() instanceof ClassificationViewer; } public String getName() { return "Cluster Analysis..."; } public String getDescription() { return "Open a cluster analysis window"; } public ImageIcon getIcon() { return ResourceManager.getIcon("Network16.gif"); } public boolean isCritical() { return true; } }
3,461
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowFormatterCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowFormatterCommand.java
/* * ShowFormatterCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICommand; import jloda.swing.director.IDirectableViewer; import jloda.swing.format.Formatter; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.clusteranalysis.ClusterViewer; import megan.commands.CommandBase; import megan.util.FormatterUtils; import megan.util.WindowUtilities; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; public class ShowFormatterCommand extends CommandBase implements ICommand { public String getSyntax() { return "show window=formatter;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); Formatter formatter; IDirectableViewer viewer = getViewer(); if (!(viewer instanceof ClusterViewer)) formatter = FormatterUtils.getFormatter((ViewerBase) getViewer(), getDir()); else formatter = FormatterUtils.getFormatter(((ClusterViewer) viewer).getGraphView(), getDir()); WindowUtilities.toFront(formatter.getFrame()); } public void actionPerformed(ActionEvent event) { executeImmediately(getSyntax()); } public boolean isApplicable() { return getViewer() != null && (getViewer() instanceof ViewerBase || getViewer() instanceof ClusterViewer); } public String getName() { return "Format..."; } public String getDescription() { return "Format nodes and edges"; } public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_J, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()); } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Preferences16.gif"); } public boolean isCritical() { return true; } }
2,735
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowMeganizeDialogCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowMeganizeDialogCommand.java
/* * ShowMeganizeDialogCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.CommandBase; import jloda.swing.commands.CommandManager; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.core.Director; import megan.dialogs.meganize.MeganizeDAADialog; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.InputEvent; import java.awt.event.KeyEvent; /** * meganize DAA files command * Daniel Huson, 3.2016 */ public class ShowMeganizeDialogCommand extends CommandBase implements ICommand { public ShowMeganizeDialogCommand() { } public ShowMeganizeDialogCommand(CommandManager commandManager) { super(commandManager); } /** * get command-line usage description * * @return usage */ @Override public String getSyntax() { return "show window=MeganizeDAA;"; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); final MeganizeDAADialog dialog = new MeganizeDAADialog(getViewer().getFrame(), (Director) getDir()); final String command = dialog.showAndGetCommand(); if (command != null) execute(command); } /** * action to be performed * */ @Override public void actionPerformed(ActionEvent ev) { executeImmediately(getSyntax()); } public static final String NAME = "Meganize DAA File..."; /** * get the name to be used as a menu label * * @return name */ public String getName() { return NAME; } /** * get description to be used as a tooltip * * @return description */ public String getDescription() { return "Show the 'meganize DAA file' dialog"; } /** * get icon to be used in menu or button * * @return icon */ public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Import16.gif"); } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx() | InputEvent.SHIFT_DOWN_MASK); } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return true; } }
3,656
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowChartAttributesCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowChartAttributesCommand.java
/* * ShowChartAttributesCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.core.Director; import megan.viewer.ClassificationViewer; import javax.swing.*; import java.awt.event.ActionEvent; public class ShowChartAttributesCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } public void actionPerformed(ActionEvent event) { execute("show chart drawer=BarChart data=attributes;"); } public boolean isApplicable() { return ((Director) getDir()).getDocument().getNumberOfReads() > 0 && getViewer() instanceof ClassificationViewer; } public String getName() { return "Chart Microbial Attributes..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("AttributesChart16.gif"); } public String getDescription() { return "Chart microbial attributes"; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) { } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } }
2,377
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowGroupsViewerCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowGroupsViewerCommand.java
/* * ShowGroupsViewerCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.Basic; import jloda.util.parse.NexusStreamParser; import megan.core.Director; import megan.groups.GroupsViewer; import megan.util.WindowUtilities; import megan.viewer.ClassificationViewer; import javax.swing.*; import java.awt.event.ActionEvent; public class ShowGroupsViewerCommand extends CommandBase implements ICommand { public String getSyntax() { return "show window=groups;"; } public void actionPerformed(ActionEvent event) { execute(getSyntax()); } public boolean isApplicable() { return ((Director) getDir()).getDocument().getNumberOfReads() > 0 && getViewer() instanceof ClassificationViewer; } public String getName() { return "Groups Viewer..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("JoinNodes16.gif"); } public String getDescription() { return "Show groups viewer"; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); GroupsViewer groupsViewer = (GroupsViewer) getDir().getViewerByClass(GroupsViewer.class); if (groupsViewer == null) { try { groupsViewer = new GroupsViewer((Director) getDir(), getViewer().getFrame()); getDir().addViewer(groupsViewer); WindowUtilities.toFront(groupsViewer.getFrame()); } catch (Exception e) { Basic.caught(e); } } else { groupsViewer.updateView(Director.ENABLE_STATE); WindowUtilities.toFront(groupsViewer.getFrame()); } } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } }
3,075
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowComparisonPlotCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/show/ShowComparisonPlotCommand.java
/* * ShowComparisonPlotCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.show; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.chart.ComparisonPlot; import megan.chart.gui.ChartViewer; import megan.classification.Classification; import megan.classification.ClassificationManager; import megan.commands.CommandBase; import megan.core.Director; import megan.util.WindowUtilities; import megan.viewer.ClassificationViewer; import megan.viewer.MainViewer; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.IOException; public class ShowComparisonPlotCommand extends CommandBase implements ICommand { public String getSyntax() { return "show comparisonPlot [data={" + StringUtils.toString(ClassificationManager.getAllSupportedClassifications(), "|") + "]};"; } public void apply(NexusStreamParser np) throws Exception { Director dir = getDir(); ChartViewer chartViewer; np.matchIgnoreCase("show comparisonPlot"); String data = "taxonomy"; if (np.peekMatchIgnoreCase("data")) { np.matchIgnoreCase("data="); data = np.getWordMatchesIgnoringCase(StringUtils.toString(ClassificationManager.getAllSupportedClassifications(), " ")); } np.matchIgnoreCase(";"); chartViewer = (ComparisonPlot) dir.getViewerByClassName(ComparisonPlot.getClassName(data)); if (chartViewer == null) { ClassificationViewer classificationViewer = (ClassificationViewer) dir.getViewerByClassName(ClassificationViewer.getClassName(data)); if (classificationViewer == null) throw new IOException("Viewer must be open for chart to operate"); chartViewer = new ComparisonPlot(dir, classificationViewer); getDir().addViewer(chartViewer); } else { chartViewer.sync(); } WindowUtilities.toFront(chartViewer); } public void actionPerformed(ActionEvent event) { if (getViewer() instanceof ViewerBase && ((ViewerBase) getViewer()).getSelectedNodes().size() == 0) executeImmediately("select nodes=leaves;"); if (getViewer() instanceof MainViewer) { execute("show comparisonPlot data=" + Classification.Taxonomy + ";"); } else if (getViewer() instanceof ClassificationViewer) { execute("show comparisonPlot data=" + getViewer().getClassName() + ";"); } } public boolean isApplicable() { return getDir().getDocument().getNumberOfSamples() > 1 && getViewer() instanceof ClassificationViewer; } public String getName() { return "Comparison Plot..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("Plot2D16.gif"); } public String getDescription() { return "Plot pairwise comparison of assignments to classes"; } public boolean isCritical() { return true; } }
3,852
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ColorByPositionCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/color/ColorByPositionCommand.java
/* * ColorByPositionCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.color; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICheckBoxCommand; import jloda.util.parse.NexusStreamParser; import megan.core.Director; import javax.swing.*; import java.awt.event.ActionEvent; public class ColorByPositionCommand extends CommandBase implements ICheckBoxCommand { @Override public boolean isSelected() { return ((Director) getDir()).getDocument().getChartColorManager().isColorByPosition(); } public String getSyntax() { return null; } public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { execute("set colorBy=position;"); } public boolean isApplicable() { return true; } public static final String NAME = "Color Classes By Position"; public String getName() { return NAME; } public String getDescription() { return "Color classes by their position in the chart"; } public ImageIcon getIcon() { return null; } public boolean isCritical() { return true; } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } }
2,117
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SetColorTableCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/color/SetColorTableCommand.java
/* * SetColorTableCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.color; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.director.IUsesHeatMapColors; import jloda.swing.util.ColorTableManager; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.chart.commands.ColorByRankCommand; import megan.core.Director; import megan.core.Document; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; /** * sets the color table * Daniel Huson, 1.2016 */ public class SetColorTableCommand extends CommandBase implements ICommand { /** * get command-line usage description * * @return usage */ @Override public String getSyntax() { return "set colorTable={name} [heatMap={false|true}]"; } /** * get the name to be used as a menu label * * @return name */ public String getName() { return "Colors..."; } /** * get description to be used as a tooltip * * @return description */ public String getDescription() { return "Set colors"; } /** * get icon to be used in menu or button * * @return icon */ public ImageIcon getIcon() { return ResourceManager.getIcon("ColorTable16.gif"); } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("set colorTable="); String name = np.getWordMatchesRespectingCase(ColorTableManager.getNames()); boolean isHeatMap; if (np.peekMatchIgnoreCase("heatMap")) { np.matchIgnoreCase("heatMap="); isHeatMap = np.getBoolean(); } else isHeatMap = false; np.matchIgnoreCase(";"); final Document doc = ((Director) getDir()).getDocument(); if (isHeatMap) { doc.getChartColorManager().setHeatMapTable(name); ColorTableManager.setDefaultColorTableHeatMap(name); } else { doc.getChartColorManager().setColorTable(name); ColorTableManager.setDefaultColorTable(name); } ColorByLabelCommand.updateColors(doc); doc.setDirty(true); } /** * action to be performed * */ public void actionPerformed(ActionEvent ev) { final String[] choices = ColorTableManager.getNamesOrdered(); final boolean isHeatMap = (getViewer() instanceof IUsesHeatMapColors) && ((IUsesHeatMapColors) getViewer()).useHeatMapColors(); final Document doc = ((Director) getDir()).getDocument(); final String current = isHeatMap ? doc.getChartColorManager().getHeatMapTable().getName() : doc.getChartColorManager().getColorTable().getName(); final JPopupMenu popMenu = new JPopupMenu(); for (final String name : choices) { JCheckBoxMenuItem checkBoxMenuItem = new JCheckBoxMenuItem(); checkBoxMenuItem.setAction(new AbstractAction(name) { public void actionPerformed(ActionEvent e) { if (doc.getChartColorManager().hasChangedColors()) { switch (JOptionPane.showConfirmDialog(getViewer().getFrame(), "Clear all individually set colors?", "Question", JOptionPane.YES_NO_CANCEL_OPTION)) { case JOptionPane.YES_OPTION: doc.getChartColorManager().clearChangedColors(); break; case JOptionPane.NO_OPTION: break; default: return; // canceled } } execute("set colorTable='" + name + "'" + (isHeatMap ? " heatMap=true;" : ";")); } }); checkBoxMenuItem.setSelected(name.equals(current)); checkBoxMenuItem.setIcon(ColorTableManager.getColorTable(name).makeIcon()); popMenu.add(checkBoxMenuItem); } popMenu.addSeparator(); { final JMenuItem item = getViewer().getCommandManager().getJMenuItem(ColorByLabelCommand.NAME); if (item != null) { item.setEnabled(!isHeatMap); popMenu.add(item); } } { final JMenuItem item = getViewer().getCommandManager().getJMenuItem(ColorByPositionCommand.NAME); if (item != null) { item.setEnabled(!isHeatMap); popMenu.add(item); } } { final JMenuItem item = getViewer().getCommandManager().getJMenuItem(ColorSamplesByAttributeCommand.ALT_NAME); if (item != null) { popMenu.addSeparator(); item.setEnabled(!isHeatMap); popMenu.add(item); } } { final JMenuItem item = getViewer().getCommandManager().getJMenuItem(ColorByRankCommand.NAME); if (item != null) { popMenu.addSeparator(); item.setEnabled(!isHeatMap); popMenu.add(item); } } popMenu.addSeparator(); { final JMenuItem item = getViewer().getCommandManager().getJMenuItem(UseProgramColorsCommand.NAME); if (item != null) { popMenu.add(item); } } final Point location = MouseInfo.getPointerInfo().getLocation(); SwingUtilities.convertPointFromScreen(location, getViewer().getFrame()); popMenu.show(getViewer().getFrame(), location.x, location.y); } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return true; } }
7,141
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ClearSetColorsCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/color/ClearSetColorsCommand.java
/* * ClearSetColorsCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.color; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.util.parse.NexusStreamParser; import megan.core.Director; import javax.swing.*; import java.awt.event.ActionEvent; public class ClearSetColorsCommand extends CommandBase implements ICommand { public String getSyntax() { return "clearSetColors;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); ((Director) getDir()).getDocument().getChartColorManager().clearChangedColors(); } public void actionPerformed(ActionEvent event) { if (JOptionPane.showConfirmDialog(getViewer().getFrame(), "This will discard all individually set colors, proceed?", "Question", JOptionPane.YES_NO_CANCEL_OPTION) != JOptionPane.YES_OPTION) return; // answered no or cancle execute(getSyntax()); } public boolean isApplicable() { return ((Director) getDir()).getDocument().getChartColorManager().hasChangedColors(); } private static final String NAME = "Clear Set Colors"; public String getName() { return NAME; } public String getDescription() { return "Clear all individually set colors"; } public ImageIcon getIcon() { return null; } public boolean isCritical() { return true; } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } }
2,411
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ColorSamplesByAttributeCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/color/ColorSamplesByAttributeCommand.java
/* * ColorSamplesByAttributeCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.color; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICheckBoxCommand; import jloda.util.parse.NexusStreamParser; import megan.core.Director; import megan.core.Document; import megan.samplesviewer.SamplesViewer; import javax.swing.*; import java.awt.event.ActionEvent; public class ColorSamplesByAttributeCommand extends CommandBase implements ICheckBoxCommand { @Override public boolean isSelected() { return ((Director) getDir()).getDocument().getSampleAttributeTable().isSomeSampleColored(); } public String getSyntax() { return null; } public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { if (isSelected()) { // erase all sample colors final Document doc = ((Director) getDir()).getDocument(); for (String sample : doc.getSampleNames()) { doc.getSampleAttributeTable().putSampleColor(sample, null); } execute("set colorBy=position;"); } else if (getViewer() instanceof SamplesViewer) { final SamplesViewer viewer = ((SamplesViewer) getViewer()); viewer.getFrame().toFront(); final String attribute = viewer.getSamplesTableView().getASelectedAttribute(); if (attribute != null) execute("colorBy attribute='" + attribute + "';"); } else execute("show window=samplesViewer;"); } public boolean isApplicable() { return getViewer() instanceof SamplesViewer && isSelected(); } public static final String ALT_NAME = "Color Samples By Attributes CBOX"; public String getAltName() { return ALT_NAME; } public String getName() { return "Color Samples By Attributes"; } public String getDescription() { return "Determine whether to color samples by attributes"; } public ImageIcon getIcon() { return null; } public boolean isCritical() { return true; } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } }
3,068
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
UseProgramColorsCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/color/UseProgramColorsCommand.java
/* * UseProgramColorsCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.color; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICheckBoxCommand; import jloda.util.parse.NexusStreamParser; import megan.core.Director; import megan.core.Document; import javax.swing.*; import java.awt.event.ActionEvent; public class UseProgramColorsCommand extends CommandBase implements ICheckBoxCommand { @Override public boolean isSelected() { return ((Director) getDir()).getDocument().getChartColorManager().isUsingProgramColors(); } public String getSyntax() { return "set useProgramColors={false|true};"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("set useProgramColors="); boolean use = np.getBoolean(); np.matchIgnoreCase(";"); final Document doc = ((Director) getDir()).getDocument(); if (doc.getChartColorManager().isUsingProgramColors() != use) doc.setupChartColorManager(use); } public void actionPerformed(ActionEvent event) { execute("set useProgramColors=" + (!isSelected()) + ";"); } public boolean isApplicable() { return true; } public static final String NAME = "Use Program Color Table"; public String getName() { return NAME; } public String getDescription() { return "Use program color table rather than document specific one"; } public ImageIcon getIcon() { return null; } public boolean isCritical() { return true; } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } }
2,541
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SetAttributeColorCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/color/SetAttributeColorCommand.java
/* * SetAttributeColorCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.color; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ColorUtilsSwing; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.chart.ChartColorManager; import megan.core.Director; import megan.core.Document; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; /** * set color by attribute * Daniel Huson, 7.2012 */ public class SetAttributeColorCommand extends CommandBase implements ICommand { /** * parses the given command and executes it * */ @Override public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("set color="); Color color = ColorUtilsSwing.convert(np.getColor()); np.matchIgnoreCase("attribute="); final String attribute = np.getLabelRespectCase(); np.matchIgnoreCase("state="); final String state = np.getLabelRespectCase(); if (attribute != null && state != null) { final Document doc = ((Director) getDir()).getDocument(); final ChartColorManager chartColorManager = doc.getChartColorManager(); chartColorManager.setAttributeStateColor(attribute, state, color); for (String sample : doc.getSampleNames()) { chartColorManager.setSampleColor(sample, chartColorManager.getAttributeStateColor(attribute, doc.getSampleAttributeTable().get(sample, attribute))); } doc.setDirty(true); ((Director) getDir()).updateView(Director.ALL); } np.matchIgnoreCase(";"); } /** * get command-line usage description * * @return usage */ @Override public String getSyntax() { return "set color=<color> attribute=<name> state=<name>;"; } /** * action to be performed * */ @Override public void actionPerformed(ActionEvent ev) { } public String getName() { return null; } /** * get description to be used as a tooltip * * @return description */ public String getDescription() { return "Set the color for an attribute value"; } public ImageIcon getIcon() { return ResourceManager.getIcon("YellowSquare16.gif"); } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_K, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()); } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return true; } }
3,872
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ColorByLabelCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/color/ColorByLabelCommand.java
/* * ColorByLabelCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.color; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICheckBoxCommand; import jloda.util.parse.NexusStreamParser; import megan.chart.ChartColorManager; import megan.core.Director; import megan.core.Document; import megan.core.SampleAttributeTable; import javax.swing.*; import java.awt.event.ActionEvent; import java.util.List; public class ColorByLabelCommand extends CommandBase implements ICheckBoxCommand { @Override public boolean isSelected() { return !((Director) getDir()).getDocument().getChartColorManager().isColorByPosition(); } public String getSyntax() { return "set colorBy={label|position};"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("set colorBy="); final boolean byPosition = (np.getWordMatchesRespectingCase("label position").equalsIgnoreCase("position")); np.matchIgnoreCase(";"); final Document doc = ((Director) getDir()).getDocument(); final boolean oldByPosition = doc.getChartColorManager().isColorByPosition(); doc.getChartColorManager().setColorByPosition(byPosition); updateColors(doc); if (oldByPosition != byPosition) doc.setDirty(true); } public static void updateColors (Document doc) { final boolean byPosition=doc.getChartColorManager().isColorByPosition(); final List<String> samples=doc.getSampleNames(); final ChartColorManager colorTableManager=doc.getChartColorManager(); colorTableManager.clearChangedColors(); for (int i = 0; i < doc.getNumberOfSamples(); i++) { doc.getSampleAttributeTable().put(samples.get(i), SampleAttributeTable.HiddenAttribute.Color, null); } if(byPosition) colorTableManager.setSampleColorPositions(samples); } public void actionPerformed(ActionEvent event) { execute("set colorBy=label;"); } public boolean isApplicable() { return true; } public static final String NAME = "Color Classes By Label"; public String getName() { return NAME; } public String getDescription() { return "Color classes by their labels (same label always gets same color)"; } public ImageIcon getIcon() { return null; } public boolean isCritical() { return true; } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } }
3,411
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SelectInvertCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/select/SelectInvertCommand.java
/* * SelectInvertCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.select; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import javax.swing.*; import java.awt.event.ActionEvent; /** * * selection command * * Daniel Huson, 11.2010 */ public class SelectInvertCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { execute("select nodes=invert;"); } public boolean isApplicable() { return true; } public String getName() { return "Invert"; } public String getDescription() { return "Invert selection"; } public ImageIcon getIcon() { return ResourceManager.getIcon("Empty16.gif"); } public boolean isCritical() { return true; } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } }
2,034
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SelectLeavesBelowCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/select/SelectLeavesBelowCommand.java
/* * SelectLeavesBelowCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.select; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.util.parse.NexusStreamParser; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.event.ActionEvent; /** * * selection command * * Daniel Huson, 11.2010 */ public class SelectLeavesBelowCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { execute("select nodes=leavesBelow;"); } public boolean isApplicable() { return getViewer() != null && ((ViewerBase) getViewer()).getSelectedNodes().size() > 0; } public String getName() { return "Leaves Below"; } public String getDescription() { return "Select all leaves below currently selected nodes"; } public ImageIcon getIcon() { return null; } public boolean isCritical() { return true; } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } }
2,119
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SelectInternalNodesCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/select/SelectInternalNodesCommand.java
/* * SelectInternalNodesCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.select; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import javax.swing.*; import java.awt.event.ActionEvent; /** * * selection command * * Daniel Huson, 11.2010 */ public class SelectInternalNodesCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } public void actionPerformed(ActionEvent event) { execute("select nodes=internal;"); } public boolean isApplicable() { return true; } public String getName() { return "All Internal Nodes"; } public String getDescription() { return "Select all internal nodes"; } public ImageIcon getIcon() { return ResourceManager.getIcon("Empty16.gif"); } public boolean isCritical() { return true; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) { } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } }
2,071
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SelectNodesByNameCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/select/SelectNodesByNameCommand.java
/* * SelectNodesByNameCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.select; import jloda.swing.commands.ICommand; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.event.ActionEvent; import java.util.HashSet; import java.util.Set; /** * select by name * Daniel Huson, 2.2011 */ public class SelectNodesByNameCommand extends CommandBase implements ICommand { public String getSyntax() { return "select name=<name> <name> ... [state={true|false}];"; } public void apply(NexusStreamParser np) throws Exception { ViewerBase viewer = (ViewerBase) getViewer(); np.matchIgnoreCase("select"); np.matchIgnoreCase("name="); Set<String> names = new HashSet<>(); while (!np.peekMatchAnyTokenIgnoreCase("state ;")) { names.add(np.getWordRespectCase()); } boolean state = true; if (np.peekMatchIgnoreCase("state")) { np.matchIgnoreCase("state="); state = np.getBoolean(); } np.matchRespectCase(";"); viewer.selectNodesByLabels(names, state); viewer.repaint(); } /** * action to be performed * */ @Override public void actionPerformed(ActionEvent ev) { String result = JOptionPane.showInputDialog(getViewer().getFrame(), "Enter name", "Select Node", JOptionPane.QUESTION_MESSAGE); if (result != null) execute("select name=" + result + ";"); } /** * get the name to be used as a menu label * * @return name */ public String getName() { return "Select By Name..."; } /** * get description to be used as a tooltip * * @return description */ public String getDescription() { return "Select the named nodes"; } /** * get icon to be used in menu or button * * @return icon */ public ImageIcon getIcon() { return null; } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { ViewerBase viewer = (ViewerBase) getViewer(); return viewer.getGraph().getNumberOfNodes() > 0; } }
3,335
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SelectNodesAboveCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/select/SelectNodesAboveCommand.java
/* * SelectNodesAboveCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.select; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.util.parse.NexusStreamParser; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.event.ActionEvent; /** * * selection command * * Daniel Huson, 11.2010 */ public class SelectNodesAboveCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { execute("select nodes=nodesAbove;"); } public boolean isApplicable() { return getViewer() != null && ((ViewerBase) getViewer()).getSelectedNodes().size() > 0; } public String getName() { return "Nodes Above"; } public String getDescription() { return "Select all nodes above the currently selected nodes"; } public ImageIcon getIcon() { return null; } public boolean isCritical() { return true; } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } }
2,118
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SelectAllNodesCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/select/SelectAllNodesCommand.java
/* * SelectAllNodesCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.select; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.director.ProjectManager; import jloda.swing.util.ResourceManager; import jloda.swing.window.NotificationsInSwing; import jloda.util.parse.NexusStreamParser; import megan.clusteranalysis.ClusterViewer; import megan.groups.GroupsViewer; import megan.viewer.ClassificationViewer; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; /** * * selection command * * Daniel Huson, 11.2010 */ public class SelectAllNodesCommand extends CommandBase implements ICommand { public String getSyntax() { return "select nodes={all|none|leaves|internal|previous|subtree|leavesBelow|nodesAbove|intermediate|invert}"; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("select nodes="); String what = np.getWordMatchesIgnoringCase("all none leaves internal previous subTree leavesBelow subLeaves nodesAbove intermediate invert positiveAssigned"); np.matchRespectCase(";"); final ViewerBase viewer; if (getViewer() instanceof ViewerBase) viewer = (ViewerBase) getViewer(); else if (getViewer() instanceof ClusterViewer && ((ClusterViewer) getViewer()).getGraphView() instanceof ViewerBase) viewer = (ViewerBase) ((ClusterViewer) getViewer()).getGraphView(); else if (getViewer() instanceof ClusterViewer && ((ClusterViewer) getViewer()).getTabbedIndex() == ClusterViewer.MATRIX_TAB_INDEX && what.equalsIgnoreCase("previous")) { ((ClusterViewer) getViewer()).getMatrixTab().selectByLabels(ProjectManager.getPreviouslySelectedNodeLabels()); return; } else if (getViewer() instanceof GroupsViewer) { switch (what.toLowerCase()) { case "previous" -> ((GroupsViewer) getViewer()).selectFromPrevious(ProjectManager.getPreviouslySelectedNodeLabels()); case "all" -> ((GroupsViewer) getViewer()).getGroupsPanel().selectAll(); case "none" -> ((GroupsViewer) getViewer()).getGroupsPanel().selectNone(); } return; } else return; if (what.equalsIgnoreCase("all")) viewer.selectAllNodes(true); else if (what.equals("none")) viewer.selectAllNodes(false); else if (what.equals("leaves")) viewer.selectAllLeaves(); else if (what.equals("internal")) viewer.selectAllInternal(); else if (what.equals("previous")) viewer.selectNodesByLabels(ProjectManager.getPreviouslySelectedNodeLabels(), true); else if (what.equalsIgnoreCase("subTree")) viewer.selectSubTreeNodes(); else if (what.equals("subLeaves") || what.equals("leavesBelow")) viewer.selectLeavesBelow(); else if (what.equals("nodesAbove")) viewer.selectNodesAbove(); else if (what.equals("intermediate")) viewer.selectAllIntermediateNodes(); else if (what.equals("invert")) viewer.invertNodeSelection(); else if (what.equals("positiveAssigned")) { if (viewer instanceof ClassificationViewer) ((ClassificationViewer) viewer).selectNodesPositiveAssigned(); else NotificationsInSwing.showWarning("select nodes=" + what + ": not implemented for this type of viewer"); } System.err.println("Number of nodes selected: " + viewer.getNumberSelectedNodes()); viewer.repaint(); } public void actionPerformed(ActionEvent event) { executeImmediately("select nodes=all;"); } public boolean isApplicable() { return true; } public String getName() { return "All Nodes"; } public String getDescription() { return "Select nodes"; } public ImageIcon getIcon() { return ResourceManager.getIcon("Empty16.gif"); } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()); } }
5,202
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SelectNodesByIdsCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/select/SelectNodesByIdsCommand.java
/* * SelectNodesByIdsCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.select; import jloda.graph.Node; import jloda.swing.commands.ICommand; import jloda.util.NumberUtils; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.event.ActionEvent; import java.util.HashSet; import java.util.Set; /** * select by name * Daniel Huson, 2.2011 */ public class SelectNodesByIdsCommand extends CommandBase implements ICommand { public String getSyntax() { return "select id=<number> ...;"; } public void apply(NexusStreamParser np) throws Exception { ViewerBase viewer = ((ViewerBase) getViewer()); np.matchIgnoreCase("select id="); Set<Integer> ids = new HashSet<>(); while (!np.peekMatchAnyTokenIgnoreCase(";")) { ids.add(NumberUtils.parseInt(np.getWordRespectCase())); } np.matchRespectCase(";"); Set<Node> nodes = new HashSet<>(); for (Integer id : ids) { if (id != null) { Set<Node> add = viewer.getNodes(id); if (add != null && add.size() > 0) nodes.addAll(add); } } viewer.getSelectedNodes().addAll(nodes); viewer.repaint(); } /** * action to be performed * */ public void actionPerformed(ActionEvent ev) { String result = JOptionPane.showInputDialog(getViewer().getFrame(), "Enter Id", "Select Node by Id", JOptionPane.QUESTION_MESSAGE); if (result != null) execute("select id=" + result + ";"); } /** * get the name to be used as a menu label * * @return name */ public String getName() { return "Select By Id..."; } /** * get description to be used as a tooltip * * @return description */ public String getDescription() { return "Select the nodes for the given ids"; } /** * get icon to be used in menu or button * * @return icon */ public ImageIcon getIcon() { return null; } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { ViewerBase viewer = (ViewerBase) getViewer(); return viewer.getGraph().getNumberOfNodes() > 0; } }
3,445
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SelectFromPreviousWindowCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/select/SelectFromPreviousWindowCommand.java
/* * SelectFromPreviousWindowCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.select; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; /** * * selection command * * Daniel Huson, 11.2010 */ public class SelectFromPreviousWindowCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { execute("select nodes=previous;"); } public boolean isApplicable() { return true; } public String getName() { return "From Previous Window"; } public String getDescription() { return "Select from previous window"; } public ImageIcon getIcon() { return ResourceManager.getIcon("Empty16.gif"); } public boolean isCritical() { return true; } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()); } }
2,147
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SelectNoneCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/select/SelectNoneCommand.java
/* * SelectNoneCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.select; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import javax.swing.*; import java.awt.event.ActionEvent; /** * * selection command * * Daniel Huson, 11.2010 */ public class SelectNoneCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { execute("select nodes=none;"); } public boolean isApplicable() { return true; } public String getName() { return "None"; } public String getDescription() { return "Deselect all nodes"; } public ImageIcon getIcon() { return ResourceManager.getIcon("Empty16.gif"); } public boolean isCritical() { return true; } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } }
2,028
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SelectSubtreeCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/select/SelectSubtreeCommand.java
/* * SelectSubtreeCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.select; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.event.ActionEvent; /** * * selection command * * Daniel Huson, 11.2010 */ public class SelectSubtreeCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { execute("select nodes=subTree;"); } public boolean isApplicable() { return getViewer() != null && ((ViewerBase) getViewer()).getSelectedNodes().size() > 0; } public String getName() { return "Subtree"; } public String getDescription() { return "Select subtree"; } public ImageIcon getIcon() { return ResourceManager.getIcon("Empty16.gif"); } public boolean isCritical() { return true; } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } }
2,143
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SelectLeavesCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/select/SelectLeavesCommand.java
/* * SelectLeavesCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.select; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; /** * * selection command * * Daniel Huson, 11.2010 */ public class SelectLeavesCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { executeImmediately("select nodes=leaves;"); } public boolean isApplicable() { return true; } public String getName() { return "All Leaves"; } public String getDescription() { return "Select all leaves (except Not Assigned, No Hits and Low Complexity)"; } public ImageIcon getIcon() { return ResourceManager.getIcon("Empty16.gif"); } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()); } }
2,134
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SelectIntermediateNodesCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/select/SelectIntermediateNodesCommand.java
/* * SelectIntermediateNodesCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.select; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.util.parse.NexusStreamParser; import javax.swing.*; import java.awt.event.ActionEvent; /** * * selection command * * Daniel Huson, 11.2010 */ public class SelectIntermediateNodesCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { executeImmediately("select nodes=intermediate;"); } public boolean isApplicable() { return true; } public String getName() { return "All Intermediate Nodes"; } public String getDescription() { return "Select all intermediate nodes"; } public ImageIcon getIcon() { return null; } public boolean isCritical() { return true; } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } }
2,027
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportAlignmentsCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportAlignmentsCommand.java
/* * ExportAlignmentsCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.swing.commands.ICommand; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.swing.window.NotificationsInSwing; import jloda.util.NumberUtils; import jloda.util.Pair; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.alignment.AlignmentExporter; import megan.classification.Classification; import megan.classification.ClassificationManager; import megan.commands.CommandBase; import megan.core.ClassificationType; import megan.core.Document; import megan.viewer.ClassificationViewer; import megan.viewer.MainViewer; import megan.viewer.TaxonomyData; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.io.File; import java.util.HashSet; import java.util.Set; /** * export all alignments for the selected nodes */ public class ExportAlignmentsCommand extends CommandBase implements ICommand { public String getSyntax() { return "export what=alignment file=<filename> data={" + StringUtils.toString(ClassificationManager.getAllSupportedClassifications(), "|") + "}" + " classId={number[,number...]|selected} [asConsensus={false|true}]\n" + "\t[useEachReadOnlyOnce={true|false}] [useEachReferenceOnlyOnce={true|false}] [includeInsertions={true|false}]\n" + "\t[refSeqOnly={false|true}] [contractGaps={false|true}] [translateCDNA={false|true}] [minReads={number}] [minLength={number}] [minCoverage={number}];"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("export what=alignment file="); String fileName = np.getWordFileNamePunctuation(); np.matchIgnoreCase("data="); String classificationName = np.getWordMatchesRespectingCase(StringUtils.toString(ClassificationManager.getAllSupportedClassifications(), " ")); np.matchIgnoreCase("classId="); boolean useSelected = false; Set<Integer> classIds = new HashSet<>(); if (np.peekMatchIgnoreCase("selected")) { np.matchIgnoreCase("selected"); useSelected = true; } else { while (true) { classIds.add(np.getInt()); if (!np.peekMatchIgnoreCase(",")) break; np.matchIgnoreCase(","); } } boolean asConsensus = false; if (np.peekMatchIgnoreCase("asConsensus")) { np.matchIgnoreCase("asConsensus="); asConsensus = np.getBoolean(); ProgramProperties.put("ExAlignmentAsConsensus", asConsensus); } boolean useEachReadOnlyOnce = true; if (np.peekMatchIgnoreCase("useEachReadOnlyOnce")) { np.matchIgnoreCase("useEachReadOnlyOnce="); useEachReadOnlyOnce = np.getBoolean(); ProgramProperties.put("ExAlignmentUseEachReadOnce", useEachReadOnlyOnce); } boolean useEachReferenceOnlyOnce = false; if (np.peekMatchIgnoreCase("useEachReferenceOnlyOnce")) { np.matchIgnoreCase("useEachReferenceOnlyOnce="); useEachReferenceOnlyOnce = np.getBoolean(); ProgramProperties.put("ExAlignmentUseEachRefOnce", useEachReferenceOnlyOnce); } /* boolean includeInsertions = true; if (np.peekMatchIgnoreCase("includeInsertions")) { np.matchIgnoreCase("includeInsertions="); includeInsertions = np.getBoolean(); } */ boolean refSeqOnly = false; if (np.peekMatchIgnoreCase("refSeqOnly")) { np.matchIgnoreCase("refSeqOnly="); refSeqOnly = np.getBoolean(); ProgramProperties.put("ExAlignmentUseRefSeqOnly", refSeqOnly); } /* boolean contractGaps = false; if (np.peekMatchIgnoreCase("contractGaps")) { np.matchIgnoreCase("contractGaps="); contractGaps = np.getBoolean(); } */ boolean blastXAsProtein = false; if (np.peekMatchIgnoreCase("translateCDNA")) { np.matchIgnoreCase("translateCDNA="); blastXAsProtein = np.getBoolean(); ProgramProperties.put("ExAlignmentTranslateCDNA", blastXAsProtein); } int minReads = 0; if (np.peekMatchIgnoreCase("minReads")) { np.matchIgnoreCase("minReads="); minReads = np.getInt(0, 1000000); ProgramProperties.put("ExAlignmentMinReads", minReads); } int minLength = 0; if (np.peekMatchIgnoreCase("minLength")) { np.matchIgnoreCase("minLength="); minLength = np.getInt(0, 1000000000); ProgramProperties.put("ExAlignmentMinLength", minLength); } double minCoverage = 0; if (np.peekMatchIgnoreCase("minCoverage")) { np.matchIgnoreCase("minCoverage="); minCoverage = np.getDouble(0, 1000000); ProgramProperties.put("ExAlignmentMinCoverage", (float) minCoverage); } np.matchIgnoreCase(";"); if (useSelected) { if (classificationName.equals(ClassificationType.Taxonomy.toString())) { MainViewer mainViewer = getDir().getMainViewer(); classIds.addAll(mainViewer.getSelectedNodeIds()); } else { ClassificationViewer viewer = (ClassificationViewer) getDir().getViewerByClassName(classificationName); if (viewer != null) { classIds.addAll(viewer.getSelectedNodeIds()); } } } int totalReads = 0; int totalFiles = 0; if (classIds.size() > 0) { final Document doc = getDir().getDocument(); doc.getProgressListener().setTasks("Alignment export", ""); AlignmentExporter alignmentExporter = new AlignmentExporter(doc, getViewer().getFrame()); alignmentExporter.setUseEachReferenceOnlyOnce(useEachReferenceOnlyOnce); Classification classification = (classificationName.equals(Classification.Taxonomy) ? null : ClassificationManager.get(classificationName, true)); for (Integer classId : classIds) { final String className; if (getViewer() instanceof MainViewer) { className = TaxonomyData.getName2IdMap().get(classId); } else if (classification != null) { className = classification.getName2IdMap().get(classId); } else className = "Unknown"; alignmentExporter.loadData(classificationName, classId, className, refSeqOnly, doc.getProgressListener()); Pair<Integer, Integer> numberOfReadsAndFiles = alignmentExporter.exportToFiles(totalFiles, fileName, useEachReadOnlyOnce, blastXAsProtein, asConsensus, minReads, minLength, minCoverage, doc.getProgressListener()); totalReads += numberOfReadsAndFiles.getFirst(); totalFiles = numberOfReadsAndFiles.getSecond(); } doc.getProgressListener().close(); NotificationsInSwing.showInformation(getViewer().getFrame(), "Wrote " + totalReads + " sequences to " + totalFiles + " files"); } System.err.println("Export Alignments: done"); } public void actionPerformed(ActionEvent event) { final String classificationName; if (getViewer() instanceof MainViewer) classificationName = ClassificationType.Taxonomy.toString(); else if (getViewer() instanceof ClassificationViewer) { ClassificationViewer viewer = (ClassificationViewer) getViewer(); classificationName = viewer.getClassName(); } else return; final JDialog dialog = new JDialog(getViewer().getFrame()); dialog.setModal(true); dialog.setLocationRelativeTo(getViewer().getFrame()); dialog.setSize(500, 400); dialog.setTitle("Export Alignments for " + classificationName + " - " + ProgramProperties.getProgramName()); final JTextField outDirectory = new JTextField(); outDirectory.setText(ProgramProperties.get("ExAlignmentDir", System.getProperty("user.home"))); final JTextField outFileTemplate = new JTextField(); outFileTemplate.setText(ProgramProperties.get("ExAlignmentFile", "alignment-%c-%r.fasta")); JPanel mainPanel = new JPanel(); mainPanel.setLayout(new BorderLayout()); JPanel topMiddlePanel = new JPanel(); topMiddlePanel.setLayout(new BoxLayout(topMiddlePanel, BoxLayout.Y_AXIS)); JPanel middlePanel = new JPanel(); middlePanel.setBorder(BorderFactory.createTitledBorder( BorderFactory.createEtchedBorder(), "Output files")); middlePanel.setLayout(new BoxLayout(middlePanel, BoxLayout.Y_AXIS)); JPanel m1 = new JPanel(); m1.setLayout(new BorderLayout()); m1.add(new JLabel("Directory:"), BorderLayout.WEST); m1.add(outDirectory, BorderLayout.CENTER); outDirectory.setToolTipText("Set directory for files to be written to"); m1.add(new JButton(new AbstractAction("Browse...") { public void actionPerformed(ActionEvent actionEvent) { File file = chooseDirectory(actionEvent, outDirectory.getText()); if (file != null) outDirectory.setText(file.getPath()); } }), BorderLayout.EAST); middlePanel.add(m1); JPanel m2 = new JPanel(); m2.setLayout(new BorderLayout()); m2.add(new JLabel("File name:"), BorderLayout.WEST); m2.add(outFileTemplate, BorderLayout.CENTER); outFileTemplate.setToolTipText("Set name of file to save to. A %c is replaced by node name, %r by reference name and %n by file number."); middlePanel.add(m2); JPanel buttons = new JPanel(); buttons.setLayout(new BoxLayout(buttons, BoxLayout.Y_AXIS)); final JCheckBox useEachReadOnlyOnce = new JCheckBox(new AbstractAction("Use Each Read Only Once") { public void actionPerformed(ActionEvent actionEvent) { } }); useEachReadOnlyOnce.setSelected(ProgramProperties.get("ExAlignmentUseEachReadOnce", true)); useEachReadOnlyOnce.setToolTipText("Allow each read only to occur in one alignment, the deepest one containing it"); buttons.add(useEachReadOnlyOnce); final JCheckBox useEachReferenceOnlyOnce = new JCheckBox(new AbstractAction("Use Each Reference Only Once") { public void actionPerformed(ActionEvent actionEvent) { } }); useEachReferenceOnlyOnce.setSelected(ProgramProperties.get("ExAlignmentUseEachRefOnce", true)); useEachReferenceOnlyOnce.setToolTipText("Allow each reference sequence to appear only once (and not for multiple nodes)"); buttons.add(useEachReferenceOnlyOnce); /* final JCheckBox includeInsertions = new JCheckBox(new AbstractAction("Include Insertions") { public void actionPerformed(ActionEvent actionEvent) { } }); includeInsertions.setSelected(true); includeInsertions.setToolTipText("Include insertions into the reference sequence in alignment"); buttons.add(includeInsertions); */ final JCheckBox refSeqOnly = new JCheckBox(new AbstractAction("Use Only Matches to RefSeqs") { public void actionPerformed(ActionEvent actionEvent) { } }); refSeqOnly.setSelected(ProgramProperties.get("ExAlignmentUseRefSeqOnly", false)); refSeqOnly.setToolTipText("Only alignment to reference sequences that have a refSeq id"); buttons.add(refSeqOnly); /* final JCheckBox contractGaps = new JCheckBox(new AbstractAction("Contract Gaps") { public void actionPerformed(ActionEvent actionEvent) { } }); contractGaps.setSelected(false); contractGaps.setToolTipText("Contract runs of gaps and replace by length in square brackets"); buttons.add(contractGaps); */ final JCheckBox cDNAAsProteins = new JCheckBox(new AbstractAction("Translate cDNA as proteins") { public void actionPerformed(ActionEvent actionEvent) { } }); cDNAAsProteins.setSelected(ProgramProperties.get("ExAlignmentTranslateCDNA", false)); cDNAAsProteins.setToolTipText("Translate cDNA sequences to proteins"); buttons.add(cDNAAsProteins); final JCheckBox asConsensus = new JCheckBox(new AbstractAction("As Consensus") { public void actionPerformed(ActionEvent actionEvent) { } }); asConsensus.setSelected(ProgramProperties.get("ExAlignmentAsConsensus", false)); asConsensus.setToolTipText("Save consensus "); buttons.add(asConsensus); buttons.add(Box.createVerticalStrut(20)); final JPanel numbersPanel = new JPanel(); numbersPanel.setLayout(new GridLayout(3, 4)); buttons.add(numbersPanel); final JTextField minReadsField = new JTextField(6); minReadsField.setMaximumSize(new Dimension(100, 20)); minReadsField.setText("" + ProgramProperties.get("ExAlignmentMinReads", 1)); numbersPanel.add(newSingleLine(Box.createHorizontalGlue(), new JLabel("Minimum reads: "))); numbersPanel.add(newSingleLine(minReadsField, Box.createHorizontalGlue())); minReadsField.setToolTipText("Discard all alignments that do not have the specify minimum number of reads"); final JTextField minLengthField = new JTextField(6); minLengthField.setMaximumSize(new Dimension(100, 20)); minLengthField.setText("" + ProgramProperties.get("ExAlignmentMinLength", 1)); numbersPanel.add(newSingleLine(Box.createHorizontalGlue(), new JLabel("Minimum length: "))); numbersPanel.add(newSingleLine(minLengthField, Box.createHorizontalGlue())); minLengthField.setToolTipText("Discard all alignments that do not have the specify minimum length"); final JTextField minCoverageField = new JTextField(6); minCoverageField.setMaximumSize(new Dimension(100, 20)); minCoverageField.setText("" + (float) (ProgramProperties.get("ExAlignmentMinCoverage", 1.0))); numbersPanel.add(newSingleLine(Box.createHorizontalGlue(), new JLabel("Minimum Coverage: "))); numbersPanel.add(newSingleLine(minCoverageField, Box.createHorizontalGlue())); minCoverageField.setToolTipText("Discard all alignments that do not have the specify minimum coverage"); middlePanel.add(buttons); topMiddlePanel.add(middlePanel); mainPanel.add(topMiddlePanel, BorderLayout.NORTH); JPanel bottomPanel = new JPanel(); bottomPanel.setBorder(BorderFactory.createEtchedBorder()); bottomPanel.setLayout(new BorderLayout()); JPanel b1 = new JPanel(); b1.add(new JButton(new AbstractAction("Cancel") { public void actionPerformed(ActionEvent actionEvent) { dialog.setVisible(false); } })); b1.setLayout(new BoxLayout(b1, BoxLayout.X_AXIS)); JButton applyButton = new JButton(new AbstractAction("Apply") { public void actionPerformed(ActionEvent actionEvent) { dialog.setVisible(false); String fileName = (new File(outDirectory.getText().trim(), outFileTemplate.getText().trim())).getPath(); if (fileName.length() > 0) { String command = "export what=alignment file='" + fileName + "'"; command += " data=" + classificationName; command += " classId=selected"; command += " asConsensus=" + asConsensus.isSelected(); command += " useEachReadOnlyOnce=" + useEachReadOnlyOnce.isSelected(); command += " useEachReferenceOnlyOnce=" + useEachReferenceOnlyOnce.isSelected(); // command += " includeInsertions=" + includeInsertions.isSelected(); command += " refSeqOnly=" + refSeqOnly.isSelected(); // command += " contractGaps=" + contractGaps.isSelected(); command += " translateCDNA=" + cDNAAsProteins.isSelected(); { final String text = minReadsField.getText(); if (NumberUtils.isInteger(text) && NumberUtils.parseInt(text) > 0) command += " minReads=" + text; } { final String text = minLengthField.getText(); if (NumberUtils.isInteger(text) && NumberUtils.parseInt(text) > 0) command += " minLength=" + text; } { final String text = minCoverageField.getText(); if (NumberUtils.isDouble(text) && NumberUtils.parseDouble(text) > 0) command += " minCoverage=" + text; } command += ";"; ProgramProperties.put("ExAlignmentDir", outDirectory.getText().trim()); ProgramProperties.put("ExAlignmentFile", outFileTemplate.getText().trim()); execute(command); } } }); b1.add(applyButton); dialog.getRootPane().setDefaultButton(applyButton); bottomPanel.add(b1, BorderLayout.EAST); mainPanel.add(bottomPanel, BorderLayout.SOUTH); dialog.getContentPane().setLayout(new BorderLayout()); dialog.getContentPane().add(mainPanel, BorderLayout.CENTER); dialog.validate(); dialog.setVisible(true); } private static JPanel newSingleLine(Component left, Component right) { final JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.X_AXIS)); panel.add(left); panel.add(right); return panel; } /** * choose the directory for export of files * * @return directory */ private File chooseDirectory(ActionEvent event, String fileName) { File file = null; if (ProgramProperties.isMacOS() && (event != null && (event.getModifiers() & ActionEvent.SHIFT_MASK) == 0)) { //Use native file dialog on mac java.awt.FileDialog dialog = new java.awt.FileDialog(getViewer().getFrame(), "Open output directory", java.awt.FileDialog.LOAD); dialog.setFilenameFilter((dir, name) -> true); if (fileName != null) { dialog.setDirectory(fileName); //dialog.setFile(fileName); } System.setProperty("apple.awt.fileDialogForDirectories", "true"); dialog.setVisible(true); System.setProperty("apple.awt.fileDialogForDirectories", "false"); if (dialog.getFile() != null) { file = new File(dialog.getDirectory(), dialog.getFile()); } } else { JFileChooser chooser = new JFileChooser(fileName); chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); if (fileName != null) chooser.setSelectedFile(new File(fileName)); chooser.setAcceptAllFileFilterUsed(true); int result = chooser.showOpenDialog(getViewer().getFrame()); if (result == JFileChooser.APPROVE_OPTION) { file = chooser.getSelectedFile(); } } if (file != null) { if (!file.isDirectory()) file = file.getParentFile(); } return file; } public boolean isApplicable() { return getViewer() instanceof ViewerBase && getDir().getDocument().getMeganFile().hasDataConnector() && ((ViewerBase) getViewer()).getSelectedNodes().size() > 0; } private static final String NAME = "Alignments..."; public String getName() { return NAME; } public KeyStroke getAcceleratorKey() { return null; } public String getDescription() { return "Calculate and export alignments for all selected leaves"; } public boolean isCritical() { return true; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } }
21,473
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportBIOMCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportBIOMCommand.java
/* * ExportBIOMCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.swing.commands.ICommand; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.swing.window.NotificationsInSwing; import jloda.util.Basic; import jloda.util.FileUtils; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.biom.biom1.Biom1ExportFViewer; import megan.biom.biom1.Biom1ExportTaxonomy; import megan.classification.Classification; import megan.classification.ClassificationManager; import megan.commands.CommandBase; import megan.core.Director; import megan.core.Document; import megan.util.BiomFileFilter; import megan.viewer.ClassificationViewer; import megan.viewer.MainViewer; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.File; /** * export BIOM 1.0 format * Daniel Huson, 2012 */ public class ExportBIOMCommand extends CommandBase implements ICommand { public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("export format=biom"); Director dir = getDir(); Document doc = dir.getDocument(); np.matchIgnoreCase("data="); String data = np.getWordMatchesIgnoringCase(StringUtils.toString(ClassificationManager.getAllSupportedClassifications(), " ")); np.matchIgnoreCase("file="); String outputFile = np.getAbsoluteFileName(); boolean officialRanksOnly = true; if (np.peekMatchIgnoreCase("officialRanksOnly")) { np.matchIgnoreCase("officialRanksOnly="); officialRanksOnly = np.getBoolean(); } np.matchIgnoreCase(";"); if (data.equalsIgnoreCase(Classification.Taxonomy)) { try { int numberOfRows = Biom1ExportTaxonomy.apply(dir, new File(outputFile), officialRanksOnly, doc.getProgressListener()); NotificationsInSwing.showInformation(getViewer().getFrame(), String.format("Exported %,d rows in BIOM1 format", numberOfRows)); } catch (Throwable th) { Basic.caught(th); } } else { int numberOfRows = Biom1ExportFViewer.apply(getDir(), data, new File(outputFile), doc.getProgressListener()); NotificationsInSwing.showInformation(getViewer().getFrame(), String.format("Exported %,d rows in BIOM1 format", numberOfRows)); } } public boolean isApplicable() { return getDoc().getNumberOfReads() > 0 && getViewer() instanceof ViewerBase && ((ViewerBase) getViewer()).getSelectedNodes().size() > 0; } public boolean isCritical() { return true; } public String getSyntax() { return "export format=biom data={" + StringUtils.toString(ClassificationManager.getAllSupportedClassifications(), "|") + "} file=<filename> [officialRanksOnly={true|false}];"; } public void actionPerformed(ActionEvent event) { final Director dir = getDir(); boolean officialRanksOnly = false; String choice; if (getViewer() instanceof MainViewer) { choice = Classification.Taxonomy; switch (JOptionPane.showConfirmDialog(getViewer().getFrame(), "Export taxa at offical ranks only (KPCOFGS)?", "Setup biom export", JOptionPane.YES_NO_CANCEL_OPTION)) { case JOptionPane.CANCEL_OPTION: return; case JOptionPane.YES_OPTION: officialRanksOnly = true; } } else if (getViewer() instanceof ClassificationViewer) choice = getViewer().getClassName(); else return; String name = FileUtils.replaceFileSuffix(dir.getDocument().getTitle(), "-" + choice + ".biom"); File lastOpenFile = new File(name); String lastDir = ProgramProperties.get("BiomDirectory", ""); if (lastDir.length() > 0) { lastOpenFile = new File(lastDir, name); } File file = ChooseFileDialog.chooseFileToSave(getViewer().getFrame(), lastOpenFile, new BiomFileFilter(BiomFileFilter.Version.V1), new BiomFileFilter(BiomFileFilter.Version.V1), event, "Save as BIOM 1.0.0 file (JSON format)", ".txt"); if (file != null) { if (getViewer() instanceof ViewerBase && ((ViewerBase) getViewer()).getSelectedNodes().size() == 0) executeImmediately("select nodes=leaves;"); ProgramProperties.put("BiomDirectory", file.getParent()); execute("export format=biom data=" + choice + " file='" + file.getPath() + "'" + (choice.equals(Classification.Taxonomy) ? " officialRanksOnly=" + officialRanksOnly + ";" : ";")); } } public String getName() { return "BIOM1 Format..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public String getDescription() { return "Export data in BIOM 1.0.0 (JSON) format (see http://biom-format.org/documentation/format_versions/biom-1.0.html)"; } }
5,900
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportTreeCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportTreeCommand.java
/* * ExportTreeCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.swing.commands.ICommand; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.swing.util.TextFileFilter; import jloda.swing.window.NotificationsInSwing; import jloda.util.FileUtils; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.dialogs.export.ExportTree; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.BufferedWriter; import java.io.File; import java.io.FileWriter; public class ExportTreeCommand extends CommandBase implements ICommand { public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("export what=tree"); np.matchIgnoreCase("file="); String outputFile = np.getAbsoluteFileName(); var simplify = false; if (np.peekMatchIgnoreCase("simplify")) { np.matchIgnoreCase("simplify="); simplify = np.getBoolean(); } var showInternalLabels = true; if (np.peekMatchIgnoreCase("showInternalLabels")) { np.matchIgnoreCase("showInternalLabels="); showInternalLabels = np.getBoolean(); } var showUnassigned = true; if (np.peekMatchIgnoreCase("showUnassigned")) { np.matchIgnoreCase("showUnassigned="); showUnassigned = np.getBoolean(); } var useIds = false; if (np.peekMatchIgnoreCase("useIds")) { np.matchIgnoreCase("useIds="); useIds = np.getBoolean(); } np.matchIgnoreCase(";"); if (getViewer() instanceof ViewerBase) { var viewer = (ViewerBase) getViewer(); try(var w = new BufferedWriter(new FileWriter(outputFile))) { var count=ExportTree.apply(viewer, w, useIds,showInternalLabels, showUnassigned, simplify); if(count==0) NotificationsInSwing.showWarning("Export tree failed: Empty tree"); else NotificationsInSwing.showInformation("Export tree: %,d nodes".formatted(count)); } } else System.err.println("Invalid command"); } public boolean isApplicable() { return getViewer() instanceof ViewerBase && ((ViewerBase) getViewer()).getSelectedNodes().size() > 0; } public boolean isCritical() { return true; } public String getSyntax() { return "export what=tree file=<filename> [simplify={false|true}] [showInternalLabels={true|false}] [showUassigned={true|false}] [useIds={false|true}];"; } public void actionPerformed(ActionEvent event) { var dir = getDir(); var name = FileUtils.replaceFileSuffix(dir.getDocument().getTitle(), ".tre"); var lastOpenFile = new File(name); var lastDir = ProgramProperties.get("TreeDirectory", ""); if (lastDir.length() > 0) { lastOpenFile = new File(lastDir, name); } var file = ChooseFileDialog.chooseFileToSave(getViewer().getFrame(), lastOpenFile, new TextFileFilter(), new TextFileFilter(), event, "Save as tree", ".txt"); if (file != null) { execute("export what=tree file='" + file.getPath() + "' showInternalLabels=true showUnassigned=true useIds=false;"); ProgramProperties.put("TreeDirectory", file.getParent()); } } public String getName() { return "Tree..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public String getDescription() { return "Export induced tree (in Newick format)"; } }
4,543
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportReadsToLengthAndCoverageCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportReadsToLengthAndCoverageCommand.java
/* * ExportReadsToLengthAndCoverageCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.swing.util.TextFileFilter; import jloda.util.FileUtils; import jloda.util.parse.NexusStreamParser; import megan.core.Director; import megan.core.Document; import megan.dialogs.export.ExportReads2LengthAndAlignmentCoverage; import megan.viewer.ClassificationViewer; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.File; /** * export reads in length and amount covered * Daniel Huson, 3.2017 */ public class ExportReadsToLengthAndCoverageCommand extends CommandBase implements ICommand { /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("export what=lengthAndCovered file="); final String fileName = np.getWordFileNamePunctuation(); np.matchIgnoreCase(";"); if (getViewer() instanceof ClassificationViewer) { final ClassificationViewer viewer = (ClassificationViewer) getViewer(); final Document doc = viewer.getDocument(); System.err.println("Writing file: " + fileName); int lines = ExportReads2LengthAndAlignmentCoverage.apply(viewer, new File(fileName), doc.getProgressListener()); System.err.println("done (" + lines + ")"); } } public String getSyntax() { return "export what=lengthAndCovered file=<file-name>"; } public void actionPerformed(ActionEvent event) { final Director dir = (Director) getDir(); String name = FileUtils.replaceFileSuffix(dir.getDocument().getTitle(), ".txt"); String lastGFFFile = ProgramProperties.get("lastExportFile", ""); File lastOpenFile = new File((new File(lastGFFFile)).getParent(), name); final File file = ChooseFileDialog.chooseFileToSave(getViewer().getFrame(), lastOpenFile, new TextFileFilter(), new TextFileFilter(), event, "Save read length and covered bases", ".txt"); if (file != null) { ProgramProperties.put("lastExportFile", file.getPath()); execute("export what=lengthAndCovered file='" + file.getPath() + "';"); } } public boolean isApplicable() { return getViewer() instanceof ClassificationViewer && ((ClassificationViewer) getViewer()).getNumberSelectedNodes() > 0; } private static final String NAME = "Export Read Lengths and Coverage..."; public String getName() { return NAME; } public String getDescription() { return "Export length and number of bases covered for all selected reads"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return null; } }
3,866
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportStampProfileCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportStampProfileCommand.java
/* * ExportStampProfileCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.swing.commands.ICommand; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.swing.window.NotificationsInSwing; import jloda.util.FileUtils; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.classification.Classification; import megan.classification.ClassificationManager; import megan.commands.CommandBase; import megan.core.Director; import megan.core.Document; import megan.util.ExportStamp; import megan.util.StampFileFilter; import megan.viewer.MainViewer; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.File; /** * export as STAMP profile * Daniel Huson, 1.2016 */ public class ExportStampProfileCommand extends CommandBase implements ICommand { public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("export format=stamp"); Director dir = getDir(); Document doc = dir.getDocument(); np.matchIgnoreCase("data="); String data = np.getWordMatchesIgnoringCase(StringUtils.toString(ClassificationManager.getAllSupportedClassifications(), " ")); np.matchIgnoreCase("file="); String outputFile = np.getAbsoluteFileName(); boolean allLevels = false; if (np.peekMatchIgnoreCase("allLevels")) { np.matchIgnoreCase("allLevels="); allLevels = np.getBoolean(); } np.matchIgnoreCase(";"); final int numberOfRows = ExportStamp.apply(getDir(), data, new File(outputFile), allLevels, doc.getProgressListener()); NotificationsInSwing.showInformation(getViewer().getFrame(), String.format("Exported %,d rows in STAMP profile format", numberOfRows)); } public boolean isApplicable() { return getDoc().getNumberOfReads() > 0 && getViewer() instanceof ViewerBase && ((ViewerBase) getViewer()).getSelectedNodes().size() > 0; } public boolean isCritical() { return true; } public String getSyntax() { return "export format=stamp data={" + StringUtils.toString(ClassificationManager.getAllSupportedClassifications(), "|") + "} file=<filename>;"; } public void actionPerformed(ActionEvent event) { if (!(getViewer() instanceof ViewerBase)) return; final ViewerBase viewer = (ViewerBase) getViewer(); final Director dir = getDir(); final String choice; if (viewer instanceof MainViewer) choice = Classification.Taxonomy; else choice = (getViewer()).getClassName(); boolean allLevels = false; switch (JOptionPane.showConfirmDialog(viewer.getFrame(), "Export all levels above selected nodes as well?", "Export to STAMP option", JOptionPane.YES_NO_CANCEL_OPTION)) { case JOptionPane.CANCEL_OPTION: return; case JOptionPane.YES_OPTION: allLevels = true; } String name = FileUtils.replaceFileSuffix(dir.getDocument().getTitle(), "-" + choice + ".spf"); File lastOpenFile = new File(name); String lastDir = ProgramProperties.get("StampDirectory", ""); if (lastDir.length() > 0) { lastOpenFile = new File(lastDir, name); } final File file = ChooseFileDialog.chooseFileToSave(getViewer().getFrame(), lastOpenFile, new StampFileFilter(), new StampFileFilter(), event, "Save as STAMP profile file", ".spf"); if (file != null) { if (viewer.getSelectedNodes().size() == 0) executeImmediately("select nodes=leaves;"); ProgramProperties.put("StampDirectory", file.getParent()); execute("export format=stamp data=" + choice + " file='" + file.getPath() + "' allLevels=" + allLevels + ";"); } } public static String NAME="STAMP Format..."; public String getName() { return NAME; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public String getDescription() { return "Export selected nodes as a STAMP profile file (.spf)"; } }
5,063
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportCSVCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportCSVCommand.java
/* * ExportCSVCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.swing.commands.ICommand; import jloda.swing.director.IDirectableViewer; import jloda.swing.util.*; import jloda.swing.window.NotificationsInSwing; import jloda.util.FileUtils; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.classification.Classification; import megan.commands.CommandBase; import megan.core.Director; import megan.core.Document; import megan.dialogs.export.CSVExporter; import megan.viewer.ClassificationViewer; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.io.File; import java.util.List; import java.util.Objects; public class ExportCSVCommand extends CommandBase implements ICommand { private static final String EXPORT_CHOICE = "CSVExportChoice"; private static final String COUNT_CHOICE = "CSVCount"; private static final String SEPARATOR_CHOICE = "CSVSeparator"; public enum Choice {assigned, summarized} public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("export what=csv"); final Director dir = getDir(); final IDirectableViewer viewer = getViewer(); final Document doc = dir.getDocument(); final String classificationName; if (viewer instanceof ClassificationViewer) classificationName = viewer.getClassName(); else classificationName = Classification.Taxonomy; final List<String> formats = CSVExporter.getFormats(classificationName, doc); np.matchIgnoreCase("format="); final String format = np.getWordMatchesIgnoringCase(StringUtils.toString(formats, " ")); char separator = '\t'; if (np.peekMatchIgnoreCase("separator")) { np.matchIgnoreCase("separator="); if (np.getWordMatchesIgnoringCase("comma tab").equalsIgnoreCase("comma")) separator = ','; } boolean reportSummarized = false; if (np.peekMatchIgnoreCase("counts")) { np.matchIgnoreCase("counts="); if (np.getWordMatchesIgnoringCase(StringUtils.toString(Choice.values(), " ")).equalsIgnoreCase(Choice.summarized.toString())) reportSummarized = true; } np.matchIgnoreCase("file="); String outputFile = np.getAbsoluteFileName(); np.matchIgnoreCase(";"); int count = CSVExporter.apply(dir, doc.getProgressListener(), new File(outputFile), format, separator, reportSummarized); NotificationsInSwing.showInformation(getViewer().getFrame(), "Wrote " + count + " line(s) to file: " + outputFile); } public boolean isApplicable() { return getViewer() instanceof ViewerBase && ((ViewerBase) getViewer()).getSelectedNodes().size() > 0; } public boolean isCritical() { return true; } public String getSyntax() { return "export what=CSV format={format} [separator={comma|tab}] [counts={assigned|summarized}] file=<filename>;"; } public void actionPerformed(ActionEvent event) { final Director dir = getDir(); final String[] choice = showChoices(getViewer().getFrame(), dir.getDocument(), getViewer().getClassName()); if (choice == null) return; final String formatName = choice[0]; final String countChoice = choice[1]; final String separator = choice[2]; final String name = FileUtils.replaceFileSuffix(dir.getDocument().getTitle(), "-ex.txt"); File lastOpenFile = new File(name); final String lastDir = ProgramProperties.get("CSVDirectory", ""); if (lastDir.length() > 0) { lastOpenFile = new File(lastDir, name); } final File file = ChooseFileDialog.chooseFileToSave(getViewer().getFrame(), lastOpenFile, new TextFileFilter(), new TextFileFilter(), event, "Save as CSV (delimiter-separated values)", ".txt"); if (file != null) { final String cmd = ("export what=CSV format=" + formatName + " separator=" + separator + (countChoice == null ? "" : " counts=" + countChoice) + " file='" + file.getPath() + "';"); execute(cmd); ProgramProperties.put("CSVDirectory", file.getParent()); } } public String getName() { return "Text (CSV) Format..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public String getDescription() { return "Export assignments of reads to nodes to a CSV (comma or tab-separated value) file"; } /** * show the choices dialog * * @return choices or null */ private static String[] showChoices(Component parent, Document doc, String classification) { final boolean doTaxonomy = classification.equalsIgnoreCase(Classification.Taxonomy); final List<String> formats = CSVExporter.getFormats(classification, doc); final JLabel label0 = new JLabel("Choose data to export: "); label0.setToolTipText("Choose data to export"); final RememberingComboBox choice0 = new RememberingComboBox(); choice0.setEditable(false); choice0.addItems(formats); choice0.setToolTipText("Choose data to export"); if (choice0.getItemCount() > 0) choice0.setSelectedItem(ProgramProperties.get(EXPORT_CHOICE, choice0.getItemAt(0))); final JLabel label1 = new JLabel("Choose count to use: "); label1.setToolTipText("Choose count to use, summarized or assigned"); final RememberingComboBox choice1 = new RememberingComboBox(); choice1.setEditable(false); choice1.addItem(Choice.assigned.toString()); choice1.addItem(Choice.summarized.toString()); choice1.setToolTipText("Choose count to use, summarized or assigned"); if (choice1.getItemCount() > 0) choice1.setSelectedItem(ProgramProperties.get(COUNT_CHOICE, choice1.getItemAt(0))); final JLabel label2 = new JLabel("Choose separator to use: "); label2.setToolTipText("Choose separator to use"); final RememberingComboBox choice2 = new RememberingComboBox(); choice2.setEditable(false); choice2.addItem("tab"); choice2.addItem("comma"); choice2.setToolTipText("Choose separator to use"); if (choice2.getItemCount() > 0) choice2.setSelectedItem(ProgramProperties.get(SEPARATOR_CHOICE, choice2.getItemAt(0))); final JPanel myPanel = new JPanel(); myPanel.setLayout(new GridLayout((doTaxonomy ? 3 : 2), 2)); myPanel.add(label0); myPanel.add(choice0); if (doTaxonomy) { myPanel.add(label1); myPanel.add(choice1); } myPanel.add(label2); myPanel.add(choice2); final int result = JOptionPane.showConfirmDialog(parent, myPanel, "MEGAN - Export to CSV", JOptionPane.OK_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, ProgramProperties.getProgramIcon()); if (result == JOptionPane.OK_OPTION) { ProgramProperties.put(EXPORT_CHOICE, Objects.requireNonNull(choice0.getSelectedItem()).toString()); ProgramProperties.put(COUNT_CHOICE, Objects.requireNonNull(choice1.getSelectedItem()).toString()); ProgramProperties.put(SEPARATOR_CHOICE, Objects.requireNonNull(choice2.getSelectedItem()).toString()); return new String[]{choice0.getCurrentText(false), choice1.getCurrentText(false), choice2.getCurrentText(false)}; } return null; } }
8,413
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportCSVForAllLevelsCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportCSVForAllLevelsCommand.java
/* * ExportCSVForAllLevelsCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.core.ClassificationType; import megan.core.DataTable; import megan.viewer.TaxonomicLevels; import megan.viewer.TaxonomyData; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.*; import java.util.List; import java.util.Map; import java.util.Map.Entry; public class ExportCSVForAllLevelsCommand extends CommandBase implements ICommand { public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("export taxonname_count"); char separator = '\t'; if (np.peekMatchIgnoreCase("separator")) { np.matchIgnoreCase("separator="); if (np.getWordMatchesIgnoringCase("comma tab").equalsIgnoreCase("comma")) separator = ','; } np.matchIgnoreCase("folder="); String outputFile = np.getAbsoluteFileName().trim(); np.matchIgnoreCase("file="); String rmaFile = np.getAbsoluteFileName(); np.matchIgnoreCase(";"); DataTable table = new DataTable(); BufferedReader reader = new BufferedReader(new FileReader(rmaFile)); table.read(reader, false); reader.close(); List<String> levels = TaxonomicLevels.getAllNames(); for (String level : levels) { try (BufferedWriter w = new BufferedWriter(new FileWriter(outputFile + "/" + new File(rmaFile).getName() + "." + level + ".txt"))) { Map<Integer, float[]> tab = table.getClass2Counts(ClassificationType.Taxonomy.toString()); for (Entry<Integer, float[]> taxid2count : tab.entrySet()) { Integer taxId = taxid2count.getKey(); float count = taxid2count.getValue()[0]; if (TaxonomyData.getTaxonomicRank(taxId) != TaxonomicLevels.getId(level)) { continue; } if (count == 0) { continue; } w.write("\"" + TaxonomyData.getName2IdMap().get(taxId) + "\""); w.write(separator + "" + count); w.write("\n"); } } } } public boolean isApplicable() { return getDoc().getNumberOfReads() > 0; } public boolean isCritical() { return true; } public String getSyntax() { return "export taxonname_count separator={comma|tab} folder=<foldername>"; } public void actionPerformed(ActionEvent event) { } public String getName() { return "Export Taxon_Path Format..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public String getDescription() { return "Export assignments"; } }
3,787
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportTaxonParentMappingCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportTaxonParentMappingCommand.java
/* * ExportTaxonParentMappingCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.swing.util.TextFileFilter; import jloda.swing.window.NotificationsInSwing; import jloda.util.Single; import jloda.util.parse.NexusStreamParser; import megan.core.Director; import megan.viewer.TaxonomyData; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.BufferedWriter; import java.io.File; import java.io.FileWriter; import java.io.IOException; /** * exports the parent to node mapping * Daniel Huson. 7.2021 */ public class ExportTaxonParentMappingCommand extends CommandBase implements ICommand { @Override public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("export what=taxonParentMap file="); var file = np.getWordFileNamePunctuation(); boolean top; if (np.peekMatchIgnoreCase("toTop")) { np.matchIgnoreCase("toTop="); top = np.getBoolean(); } else top = true; boolean names; if(np.peekMatchIgnoreCase("names")) { np.matchIgnoreCase("names="); names=np.getBoolean(); } else names=false; np.matchIgnoreCase(";"); var exception=new Single<Exception>(); var progress=((Director)getDir()).getDocument().getProgressListener(); progress.setTasks("Export","Taxon-parent mapping"); progress.setProgress(0); progress.setMaximum(TaxonomyData.getTree().getNumberOfNodes()); try(var writer=new BufferedWriter(new FileWriter(file))) { var root=TaxonomyData.getTree().getRoot(); var cellularOrganisms=131567; var topNode=new Single<>(root); TaxonomyData.getTree().preorderTraversal(v -> { if (exception.isNull() && v.getParent() != null) { try { progress.incrementProgress(); var id = (int) v.getInfo(); int other; if (top) { if (v.getParent() == root || (int) v.getParent().getInfo() == cellularOrganisms) topNode.set(v); other = (int) topNode.get().getInfo(); } else { other = (int) v.getParent().getInfo(); } if(names) writer.write(String.format("%s\t%s%n", TaxonomyData.getName2IdMap().get(id), TaxonomyData.getName2IdMap().get(other))); writer.write(String.format("%d\t%d%n", id, other)); } catch(IOException ex) { exception.setIfCurrentValueIsNull(ex); } } } ); progress.reportTaskCompleted(); } catch(IOException ex) { exception.setIfCurrentValueIsNull(ex); } if(exception.isNotNull()) { NotificationsInSwing.showError("Write failed: "+exception.get().getMessage()); } } @Override public String getSyntax() { return "export what=taxonParentMap file=<output-file> [toTop={false|true}] [names={false|true}];"; } @Override public void actionPerformed(ActionEvent ev) { var lastOpenFile = new File(ProgramProperties.get("TaxonParentFile","taxon-parent.txt")); var file = ChooseFileDialog.chooseFileToSave(getViewer().getFrame(), lastOpenFile, new TextFileFilter(), new TextFileFilter(), ev, "Save", ".txt"); if (file != null) { execute("export what=taxonParentMap file='" + file.getPath() + "' toTop=true names=false;"); ProgramProperties.put("TaxonParentFile", file); } } @Override public String getName() { return "Taxon-Parent Mapping..."; } @Override public String getDescription() { return "Export taxonomy as node-to-parent mapping"; } @Override public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } @Override public KeyStroke getAcceleratorKey() { return null; } @Override public boolean isCritical() { return true; } @Override public boolean isApplicable() { return true; } }
5,203
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportSummaryCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportSummaryCommand.java
/* * ExportSummaryCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.swing.commands.ICommand; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.util.FileUtils; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.core.Director; import megan.main.MeganProperties; import megan.util.MeganFileFilter; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.File; public class ExportSummaryCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } public void apply(NexusStreamParser np) { // no need to implement, never called } public void actionPerformed(ActionEvent event) { Director dir = getDir(); if (dir.getDocument().getMeganFile().hasDataConnector()) { final File savedFile = ProgramProperties.getFile(MeganProperties.SAVEFILE); final File directory = (savedFile != null ? savedFile.getParentFile() : null); final File lastOpenFile = FileUtils.replaceFileSuffix(new File(directory, dir.getTitle()), ".megan"); final File file = ChooseFileDialog.chooseFileToSave(getViewer().getFrame(), lastOpenFile, new MeganFileFilter(), new MeganFileFilter(), event, "Save MEGAN summary file", ".megan"); if (file != null) { ProgramProperties.put(MeganProperties.SAVEFILE, file); String cmd; cmd = ("save file='" + file.getPath() + "' summary=true;"); execute(cmd); } } } // if in ask to save summary, modify event source to tell calling method can see that user has canceled void replyUserHasCanceledInAskToSavesummary(ActionEvent event) { ((Boolean[]) event.getSource())[0] = true; } public boolean isApplicable() { return getDoc().getNumberOfReads() > 0 && getDoc().getMeganFile().hasDataConnector(); } public String getName() { return "MEGAN Summary File..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public String getDescription() { return "Export as summary file"; } public boolean isCritical() { return true; } }
3,104
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportImageCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportImageCommand.java
/* * ExportImageCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.fx.util.IHasJavaFXStageAndRoot; import jloda.swing.commands.ICommand; import jloda.swing.director.IDirectableViewer; import jloda.swing.export.*; import jloda.swing.graphview.GraphView; import jloda.swing.graphview.NodeView; import jloda.swing.util.IViewerWithJComponent; import jloda.swing.util.ResourceManager; import jloda.util.Basic; import jloda.util.parse.NexusStreamParser; import megan.chart.gui.ChartViewer; import megan.clusteranalysis.ClusterViewer; import megan.commands.CommandBase; import megan.core.Document; import megan.util.JPanelWithFXStageAndRoot; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; import java.io.File; import java.io.FileWriter; import java.io.IOException; public class ExportImageCommand extends CommandBase implements ICommand { public String getSyntax() { return "exportImage file=<filename> [descriptionFile=<filename>] [format={bmp|eps|gif|jpg|pdf|png|svg}] [replace={false|true}]\n" + "\t[visibleOnly]={false|true}] [textAsShapes={false|true}] [title=<string>];"; } public void apply(NexusStreamParser np) throws Exception { if (getViewer() != null) { final IDirectableViewer viewer = getViewer(); np.matchIgnoreCase("exportImage file="); String cname = np.getWordFileNamePunctuation(); if (cname == null) throw new IOException("exportImage: Must specify FILE=filename"); String nodeLabelDescriptionFile = null; if (np.peekMatchIgnoreCase("descriptionFile")) { np.matchIgnoreCase("descriptionFile="); nodeLabelDescriptionFile = np.getAbsoluteFileName(); } java.util.List<String> tokens; try { np.pushPunctuationCharacters("=;"); // filename punctuation tokens = np.getTokensRespectCase(null, ";"); } finally { np.popPunctuationCharacters(); } String format = np.findIgnoreCase(tokens, "format=", "svg gif png jpg pdf eps bmp file-suffix", "file-suffix"); boolean visibleOnly = np.findIgnoreCase(tokens, "visibleOnly=", "true false", "false").equals("true"); boolean text2shapes = np.findIgnoreCase(tokens, "textAsShapes=", "true false", "false").equals("true"); String title = np.findIgnoreCase(tokens, "title=", null, "none"); boolean replace = np.findIgnoreCase(tokens, "replace=", "true false", "false").equals("true"); np.checkFindDone(tokens); File file = new File(cname); if (!replace && file.exists()) throw new IOException("File exists: " + cname + ", use REPLACE=true to overwrite"); try { final ExportGraphicType graphicsType; if (format.equalsIgnoreCase("eps")) { graphicsType = new EPSExportType(); ((EPSExportType) graphicsType).setDrawTextAsOutlines(!text2shapes); } else if (format.equalsIgnoreCase("png")) graphicsType = new PNGExportType(); else if (format.equalsIgnoreCase("pdf")) graphicsType = new PDFExportType(); else if (format.equalsIgnoreCase("svg")) graphicsType = new SVGExportType(); else if (format.equalsIgnoreCase("gif")) graphicsType = new GIFExportType(); else if (format.equalsIgnoreCase("bmp")) graphicsType = new RenderedExportType(); else if (format.equalsIgnoreCase("jpg") || format.equalsIgnoreCase("jpeg")) graphicsType = new JPGExportType(); else throw new IOException("Unsupported graphics format: " + format); JPanel panel; JScrollPane scrollPane = null; if (viewer instanceof ViewerBase) { panel = ((ViewerBase) viewer).getPanel(); scrollPane = ((ViewerBase) viewer).getScrollPane(); } else if (viewer instanceof ChartViewer) { panel = ((ChartViewer) viewer).getContentPanel(); scrollPane = ((ChartViewer) viewer).getScrollPane(); } else if (viewer instanceof ClusterViewer) { panel = ((ClusterViewer) viewer).getPanel(); GraphView graphView = ((ClusterViewer) viewer).getGraphView(); if (graphView != null) scrollPane = graphView.getScrollPane(); } else if (viewer instanceof IHasJavaFXStageAndRoot) { final IHasJavaFXStageAndRoot component = (IHasJavaFXStageAndRoot) viewer; panel = new JPanelWithFXStageAndRoot(component.getJavaFXRoot(), component.getJavaFXStage()) { @Override public void paint(Graphics g) { if (viewer instanceof IViewerWithJComponent) ((IViewerWithJComponent) viewer).getComponent().paint(g); } }; } else if (viewer instanceof IViewerWithJComponent) { final JComponent component = ((IViewerWithJComponent) viewer).getComponent(); System.err.println("Size: " + component.getSize()); panel = new JPanel() { public void paint(Graphics gc) { component.paint(gc); } }; panel.setSize(component.getSize()); } else { final JFrame frame = viewer.getFrame(); panel = new JPanel() { public void paint(Graphics gc) { frame.paint(gc); } }; panel.setSize(frame.getContentPane().getSize()); } if (!visibleOnly && scrollPane != null) { // need to adjust bounds and color background if (!panel.getBounds().contains(scrollPane.getBounds())) { final JPanel fpanel = panel; final JScrollPane fScrollPane = scrollPane; panel = new JPanel() { @Override public void paint(Graphics g) { Rectangle rectangle = new Rectangle(getBounds()); final Point apt = fScrollPane.getViewport().getViewPosition(); rectangle.x += apt.x; rectangle.y += apt.y; g.setColor(Color.WHITE); ((Graphics2D) g).fill(rectangle); fpanel.paint(g); } }; panel.setBounds(fpanel.getBounds().x, fpanel.getBounds().y, Math.max(fpanel.getBounds().width, scrollPane.getBounds().width), Math.max(fpanel.getBounds().height, scrollPane.getBounds().height)); } } ensureReasonableBounds(panel); ensureReasonableBounds(scrollPane); NodeView.descriptionWriter = null; if (nodeLabelDescriptionFile != null) { try { NodeView.descriptionWriter = new FileWriter(nodeLabelDescriptionFile); } catch (Exception ex) { Basic.caught(ex); } } try { /* todo: find out why no printer is found... if(graphicsType instanceof PDFExportType && panel instanceof IHasJavaFXStageAndRoot) { JavaFX2PDF javaFX2PDF = new JavaFX2PDF(((IHasJavaFXStageAndRoot) panel).getJavaFXRoot(), ((IHasJavaFXStageAndRoot) panel).getJavaFXStage()); javaFX2PDF.print(); } else */ graphicsType.writeToFile(file, panel, scrollPane, !visibleOnly); } finally { if (NodeView.descriptionWriter != null) { NodeView.descriptionWriter.close(); NodeView.descriptionWriter = null; } } System.err.println("Exported image to file: " + file); } catch (Exception ex) { throw new IOException(ex); } } else { np.matchWordIgnoreCase("exportImage"); throw new IOException("ExportImage not implemented for this type of window: " + (Basic.getShortName(getParent().getClass()))); } } /** * if width or height unreasonably big (>100000) or small (<=0), sets to 1000 * */ private static void ensureReasonableBounds(JPanel panel) { panel.setSize(new Dimension((panel.getWidth() <= 0 || panel.getWidth() > 100000 ? 1000 : panel.getWidth()), (panel.getHeight() <= 0 || panel.getHeight() > 100000 ? 1000 : panel.getHeight()))); } /** * if width or height unreasonably big or small, sets to 1000 * */ private void ensureReasonableBounds(JScrollPane panel) { if (panel != null) { panel.setSize(new Dimension((panel.getWidth() <= 0 || panel.getWidth() > 100000 ? 1000 : panel.getWidth()), (panel.getHeight() <= 0 || panel.getHeight() > 100000 ? 1000 : panel.getHeight()))); final JViewport viewPort = panel.getViewport(); viewPort.setExtentSize(new Dimension((int) (viewPort.getExtentSize().getWidth() <= 0 || viewPort.getExtentSize().getWidth() > 100000 ? 1000 : viewPort.getExtentSize().getWidth()), (int) (viewPort.getExtentSize().getHeight() <= 0 || viewPort.getExtentSize().getHeight() > 100000 ? 1000 : viewPort.getExtentSize().getHeight()))); } } public void actionPerformed(ActionEvent event) { final IDirectableViewer viewer = getViewer(); // setup a good default name: the file name plus .eps: String fileName = "Untitled"; Document doc = getDir().getDocument(); if (doc.getMeganFile().getFileName() != null) fileName = doc.getMeganFile().getFileName(); final boolean allowWhole = (viewer instanceof ViewerBase || viewer instanceof ChartViewer || (viewer instanceof ClusterViewer && ((ClusterViewer) viewer).isSwingPanel())); final ExportImageDialog saveImageDialog = new ExportImageDialog(viewer.getFrame(), fileName, true, allowWhole, true, event); final String command = saveImageDialog.displayDialog(); if (command != null) executeImmediately(command); } public boolean isApplicable() { return getViewer() != null; } public String getName() { return "Export Image..."; } public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()); } public String getDescription() { return "Export content of window to an image file"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public boolean isCritical() { return true; } }
12,509
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportMetaDataCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportMetaDataCommand.java
/* * ExportMetaDataCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.swing.util.TextFileFilter; import jloda.util.FileUtils; import jloda.util.parse.NexusStreamParser; import megan.core.Director; import megan.core.Document; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.File; import java.io.FileWriter; import java.io.Writer; public class ExportMetaDataCommand extends CommandBase implements ICommand { public String getSyntax() { return "export metaData=<file> [format={metaDataMapping}];"; } public void apply(NexusStreamParser np) throws Exception { Director dir = (Director) getDir(); Document doc = dir.getDocument(); np.matchIgnoreCase("export metaData="); String fileName = np.getAbsoluteFileName(); String format = "metaDataMapping"; if (np.peekMatchIgnoreCase("format")) { np.matchIgnoreCase("format="); format = np.getWordMatchesIgnoringCase("metaDataMapping"); } np.matchIgnoreCase(";"); Writer w = new FileWriter(fileName); doc.getSampleAttributeTable().write(w, false, false); w.close(); } public void actionPerformed(ActionEvent event) { String name = ((Director) getDir()).getDocument().getMeganFile().getName(); File lastOpenFile = ProgramProperties.getFile("MetaDataFilePath"); if (lastOpenFile != null) { lastOpenFile = new File(lastOpenFile.getParent(), FileUtils.replaceFileSuffix(name, "-metadata.txt")); } else lastOpenFile = new File(FileUtils.replaceFileSuffix(name, "-metadata.txt")); File file = ChooseFileDialog.chooseFileToSave(getViewer().getFrame(), lastOpenFile, new TextFileFilter(), new TextFileFilter(), event, "Export metadata mapping file"); if (file != null) { execute("export metadata='" + file.getPath() + "';"); ProgramProperties.put("MetaDataFilePath", file.getPath()); } } public boolean isApplicable() { Director dir = (Director) getDir(); Document doc = dir.getDocument(); return doc.getNumberOfSamples() > 0; } public String getName() { return "Metadata..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public String getDescription() { return "Export a metadata mapping file (as defined in http://qiime.org/documentation/file_formats.html)"; } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return null; } }
3,613
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportMatchSignaturesCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportMatchSignaturesCommand.java
/* * ExportMatchSignaturesCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.swing.commands.ICommand; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.FastaFileFilter; import jloda.swing.util.ResourceManager; import jloda.util.FileUtils; import jloda.util.NumberUtils; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.core.Director; import megan.core.Document; import megan.dialogs.export.MatchSignaturesExporter; import megan.viewer.TaxonomicLevels; import megan.viewer.TaxonomyData; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.File; public class ExportMatchSignaturesCommand extends CommandBase implements ICommand { public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("export what=matchPatterns"); final Document doc = getDir().getDocument(); np.matchIgnoreCase("taxon="); String label = np.getWordRespectCase(); int taxonId; if (NumberUtils.isInteger(label)) taxonId = NumberUtils.parseInt(label); else taxonId = TaxonomyData.getName2IdMap().get(label); np.matchIgnoreCase("rank="); String rank = np.getWordMatchesRespectingCase(StringUtils.toString(TaxonomicLevels.getAllNames(), " ")); np.matchIgnoreCase("file="); String outputFile = np.getAbsoluteFileName(); np.matchIgnoreCase(";"); MatchSignaturesExporter.export(doc.getConnector(), taxonId, rank, doc.getMinScore(), doc.getMaxExpected(), doc.getMinPercentIdentity(), doc.getTopPercent(), outputFile, doc.getProgressListener()); } public boolean isApplicable() { return getDoc().getMeganFile().hasDataConnector() && getDir().getMainViewer().getSelectedNodeIds().size() == 1; } public boolean isCritical() { return true; } public String getSyntax() { return "export what=matchPatterns taxon=<id or name> rank=<name> file=<filename>;"; } public void actionPerformed(ActionEvent event) { Director dir = getDir(); if (!isApplicable()) return; int taxon = getDir().getMainViewer().getSelectedNodeIds().iterator().next(); String name = FileUtils.replaceFileSuffix(dir.getDocument().getTitle(), "-ex.txt"); File lastOpenFile = new File(name); File file = ChooseFileDialog.chooseFileToSave(getViewer().getFrame(), lastOpenFile, new FastaFileFilter(), new FastaFileFilter(), event, "Save all READs to file", ".fasta"); if (file != null) { String cmd; cmd = ("export what=matchPatterns taxon=" + taxon + " rank=Genus file='" + file.getPath() + "';"); execute(cmd); } } public String getName() { return "Match Signatures..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public String getDescription() { return "Export all match signatures for the select node"; } }
3,753
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportReadsToGFFCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportReadsToGFFCommand.java
/* * ExportReadsToGFFCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.seq.BlastMode; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.message.MessageWindow; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.Message; import jloda.swing.util.ResourceManager; import jloda.swing.util.TextFileFilter; import jloda.swing.window.NotificationsInSwing; import jloda.util.*; import jloda.util.parse.NexusStreamParser; import megan.classification.Classification; import megan.classification.ClassificationManager; import megan.core.Director; import megan.core.Document; import megan.dialogs.export.ExportAlignedReads2GFF3Format; import megan.dialogs.lrinspector.LRInspectorViewer; import megan.main.Version; import megan.viewer.ClassificationViewer; import megan.viewer.MainViewer; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.io.File; /** * export reads in GFF format * Daniel Huson, 3.2017 */ public class ExportReadsToGFFCommand extends CommandBase implements ICommand { public String getSyntax() { return "export what=GFF file=<file-name> [classification={all|" + StringUtils.toString(ClassificationManager.getAllSupportedClassifications(), "|") + "] [excludeIncompatible={false|true}] [excludeDominated={true|false}]"; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("export what=GFF file="); final String fileName = np.getWordFileNamePunctuation(); final String classification; if (np.peekMatchIgnoreCase("classification")) { np.matchIgnoreCase("classification="); classification = np.getWordMatchesIgnoringCase("all " + StringUtils.toString(ClassificationManager.getAllSupportedClassifications(), " ")); } else classification = "all"; final boolean excludeIncompatible; if (np.peekMatchIgnoreCase("excludeIncompatible")) { np.matchIgnoreCase("excludeIncompatible="); excludeIncompatible = np.getBoolean(); } else excludeIncompatible = false; final boolean excludeDominated; if (np.peekMatchIgnoreCase("excludeDominated")) { np.matchIgnoreCase("excludeDominated="); excludeDominated = np.getBoolean(); } else excludeDominated = true; np.matchIgnoreCase(";"); if (getViewer() instanceof final ClassificationViewer viewer) { final Document doc = viewer.getDocument(); final Pair<Long, Long> counts = ExportAlignedReads2GFF3Format.apply(viewer, new File(fileName), classification, excludeIncompatible, excludeDominated, doc.getProgressListener()); NotificationsInSwing.showInformation(viewer.getFrame(), "Number of reads exported: " + counts.getFirst() + ", alignments exported: " + counts.getSecond()); } else if (getViewer() instanceof final LRInspectorViewer viewer) { final Document doc = viewer.getDir().getDocument(); final Pair<Long, Long> counts = ExportAlignedReads2GFF3Format.apply(viewer, new File(fileName), classification, excludeIncompatible, excludeDominated, doc.getProgressListener()); NotificationsInSwing.showInformation(viewer.getFrame(), "Number of reads exported: " + counts.getFirst() + ", alignments exported: " + counts.getSecond()); } } public void actionPerformed(ActionEvent event) { final boolean canExport; final boolean canExcludeIncompatible; { if (getViewer() instanceof MainViewer) { canExcludeIncompatible = true; canExport = (((MainViewer) getViewer()).getNumberSelectedNodes() > 0); } else if (getViewer() instanceof ClassificationViewer) { canExcludeIncompatible = false; canExport = (((ClassificationViewer) getViewer()).getNumberSelectedNodes() > 0); } else if (getViewer() instanceof final LRInspectorViewer viewer) { canExcludeIncompatible = viewer.getClassificationName().equals(Classification.Taxonomy) && viewer.someSelectedItemHasTaxonLabelsShowing(); canExport=viewer.someSelectedItemHasAnyLabelsShowing(); } else { canExcludeIncompatible = false; canExport = false; } } if(!canExport) { NotificationsInSwing.showWarning("To export in GFF format, select reads(s) and activate classifications in Layout menu"); return; } final Triplet<Boolean, Boolean, String> options = getOptions(getViewer().getFrame(), canExport, canExcludeIncompatible); if (options != null) { String name = FileUtils.replaceFileSuffix(((Director) getDir()).getDocument().getTitle(), "-" + ExportAlignedReads2GFF3Format.getShortName(options.getThird()) + ".gff"); String lastGFFFile = ProgramProperties.get("lastGFFFile", ""); File lastOpenFile = new File((new File(lastGFFFile)).getParent(), name); final File file = ChooseFileDialog.chooseFileToSave(getViewer().getFrame(), lastOpenFile, new TextFileFilter(".gff"), new TextFileFilter(".gff"), event, "Save read annotations to file", ".gff"); if (file != null) { ProgramProperties.put("lastGFFFile", file.getPath()); execute("export what=GFF file='" + file.getPath() + "'" + (options.getThird() != null ? " classification=" + options.getThird() : "") + (options.getFirst() ? " excludeIncompatible=true" : "") + (options.getSecond() ? " excludeDominated=true" : "") + ";"); } } } /** * gets options from user * * @return options */ private Triplet<Boolean, Boolean, String> getOptions(JFrame frame, boolean canExport, boolean canExcludeIncompatible) { final JDialog dialog = new JDialog(); { dialog.setModal(true); dialog.setTitle("Export in GFF3 Format - " + Version.NAME); dialog.setIconImages(jloda.swing.util.ProgramProperties.getProgramIconImages()); dialog.setLocationRelativeTo(frame); dialog.setSize(500, 160); dialog.getContentPane().setLayout(new BorderLayout()); } final JPanel topPane = new JPanel(); { topPane.setLayout(new BoxLayout(topPane, BoxLayout.X_AXIS)); topPane.setBorder(BorderFactory.createEmptyBorder(2, 5, 2, 5)); topPane.add(new JLabel("Select export options:")); dialog.getContentPane().add(topPane, BorderLayout.NORTH); } final JPanel middlePanel = new JPanel(); { middlePanel.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createEmptyBorder(2, 4, 2, 4), BorderFactory.createCompoundBorder(BorderFactory.createEtchedBorder(), BorderFactory.createEmptyBorder(4, 4, 4, 4)))); middlePanel.setLayout(new BoxLayout(middlePanel, BoxLayout.Y_AXIS)); dialog.getContentPane().add(middlePanel, BorderLayout.CENTER); } final JComboBox<String> classificationCBox = new JComboBox<>(); { classificationCBox.setEditable(false); classificationCBox.addItem("All"); for (String classification : ClassificationManager.getAllSupportedClassifications()) classificationCBox.addItem(classification); classificationCBox.setSelectedItem(ProgramProperties.get("GFFExportClassification", "All")); final JPanel aLine = new JPanel(); aLine.setLayout(new BoxLayout(aLine, BoxLayout.X_AXIS)); aLine.setMaximumSize(new Dimension(256, 60)); aLine.add(new JLabel("Classification:")); aLine.add(classificationCBox); classificationCBox.setToolTipText("Choose classification to export. Use 'all' to export all alignments."); middlePanel.add(aLine); } final JCheckBox excludeIncompatible = new JCheckBox("Exclude taxonomically incompatible genes"); final JCheckBox excludeDominated = new JCheckBox("Exclude dominated genes"); { excludeIncompatible.setToolTipText("Don't report a gene if its taxon is incompatible with the taxon assigned to the read."); excludeIncompatible.setEnabled(canExport && canExcludeIncompatible); excludeIncompatible.setSelected(ProgramProperties.get("GFFExportExcludeIncompatible", false)); excludeDominated.setToolTipText("Don't report any genes that are dominated by better ones."); excludeDominated.setEnabled(canExport); excludeDominated.setSelected(ProgramProperties.get("GFFExportExcludeDominated", true)); middlePanel.add(excludeIncompatible); middlePanel.add(excludeDominated); } final JPanel bottomPanel = new JPanel(); { bottomPanel.setLayout(new BoxLayout(bottomPanel, BoxLayout.X_AXIS)); bottomPanel.add(Box.createHorizontalGlue()); if (!canExport) { bottomPanel.add(new JLabel("Nothing to export.")); } bottomPanel.add(Box.createHorizontalGlue()); dialog.getContentPane().add(bottomPanel, BorderLayout.SOUTH); } final JButton cancel = new JButton(new AbstractAction("Cancel") { @Override public void actionPerformed(ActionEvent e) { dialog.setVisible(false); } }); bottomPanel.add(cancel); final Single<Triplet<Boolean, Boolean, String>> result = new Single<>(null); final JButton apply = new JButton(new AbstractAction("Apply") { @Override public void actionPerformed(ActionEvent e) { ProgramProperties.put("GFFExportClassification", (String) classificationCBox.getSelectedItem()); ProgramProperties.put("GFFExportExcludeIncompatible", excludeIncompatible.isSelected()); ProgramProperties.put("GFFExportExcludeDominated", excludeDominated.isSelected()); result.set(new Triplet<>(excludeIncompatible.isSelected(), excludeDominated.isSelected(), (String) classificationCBox.getSelectedItem())); dialog.setVisible(false); } }); apply.setEnabled(canExport); bottomPanel.add(apply); dialog.setVisible(true); return result.get(); } public boolean isApplicable() { if (((Director) getDir()).getDocument().getBlastMode() == BlastMode.BlastX) { if (getViewer() instanceof final ClassificationViewer viewer) { return viewer.getDocument().isLongReads() && viewer.getNumberSelectedNodes() > 0; } else if (getViewer() instanceof LRInspectorViewer) { return ((LRInspectorViewer) getViewer()).getNumberOfSelectedItems() > 0; } } return false; } private static final String NAME = "Annotations in GFF Format..."; public String getName() { return NAME; } public String getDescription() { return "Export selected long reads and their aligned genes in GFF3 format"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return null; } }
12,426
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportMatchesCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportMatchesCommand.java
/* * ExportMatchesCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.swing.commands.ICommand; import jloda.swing.util.BlastFileFilter; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.ResourceManager; import jloda.swing.window.NotificationsInSwing; import jloda.util.FileUtils; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.classification.Classification; import megan.classification.ClassificationManager; import megan.commands.CommandBase; import megan.core.ClassificationType; import megan.core.Director; import megan.core.Document; import megan.dialogs.export.MatchesExporter; import megan.viewer.ClassificationViewer; import megan.viewer.MainViewer; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.File; import java.util.HashSet; import java.util.Set; public class ExportMatchesCommand extends CommandBase implements ICommand { public String getSyntax() { return "export what=matches [data={" + StringUtils.toString(ClassificationManager.getAllSupportedClassifications(), "|") + "}] file=<filename>;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("export what=matches"); Director dir = getDir(); MainViewer mainViewer = dir.getMainViewer(); Document doc = dir.getDocument(); String classificationName = ClassificationType.Taxonomy.toString(); if (np.peekMatchIgnoreCase("data")) { np.matchIgnoreCase("data="); classificationName = np.getWordMatchesRespectingCase(StringUtils.toString(ClassificationManager.getAllSupportedClassifications(), " ")); } Set<Integer> classIds = new HashSet<>(); if (classificationName.equals(Classification.Taxonomy)) classIds.addAll(mainViewer.getSelectedNodeIds()); else { ClassificationViewer viewer = (ClassificationViewer) getDir().getViewerByClassName(classificationName); if (viewer != null) { final Classification classification = ClassificationManager.get(classificationName, true); for (Integer id : viewer.getSelectedNodeIds()) { Set<Integer> ids = classification.getFullTree().getAllDescendants(id); classIds.addAll(ids); } } } np.matchIgnoreCase("file="); String outputFile = np.getAbsoluteFileName(); np.matchIgnoreCase(";"); long count; if (classIds.size() == 0) count = MatchesExporter.exportAll(doc.getBlastMode(), doc.getConnector(), outputFile, doc.getProgressListener()); else count = MatchesExporter.export(classificationName, classIds, doc.getBlastMode(), doc.getConnector(), outputFile, doc.getProgressListener()); NotificationsInSwing.showInformation(getViewer().getFrame(), "Wrote " + count + " matches to file: " + outputFile); } public boolean isApplicable() { return getDoc().getMeganFile().hasDataConnector(); } public boolean isCritical() { return true; } public void actionPerformed(ActionEvent event) { Director dir = getDir(); if (!dir.getDocument().getMeganFile().hasDataConnector()) return; String name = FileUtils.replaceFileSuffix(dir.getDocument().getTitle(), "-ex.blast"); File lastOpenFile = new File(name); File file = ChooseFileDialog.chooseFileToSave(getViewer().getFrame(), lastOpenFile, new BlastFileFilter(), new BlastFileFilter(), event, "Save all BLAST matches to file", ".blast"); String data; if (getViewer() instanceof MainViewer) { data = Classification.Taxonomy; } else if (getViewer() instanceof ClassificationViewer) { data = getViewer().getClassName(); } else return; if (file != null) { String cmd; cmd = ("export what=matches data=" + data + " file='" + file.getPath() + "';"); execute(cmd); } } public String getName() { return "Matches..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public String getDescription() { return "Export all matches to a file in BLAST text format (or only those for selected nodes, if any selected)"; } }
5,190
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportLegendCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportLegendCommand.java
/* * ExportLegendCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.swing.commands.ICommand; import jloda.swing.director.IDirectableViewer; import jloda.swing.director.IViewerWithLegend; import jloda.swing.export.*; import jloda.swing.util.ResourceManager; import jloda.util.FileUtils; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.core.Document; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.File; import java.io.IOException; public class ExportLegendCommand extends CommandBase implements ICommand { public String getSyntax() { return "exportLegend file=<filename> [format={bmp|eps|gif|jpg|pdf|png|svg}]" + " [replace={false|true}] [textAsShapes={false|true}];"; } public void apply(NexusStreamParser np) throws Exception { IDirectableViewer viewer = getViewer(); np.matchIgnoreCase("exportLegend file="); String cname = np.getWordFileNamePunctuation(); if (cname == null) throw new IOException("exportimage: Must specify FILE=filename"); String nodeLabelDescriptionFile = null; if (np.peekMatchIgnoreCase("descriptionFile")) { np.matchIgnoreCase("descriptionFile="); nodeLabelDescriptionFile = np.getAbsoluteFileName(); } java.util.List<String> tokens; try { np.pushPunctuationCharacters("=;"); // filename punctuation tokens = np.getTokensRespectCase(null, ";"); } finally { np.popPunctuationCharacters(); } String format = np.findIgnoreCase(tokens, "format=", "svg gif png jpg pdf eps bmp file-suffix", "file-suffix"); boolean visibleOnly = np.findIgnoreCase(tokens, "visibleOnly=", "true false", "false").equals("true"); boolean text2shapes = np.findIgnoreCase(tokens, "textasShapes=", "true false", "false").equals("true"); String title = np.findIgnoreCase(tokens, "title=", null, "none"); boolean replace = np.findIgnoreCase(tokens, "replace=", "true false", "false").equals("true"); np.checkFindDone(tokens); File file = new File(cname); if (!replace && file.exists()) throw new IOException("File exists: " + cname + ", use REPLACE=true to overwrite"); try { ExportGraphicType graphicsType; if (format.equalsIgnoreCase("eps")) { graphicsType = new EPSExportType(); ((EPSExportType) graphicsType).setDrawTextAsOutlines(!text2shapes); } else if (format.equalsIgnoreCase("png")) graphicsType = new PNGExportType(); else if (format.equalsIgnoreCase("pdf")) graphicsType = new PDFExportType(); else if (format.equalsIgnoreCase("svg")) graphicsType = new SVGExportType(); else if (format.equalsIgnoreCase("gif")) graphicsType = new GIFExportType(); else if (format.equalsIgnoreCase("bmp")) graphicsType = new RenderedExportType(); else if (format.equalsIgnoreCase("jpg") || format.equalsIgnoreCase("jpeg")) graphicsType = new JPGExportType(); else throw new IOException("Unsupported graphics format: " + format); if (viewer instanceof IViewerWithLegend) graphicsType.writeToFile(file, ((IViewerWithLegend) viewer).getLegendPanel(), ((IViewerWithLegend) viewer).getLegendScrollPane(), true); else throw new IOException("Export legend: not imported for this type of viewer"); System.err.println("Exported legend image to file: " + file); } catch (Exception ex) { throw new IOException(ex); } } public void actionPerformed(ActionEvent event) { IDirectableViewer viewer = getViewer(); // setup a good default name: the file name plus .eps: String fileName = "Untitled"; Document doc = getDir().getDocument(); if (doc.getMeganFile().getFileName() != null) fileName = doc.getMeganFile().getFileName(); fileName = FileUtils.replaceFileSuffix(fileName, "-legend.pdf"); ExportImageDialog saveImageDialog; if (viewer instanceof IViewerWithLegend) { saveImageDialog = new ExportImageDialog(viewer.getFrame(), fileName, false, true, true, event); String command = saveImageDialog.displayDialog(); if (command != null) { command = command.replaceAll("(?i)exportimage", "exportLegend"); execute(command); } } } public boolean isApplicable() { return getViewer() != null && getViewer() instanceof IViewerWithLegend && !((IViewerWithLegend) getViewer()).getShowLegend().equals("none"); } public String getName() { return "Export Legend..."; } public KeyStroke getAcceleratorKey() { return null; } public String getDescription() { return "Export content of legend window"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public boolean isCritical() { return true; } }
6,067
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportIndividualSamplesCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportIndividualSamplesCommand.java
/* * ExportIndividualSamplesCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.swing.commands.ICommand; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.swing.window.NotificationsInSwing; import jloda.util.FileUtils; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.core.Document; import megan.core.MeganFile; import megan.main.MeganProperties; import megan.util.MeganFileFilter; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.BufferedWriter; import java.io.File; import java.io.FileWriter; import java.io.Writer; import java.util.Collections; public class ExportIndividualSamplesCommand extends CommandBase implements ICommand { public String getSyntax() { return "extract directory=<target-directory> replace={true|false};"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("extract directory="); final String directory = np.getWordFileNamePunctuation(); final boolean replace; if (np.peekMatchIgnoreCase("replace")) { np.matchIgnoreCase("replace="); replace = np.getBoolean(); } else replace = true; np.matchIgnoreCase(";"); for (String name : getDoc().getSampleNames()) { final File file = new File(directory, name + ".megan"); if (!replace && file.exists()) { NotificationsInSwing.showWarning("File exists: " + file + ", won't replace"); } else { try (Writer w = new BufferedWriter(new FileWriter(file))) { Document newDocument = new Document(); newDocument.getMeganFile().setFile(file.getPath(), MeganFile.Type.MEGAN_SUMMARY_FILE); newDocument.extractSamples(Collections.singleton(name), getDoc()); newDocument.setNumberReads(newDocument.getDataTable().getTotalReads()); System.err.println("Number of reads: " + newDocument.getNumberOfReads()); newDocument.processReadHits(); newDocument.setTopPercent(100); newDocument.setMinScore(0); newDocument.setMaxExpected(10000); newDocument.setMinSupport(1); newDocument.getDataTable().setParameters(newDocument.getParameterString()); newDocument.getDataTable().write(w); newDocument.getSampleAttributeTable().write(w, false, true); } } } } public void actionPerformed(ActionEvent event) { if (getDoc().getMeganFile().hasDataConnector()) { final File savedFile = ProgramProperties.getFile(MeganProperties.SAVEFILE); final File directory = (savedFile != null ? savedFile.getParentFile() : null); final File lastOpenFile = FileUtils.replaceFileSuffix(new File(directory, getDoc().getSampleNames().get(0)), ".megan"); final File file = ChooseFileDialog.chooseFileToSave(getViewer().getFrame(), lastOpenFile, new MeganFileFilter(), new MeganFileFilter(), event, "Extract MEGAN files", ".megan"); if (file != null) { ProgramProperties.put(MeganProperties.SAVEFILE, file); execute("extract directory='" + file.getParent() + "' replace=true;"); } } } public boolean isApplicable() { return getDoc().getNumberOfReads() > 0 && getDoc().getMeganFile().hasDataConnector(); } public String getName() { return "All Individual Samples..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public String getDescription() { return "Extract and export all contained samples as individual files"; } public boolean isCritical() { return true; } }
4,768
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportReadsCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/export/ExportReadsCommand.java
/* * ExportReadsCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.export; import jloda.swing.commands.ICommand; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.FastaFileFilter; import jloda.swing.util.ResourceManager; import jloda.swing.window.NotificationsInSwing; import jloda.util.FileUtils; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.classification.Classification; import megan.classification.ClassificationManager; import megan.commands.CommandBase; import megan.core.ClassificationType; import megan.core.Director; import megan.core.Document; import megan.dialogs.export.ReadsExporter; import megan.dialogs.lrinspector.LRInspectorViewer; import megan.viewer.ClassificationViewer; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.File; import java.util.HashSet; import java.util.Set; public class ExportReadsCommand extends CommandBase implements ICommand { public String getSyntax() { return "export what=reads [data={" + StringUtils.toString(ClassificationManager.getAllSupportedClassifications(), "|") + "}] file=<filename>;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("export what=reads"); final String data; if (np.peekMatchIgnoreCase("data")) { np.matchIgnoreCase("data="); data = np.getWordMatchesRespectingCase(StringUtils.toString(ClassificationManager.getAllSupportedClassifications(), " ")); } else data = Classification.Taxonomy; np.matchIgnoreCase("file="); String outputFile = np.getAbsoluteFileName(); np.matchIgnoreCase(";"); final Director dir = getDir(); final Document doc = dir.getDocument(); long count; if (getViewer() instanceof ClassificationViewer) { final ClassificationViewer classificationViewer = (ClassificationViewer) dir.getViewerByClassName(data); final Set<Integer> classIds = new HashSet<>(); if (classificationViewer != null) classIds.addAll(classificationViewer.getSelectedNodeIds()); if (classIds.size() == 0) count = ReadsExporter.exportAll(doc.getConnector(), outputFile, doc.getProgressListener()); else count = ReadsExporter.export(data, classIds, doc.getConnector(), outputFile, doc.getProgressListener()); } else if (getViewer() instanceof LRInspectorViewer) { count = ((LRInspectorViewer) getViewer()).exportSelectedReads(outputFile, doc.getProgressListener()); } else count = 0; NotificationsInSwing.showInformation(getViewer().getFrame(), "Wrote " + count + " reads to file: " + outputFile); } public boolean isApplicable() { return getDoc().getMeganFile().hasDataConnector(); } public boolean isCritical() { return true; } public void actionPerformed(ActionEvent event) { Director dir = getDir(); if (!dir.getDocument().getMeganFile().hasDataConnector()) return; String name = FileUtils.replaceFileSuffix(dir.getDocument().getTitle(), "-ex.fasta"); File lastOpenFile = new File(name); final File file = ChooseFileDialog.chooseFileToSave(getViewer().getFrame(), lastOpenFile, new FastaFileFilter(), new FastaFileFilter(), event, "Save all READs to file", ".fasta"); final String data; if (getViewer() instanceof ClassificationViewer) data = getViewer().getClassName(); else data = ClassificationType.Taxonomy.toString(); if (file != null) { execute("export what=reads data=" + data + " file='" + file.getPath() + "';"); } } public String getName() { return "Reads..."; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public String getDescription() { return "Export reads to a text file"; } }
4,800
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ComputeRareBiomeCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/algorithms/ComputeRareBiomeCommand.java
/* * ComputeRareBiomeCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.algorithms; import jloda.swing.commands.ICommand; import jloda.swing.util.ProgramProperties; import jloda.swing.util.TwoInputOptionsPanel; import jloda.swing.window.NotificationsInSwing; import jloda.util.NumberUtils; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.samplesviewer.SamplesViewer; import megan.viewer.ClassificationViewer; import javax.swing.*; import java.awt.event.ActionEvent; import java.util.Collection; /** * compute rea biome * Daniel Huson, 2.2013 */ public class ComputeRareBiomeCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { final Collection<String> samples; if (getViewer() instanceof SamplesViewer) samples = ((SamplesViewer) getViewer()).getSamplesTableView().getSelectedSamples(); else if (getViewer() instanceof ClassificationViewer) samples = ((ClassificationViewer) getViewer()).getDocument().getSampleNames(); else return; if (samples.size() > 1) { float sampleThresholdPercent = (float) ProgramProperties.get("RareBiomeSampleThreshold", 10.0); float classThresholdPercent = (float) ProgramProperties.get("RareBiomeClassThreshold", 1.0); final String[] result = TwoInputOptionsPanel.show(getViewer().getFrame(), "MEGAN - Setup Compute Rare Biome", "Sample threshold (%)", "" + sampleThresholdPercent, "Maximum percent of samples in which class is present", "Class threshold (%)", "" + classThresholdPercent, "Percentage of assigned reads in sample that class must achieve to be considered present in that sample"); if (result != null) { if (NumberUtils.isFloat(result[0]) && NumberUtils.isFloat(result[1])) { sampleThresholdPercent = NumberUtils.parseFloat(result[0]); ProgramProperties.put("RareBiomeSampleThreshold", sampleThresholdPercent); classThresholdPercent = NumberUtils.parseFloat(result[1]); ProgramProperties.put("RareBiomeClassThreshold", classThresholdPercent); execute("compute biome=rare classThreshold=" + result[1] + " sampleThreshold=" + result[0] + " samples='" + StringUtils.toString(samples, "' '") + "';"); } else NotificationsInSwing.showError(getViewer().getFrame(), "Failed to parse values: " + StringUtils.toString(result, " ")); } } } public boolean isApplicable() { return getViewer() instanceof ClassificationViewer || getViewer() instanceof SamplesViewer && ((SamplesViewer) getViewer()).getSamplesTableView().getCountSelectedSamples() > 1; } public boolean isCritical() { return true; } public String getName() { return "Compute Rare Biome..."; } public ImageIcon getIcon() { return null; } public String getDescription() { return "Determine taxa and functions that appear in a minority of samples"; } }
3,976
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ReanalyzeFilesCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/algorithms/ReanalyzeFilesCommand.java
/* * ReanalyzeFilesCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.algorithms; import jloda.swing.commands.ICommand; import jloda.swing.director.IDirector; import jloda.swing.director.ProjectManager; import jloda.swing.window.NotificationsInSwing; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import jloda.util.progress.ProgressListener; import jloda.util.progress.ProgressPercentage; import megan.classification.ClassificationManager; import megan.commands.CommandBase; import megan.core.Director; import megan.core.Document; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.File; import java.util.ArrayList; import java.util.List; /** * reanalyze a set of files * Daniel Huson, 12.2019 */ public class ReanalyzeFilesCommand extends CommandBase implements ICommand { public String getSyntax() { return "reanalyzeFiles file=<name> [,<name>...] [minSupportPercent=<number>] [minSupport=<number>] [minScore=<number>] [maxExpected=<number>] [minPercentIdentity=<number>]\n" + "\t[topPercent=<number>] [minSupportPercent=<num>] [minSupport=<num>]\n" + "\t[lcaAlgorithm={" + StringUtils.toString(Document.LCAAlgorithm.values(), "|") + "}] [lcaCoveragePercent=<number>] [minPercentReadToCover=<number>] [minPercentReferenceToCover=<number>]" + " [minComplexity=<number>] [longReads={false|true}] [pairedReads={false|true}] [useIdentityFilter={false|true}]\n" + "\t[useContaminantFilter={false|true}] [loadContaminantFile=<filename>]\n" + "\t[readAssignmentMode={" + StringUtils.toString(Document.ReadAssignmentMode.values(), "|") + "} [fNames={" + StringUtils.toString(ClassificationManager.getAllSupportedClassificationsExcludingNCBITaxonomy(), "|") + "|*}];"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("reanalyzeFiles file="); final ArrayList<String> files = new ArrayList<>(); files.add(np.getWordFileNamePunctuation()); while (np.peekMatchAnyTokenIgnoreCase(",")) { np.matchIgnoreCase(","); files.add(np.getWordFileNamePunctuation()); } final ProgressListener progress = (getDoc() != null ? getDoc().getProgressListener() : new ProgressPercentage()); progress.setMaximum(files.size()); progress.setProgress(0); final List<String> tokens = np.getTokensRespectCase(null, ";"); final String fNames = np.findIgnoreCase(tokens, "fName=", null, "*"); final boolean allFNames = (fNames.equals("*")); final String recomputeParameters = StringUtils.toString(tokens, " ").replaceAll("fNames\\s*=.*", ""); for (String file : files) { progress.setTasks("Reanalyzing", file); { final Director openDir = findOpenDirector(file); if (openDir != null) { NotificationsInSwing.showWarning("File '" + file + "' is currently open, cannot reanalyze open files"); continue; } } NotificationsInSwing.showInformation("Reanalyzing file: " + file); final Director dir = Director.newProject(false, true); try { final Document doc = dir.getDocument(); doc.setOpenDAAFileOnlyIfMeganized(false); doc.getMeganFile().setFileFromExistingFile(file, false); final String fNamesToUse = (allFNames ? StringUtils.toString(StringUtils.remove(doc.getConnector().getAllClassificationNames(), "Taxonomy"), " ") : fNames).trim(); final String recomputeCommand = "recompute " + recomputeParameters + (fNamesToUse.length() > 0 ? " fNames = " + fNamesToUse : "") + ";"; dir.getDocument().setProgressListener(getDoc().getProgressListener()); dir.executeImmediately(recomputeCommand, dir.getMainViewer().getCommandManager()); } finally { dir.close(); } progress.incrementProgress(); } //getDir().close(); } public void actionPerformed(ActionEvent event) { } public boolean isApplicable() { return true; } public String getName() { return "Reanalyze Files"; } public String getDescription() { return "Reanalyze files"; } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return null; } public ImageIcon getIcon() { return null; } /** * get directory if this file is currently open * * @return directory */ private Director findOpenDirector(String daaFile) { final File file = new File(daaFile); if (file.isFile()) { for (IDirector dir : ProjectManager.getProjects()) { File aFile = new File(((Director) dir).getDocument().getMeganFile().getFileName()); if (aFile.isFile() && aFile.equals(file)) return (Director) dir; } } return null; } }
5,856
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
RemoveLowAbundancesCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/algorithms/RemoveLowAbundancesCommand.java
/* * RemoveLowAbundancesCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.algorithms; import jloda.graph.Node; import jloda.swing.commands.ICommand; import jloda.swing.window.NotificationsInSwing; import jloda.util.*; import jloda.util.parse.NexusStreamParser; import jloda.util.progress.ProgressListener; import megan.classification.Classification; import megan.classification.ClassificationManager; import megan.commands.CommandBase; import megan.core.Director; import megan.core.Document; import megan.core.MeganFile; import megan.main.MeganProperties; import megan.samplesviewer.SamplesViewer; import megan.viewer.ClassificationViewer; import megan.viewer.TaxonomyData; import megan.viewer.gui.NodeDrawer; import javax.swing.*; import java.awt.event.ActionEvent; import java.util.ArrayList; import java.util.Collection; import java.util.HashMap; import java.util.Map; /** * compute robust biome * Daniel Huson, 22022 */ public class RemoveLowAbundancesCommand extends CommandBase implements ICommand { public String getSyntax() { return "compute minAbundance=<threshold> samples=<name name...>;"; } public void apply(NexusStreamParser np) throws Exception { final var dir = getDir(); final var doc = dir.getDocument(); np.matchIgnoreCase("compute minAbundance="); var threshold = (float) np.getDouble(0, 100); final var legalSampleNames = "'" + StringUtils.toString(doc.getSampleNames(), "' '") + "' ALL"; final var selectedSamples = new ArrayList<String>(); np.matchIgnoreCase("samples="); while (!np.peekMatchIgnoreCase(";")) { selectedSamples.add(np.getWordMatchesRespectingCase(legalSampleNames)); } np.matchIgnoreCase(";"); if (selectedSamples.contains("ALL")) { selectedSamples.addAll(doc.getSampleNames()); } System.err.println("Number of samples: " + selectedSamples.size()); var newDir = Director.newProject(false); if (dir.getMainViewer() != null) { newDir.getMainViewer().getFrame().setVisible(true); newDir.getMainViewer().setDoReInduce(true); newDir.getMainViewer().setDoReset(true); } final var newDocument = newDir.getDocument(); final var tarClassification2class2counts = new HashMap<String, Map<Integer, float[]>>(); var sampleSizes = removeLowAbundance(doc, selectedSamples, threshold, tarClassification2class2counts, doc.getProgressListener()); if (tarClassification2class2counts.size() > 0) { for (var s = 0; s < selectedSamples.size(); s++) { newDocument.getDataTable().addSample(selectedSamples.get(s), sampleSizes[s], doc.getDataTable().getBlastMode(), s, tarClassification2class2counts); } newDocument.getSampleAttributeTable().addTable(doc.getSampleAttributeTable().extractTable(selectedSamples), false, true); newDocument.setNumberReads(newDocument.getDataTable().getTotalReads()); var fileName = FileUtils.replaceFileSuffix(doc.getMeganFile().getFileName(), "-min-" + threshold + ".megan"); newDocument.getMeganFile().setFile(fileName, MeganFile.Type.MEGAN_SUMMARY_FILE); System.err.printf("Total number of reads: %,d%n", newDocument.getNumberOfReads()); newDocument.processReadHits(); newDocument.setTopPercent(100); newDocument.setMinScore(0); newDocument.setMaxExpected(10000); newDocument.setMinSupport(1); newDocument.setMinSupportPercent(0); newDocument.setDirty(true); for (var classificationName : newDocument.getDataTable().getClassification2Class2Counts().keySet()) { newDocument.getActiveViewers().add(classificationName); } newDocument.getSampleAttributeTable().addTable(doc.getSampleAttributeTable().mergeSamples(selectedSamples, newDocument.getSampleNames().get(0)), false, true); if (newDocument.getNumberOfSamples() > 1) { newDir.getMainViewer().getNodeDrawer().setStyle(ProgramProperties.get(MeganProperties.COMPARISON_STYLE, ""), NodeDrawer.Style.PieChart); } NotificationsInSwing.showInformation("Filtered dataset has %,d reads".formatted(newDocument.getNumberOfReads())); newDir.execute("update reprocess=true reinduce=true;", newDir.getMainViewer().getCommandManager()); } } public void actionPerformed(ActionEvent event) { final Collection<String> samples; if (getViewer() instanceof SamplesViewer) samples = ((SamplesViewer) getViewer()).getSamplesTableView().getSelectedSamples(); else if (getViewer() instanceof ClassificationViewer) samples = ((ClassificationViewer) getViewer()).getDocument().getSampleNames(); else return; if (samples.size() > 1) { float classThresholdPercent = (float) ProgramProperties.get("LowAbundanceThreshold", 1.0); var result = JOptionPane.showInputDialog(getViewer().getFrame(), "Minimum abundance threshold (%):", "MEGAN - Remove low abundance nodes", JOptionPane.QUESTION_MESSAGE, null, null, classThresholdPercent); if (result instanceof String string && NumberUtils.isFloat(string)) { classThresholdPercent = NumberUtils.parseFloat(string); ProgramProperties.put("LowAbundanceThreshold", classThresholdPercent); execute("compute minAbundance=" + result + " samples='" + StringUtils.toString(samples, "' '") + "';"); } else NotificationsInSwing.showError(getViewer().getFrame(), "Failed to parse value: " + result); } } public boolean isApplicable() { return getViewer() instanceof ClassificationViewer || getViewer() instanceof SamplesViewer && ((SamplesViewer) getViewer()).getSamplesTableView().getCountSelectedSamples() > 1; } public boolean isCritical() { return true; } public String getName() { return "Remove Low Abundances..."; } public ImageIcon getIcon() { return null; } public String getDescription() { return "Remove taxa and functions whose abundance lie below a given percentage of assigned reads for all samples"; } /** * compute a new comparison in which low abundance items have been removed * * @param srcDoc * @param samplesToUse * @param threshold * @param tarClassification2class2counts * @param progress * @return low abundance version * @throws CanceledException */ private int[] removeLowAbundance(Document srcDoc, ArrayList<String> samplesToUse, float threshold, HashMap<String, Map<Integer, float[]>> tarClassification2class2counts, ProgressListener progress) throws CanceledException { var numberInputSamples = srcDoc.getNumberOfSamples(); var numberOutputSamples = samplesToUse.size(); final var sampleIds = srcDoc.getDataTable().getSampleIds(samplesToUse); var input2outputId = new int[sampleIds.cardinality()]; var outId = 0; for (var inId : BitSetUtils.members(sampleIds)) { input2outputId[inId] = outId++; } final var sizes = new int[numberOutputSamples]; if (numberOutputSamples > 0) { var dataTable = srcDoc.getDataTable(); for (var classificationName : dataTable.getClassification2Class2Counts().keySet()) { final var srcClass2counts = srcDoc.getDataTable().getClass2Counts(classificationName); final Node root; if (classificationName.equals(Classification.Taxonomy)) root = TaxonomyData.getTree().getRoot(); else { root = ClassificationManager.get(classificationName, true).getFullTree().getRoot(); } final int[] detectionThresholds = ComputeCoreOrRareBiome.computeDetectionThreshold(classificationName, numberInputSamples, srcClass2counts, threshold); var tarClass2counts = new HashMap<Integer, float[]>(); if (true) { var coreClass2counts = new HashMap<Integer, float[]>(); ComputeCoreOrRareBiome.computeCoreBiomeRec(sampleIds, false, srcDoc.getNumberOfSamples(), 0, detectionThresholds, root, srcClass2counts, coreClass2counts, progress); for (var classId : coreClass2counts.keySet()) { var value = coreClass2counts.get(classId)[0]; if (value > 0) { var srcCounts = srcClass2counts.get(classId); var tarCounts = new float[numberOutputSamples]; var outS = 0; for (var inS : BitSetUtils.members(sampleIds)) { tarCounts[outS++] = srcCounts[inS]; } tarClass2counts.put(classId, tarCounts); } } } else { for (var s : BitSetUtils.members(sampleIds)) { var tmpClass2counts = new HashMap<Integer, float[]>(); ComputeCoreOrRareBiome.computeCoreBiomeRec(BitSetUtils.asBitSet(s), false, srcDoc.getNumberOfSamples(), 0, detectionThresholds, root, srcClass2counts, tmpClass2counts, progress); for (var classId : tmpClass2counts.keySet()) { var value = tmpClass2counts.get(classId)[0]; var array = tarClass2counts.computeIfAbsent(classId, a -> new float[numberOutputSamples]); array[input2outputId[s]] = value; } } } tarClassification2class2counts.put(classificationName, tarClass2counts); if (classificationName.equals(Classification.Taxonomy)) { for (var counts : tarClass2counts.values()) { for (var i = 0; i < counts.length; i++) { sizes[i] += counts[i]; } } } } } return sizes; } }
9,714
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ComputeTotalBiomeCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/algorithms/ComputeTotalBiomeCommand.java
/* * ComputeTotalBiomeCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.algorithms; import jloda.swing.commands.ICommand; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.samplesviewer.SamplesViewer; import megan.viewer.ClassificationViewer; import javax.swing.*; import java.awt.event.ActionEvent; import java.util.Collection; /** * compute biome * Daniel Huson, 2.2013 */ public class ComputeTotalBiomeCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { final Collection<String> samples; if (getViewer() instanceof SamplesViewer) samples = ((SamplesViewer) getViewer()).getSamplesTableView().getSelectedSamples(); else if (getViewer() instanceof ClassificationViewer) samples = ((ClassificationViewer) getViewer()).getDocument().getSampleNames(); else return; if (samples.size() > 1) { execute("compute biome=total samples='" + StringUtils.toString(samples, "' '") + "';"); } } public boolean isApplicable() { return getViewer() instanceof ClassificationViewer || getViewer() instanceof SamplesViewer && ((SamplesViewer) getViewer()).getSamplesTableView().getCountSelectedSamples() > 1; } public boolean isCritical() { return true; } public String getName() { return "Compute Total Biome..."; } public ImageIcon getIcon() { return null; } public String getDescription() { return "Determine total (union) taxonomic and functional content"; } }
2,538
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
RecomputeCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/algorithms/RecomputeCommand.java
/* * RecomputeCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.algorithms; import jloda.swing.commands.ICommand; import jloda.swing.director.IDirectableViewer; import jloda.swing.window.NotificationsInSwing; import jloda.util.Basic; import jloda.util.CanceledException; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.classification.Classification; import megan.classification.ClassificationManager; import megan.commands.CommandBase; import megan.core.ContaminantManager; import megan.core.Document; import megan.dialogs.lrinspector.LRInspectorViewer; import megan.inspector.InspectorWindow; import megan.viewer.MainViewer; import javax.swing.*; import java.awt.event.ActionEvent; import java.util.ArrayList; /** * rerun LCA algorithm * Daniel Huson, 2010? */ public class RecomputeCommand extends CommandBase implements ICommand { public String getSyntax() { return "recompute [minScore=<number>] [maxExpected=<number>] [minPercentIdentity=<number>] [topPercent=<number>] [minSupportPercent=<number>] [minSupport=<number>]\n" + "\t[lcaAlgorithm={" + StringUtils.toString(Document.LCAAlgorithm.values(), "|") + "}] [lcaCoveragePercent=<number>] [minPercentReadToCover=<number>] [minPercentReferenceToCover=<number>]" + " [minComplexity=<number>] [longReads={false|true}] [pairedReads={false|true}] [useIdentityFilter={false|true}]\n" + "\t[useContaminantFilter={false|true}] [loadContaminantFile=<filename>]\n" + "\t[readAssignmentMode={" + StringUtils.toString(Document.ReadAssignmentMode.values(), "|") + "} [fNames={" + StringUtils.toString(ClassificationManager.getAllSupportedClassificationsExcludingNCBITaxonomy(), "|") + "];"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("recompute"); if (np.peekMatchIgnoreCase("minScore")) { np.matchIgnoreCase("minScore="); getDoc().setMinScore((float) np.getDouble(0, Float.MAX_VALUE)); } if (np.peekMatchIgnoreCase("maxExpected")) { np.matchIgnoreCase("maxExpected="); getDoc().setMaxExpected((float) np.getDouble(0, Float.MAX_VALUE)); } if (np.peekMatchIgnoreCase("minPercentIdentity")) { np.matchIgnoreCase("minPercentIdentity="); getDoc().setMinPercentIdentity((float) np.getDouble(0, 100)); } if (np.peekMatchIgnoreCase("topPercent")) { np.matchIgnoreCase("topPercent="); getDoc().setTopPercent((float) np.getDouble(0, Float.MAX_VALUE)); } if (np.peekMatchIgnoreCase("minSupportPercent")) { np.matchIgnoreCase("minSupportPercent="); getDoc().setMinSupportPercent((float) np.getDouble(0, 100)); } if (np.peekMatchIgnoreCase("minSupport")) { np.matchIgnoreCase("minSupport="); getDoc().setMinSupport(np.getInt(1, Integer.MAX_VALUE)); } if (np.peekMatchIgnoreCase("weightedLCA")) { // legacy np.matchIgnoreCase("weightedLCA="); getDoc().setLcaAlgorithm(Document.LCAAlgorithm.weighted); } else if (np.peekMatchIgnoreCase("lcaAlgorithm")) { np.matchIgnoreCase("lcaAlgorithm="); getDoc().setLcaAlgorithm(Document.LCAAlgorithm.valueOfIgnoreCase(np.getWordRespectCase())); } if (np.peekMatchAnyTokenIgnoreCase("lcaCoveragePercent weightedLCAPercent")) { np.matchAnyTokenIgnoreCase("lcaCoveragePercent weightedLCAPercent"); np.matchIgnoreCase("="); getDoc().setLcaCoveragePercent((float) np.getDouble(1, 100)); } if (np.peekMatchIgnoreCase("minPercentReadToCover")) { np.matchIgnoreCase("minPercentReadToCover="); getDoc().setMinPercentReadToCover((float) np.getDouble(0, 100)); } if (np.peekMatchIgnoreCase("minPercentReferenceToCover")) { np.matchIgnoreCase("minPercentReferenceToCover="); getDoc().setMinPercentReferenceToCover((float) np.getDouble(0, 100)); } if (np.peekMatchIgnoreCase("minComplexity")) { np.matchIgnoreCase("minComplexity="); getDoc().setMinComplexity((float) np.getDouble(-1.0, 1.0)); } if (np.peekMatchIgnoreCase("minReadLength")) { np.matchIgnoreCase("minReadLength="); getDoc().setMinReadLength(np.getInt(0,Integer.MAX_VALUE)); } if (np.peekMatchIgnoreCase("longReads")) { np.matchIgnoreCase("longReads="); getDoc().setLongReads(np.getBoolean()); } if (np.peekMatchIgnoreCase("pairedReads")) { np.matchIgnoreCase("pairedReads="); getDoc().setPairedReads(np.getBoolean()); } if (np.peekMatchIgnoreCase("useIdentityFilter")) { np.matchIgnoreCase("useIdentityFilter="); getDoc().setUseIdentityFilter(np.getBoolean()); } if (np.peekMatchIgnoreCase("useContaminantFilter")) { np.matchIgnoreCase("useContaminantFilter="); getDoc().setUseContaminantFilter(np.getBoolean()); } else getDoc().setUseContaminantFilter(false); if (np.peekMatchIgnoreCase("loadContaminantFile")) { np.matchIgnoreCase("loadContaminantFile="); final String fileName = np.getWordFileNamePunctuation(); final ContaminantManager contaminantManager = new ContaminantManager(); System.err.println("Loading contaminant file: " + fileName); contaminantManager.read(fileName); System.err.println("Contaminants: " + contaminantManager.inputSize()); getDoc().getDataTable().setContaminants(contaminantManager.getTaxonIdsString()); getDoc().setUseContaminantFilter(true); } if (np.peekMatchIgnoreCase("readAssignmentMode")) { np.matchIgnoreCase("readAssignmentMode="); getDoc().setReadAssignmentMode(Document.ReadAssignmentMode.valueOfIgnoreCase(np.getWordMatchesIgnoringCase(StringUtils.toString(Document.ReadAssignmentMode.values(), " ")))); } if (np.peekMatchIgnoreCase("fNames")) { getDoc().getActiveViewers().clear(); getDoc().getActiveViewers().add(Classification.Taxonomy); np.matchIgnoreCase("fNames="); while (!np.peekMatchIgnoreCase(";")) { final String cName = np.getWordRespectCase(); if (ClassificationManager.getAllSupportedClassificationsExcludingNCBITaxonomy().contains(cName)) getDoc().getActiveViewers().add(cName); else System.err.println("Warning: Unknown classification: " + cName); } } np.matchIgnoreCase(";"); final InspectorWindow inspectorWindow = (InspectorWindow) getDir().getViewerByClass(InspectorWindow.class); if (inspectorWindow != null && inspectorWindow.getDataTree().getRowCount() > 1) { SwingUtilities.invokeLater(inspectorWindow::clear); } final ArrayList<LRInspectorViewer> toClose = new ArrayList<>(); for (IDirectableViewer viewer : getDir().getViewers()) { if (viewer instanceof LRInspectorViewer) toClose.add((LRInspectorViewer) viewer); } for (final IDirectableViewer viewer : toClose) { SwingUtilities.invokeLater(() -> { try { viewer.destroyView(); } catch (CanceledException e) { Basic.caught(e); } }); } getDoc().processReadHits(); getDoc().setDirty(true); if (getViewer() instanceof MainViewer) ((MainViewer) getViewer()).setDoReInduce(true); NotificationsInSwing.showInformation(String.format("Classified %,d reads", +getDoc().getNumberOfReads())); } public void actionPerformed(ActionEvent event) { } public boolean isApplicable() { Document doc = getDoc(); return !doc.getMeganFile().isReadOnly() && doc.getMeganFile().hasDataConnector() && !doc.getMeganFile().isMeganSummaryFile(); } public String getName() { return null; } public String getDescription() { return "Rerun the LCA analysis with different parameters"; } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return null; } public ImageIcon getIcon() { return null; } }
9,336
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ComputeCoreBiomeCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/algorithms/ComputeCoreBiomeCommand.java
/* * ComputeCoreBiomeCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.algorithms; import jloda.swing.commands.ICommand; import jloda.swing.util.ProgramProperties; import jloda.swing.util.TwoInputOptionsPanel; import jloda.swing.window.NotificationsInSwing; import jloda.util.NumberUtils; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.samplesviewer.SamplesViewer; import megan.viewer.ClassificationViewer; import javax.swing.*; import java.awt.event.ActionEvent; import java.util.Collection; /** * compute biome * Daniel Huson, 2.2013, 7.2016 */ public class ComputeCoreBiomeCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } public void apply(NexusStreamParser np) { } public boolean isCritical() { return true; } public void actionPerformed(ActionEvent event) { final Collection<String> samples; if (getViewer() instanceof SamplesViewer) samples = ((SamplesViewer) getViewer()).getSamplesTableView().getSelectedSamples(); else if (getViewer() instanceof ClassificationViewer) samples = ((ClassificationViewer) getViewer()).getDocument().getSampleNames(); else return; if (samples.size() > 1) { float sampleThresholdPercent = (float) ProgramProperties.get("CoreBiomeSampleThreshold", 50.0); float classThresholdPercent = (float) ProgramProperties.get("CoreBiomeClassThreshold", 1.0); final String[] result = TwoInputOptionsPanel.show(getViewer().getFrame(), "MEGAN - Setup Compute Core Biome", "Sample threshold (%)", "" + sampleThresholdPercent, "Minimum percent of samples in which class must be present", "Class threshold (%)", "" + classThresholdPercent, "Percentage of assigned reads in sample that class must achieve to be considered present in that sample"); if (result != null) { if (NumberUtils.isFloat(result[0]) && NumberUtils.isFloat(result[1])) { sampleThresholdPercent = NumberUtils.parseFloat(result[0]); ProgramProperties.put("CoreBiomeSampleThreshold", sampleThresholdPercent); classThresholdPercent = NumberUtils.parseFloat(result[1]); ProgramProperties.put("CoreBiomeClassThreshold", classThresholdPercent); execute("compute biome=core classThreshold=" + result[1] + " sampleThreshold=" + result[0] + " samples='" + StringUtils.toString(samples, "' '") + "';"); } else NotificationsInSwing.showError(getViewer().getFrame(), "Failed to parse values: " + StringUtils.toString(result, " ")); } } } public boolean isApplicable() { return (getViewer() instanceof ClassificationViewer && ((ClassificationViewer) getViewer()).getDocument().getNumberOfSamples() > 1) || (getViewer() instanceof SamplesViewer && ((SamplesViewer) getViewer()).getSamplesTableView().getCountSelectedSamples() > 1); } public String getName() { return "Compute Core Biome..."; } public ImageIcon getIcon() { return null; } public String getDescription() { return "Determine taxa and functions that appear in a majority of the samples"; } }
4,071
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ComputeCoreOrRareBiome.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/algorithms/ComputeCoreOrRareBiome.java
/* * ComputeCoreOrRareBiome.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.algorithms; import jloda.graph.Edge; import jloda.graph.Node; import jloda.util.CanceledException; import jloda.util.progress.ProgressListener; import megan.classification.Classification; import megan.classification.ClassificationManager; import megan.core.ClassificationType; import megan.core.DataTable; import megan.core.Document; import megan.viewer.TaxonomyData; import java.util.BitSet; import java.util.Collection; import java.util.HashMap; import java.util.Map; /** * computes the core or rare biome for a set of samples * Reads summarized by a node are used to decide whether to keep node, reads assigned to node are used as counts * Daniel Huson, 2.2013 */ public class ComputeCoreOrRareBiome { /** * computes core biome for a given threshold * * @param asUpperBound if true, keep rare taxa in which the sample threshold is an upper bound * @param samplesThreshold number of samples that must contain a taxon so that it appears in the output, or max, if asUpperBound is true * @return sampleSize */ public static int apply(Document srcDoc, Collection<String> samplesToUse, boolean asUpperBound, int samplesThreshold, float taxonDetectionThresholdPercent, Map<String, Map<Integer, float[]>> tarClassification2class2counts, ProgressListener progress) throws CanceledException { final BitSet sampleIds = srcDoc.getDataTable().getSampleIds(samplesToUse); int size = 0; if (sampleIds.cardinality() > 0) { DataTable dataTable = srcDoc.getDataTable(); for (String classificationName : dataTable.getClassification2Class2Counts().keySet()) { final Map<Integer, float[]> srcClass2counts = srcDoc.getDataTable().getClass2Counts(classificationName); final Node root; if (classificationName.equals(Classification.Taxonomy)) root = TaxonomyData.getTree().getRoot(); else { root = ClassificationManager.get(classificationName, true).getFullTree().getRoot(); } final Map<Integer, float[]> tarClass2counts = new HashMap<>(); tarClassification2class2counts.put(classificationName, tarClass2counts); final int[] detectionThreshold = computeDetectionThreshold(classificationName, srcDoc.getNumberOfSamples(), srcClass2counts, taxonDetectionThresholdPercent); computeCoreBiomeRec(sampleIds, asUpperBound, srcDoc.getNumberOfSamples(), samplesThreshold, detectionThreshold, root, srcClass2counts, tarClass2counts, progress); // System.err.println(classificationName + ": " + tarClassification2class2counts.size()); } final Map<Integer, float[]> taxId2counts = tarClassification2class2counts.get(ClassificationType.Taxonomy.toString()); if (taxId2counts != null) { for (Integer taxId : taxId2counts.keySet()) { if (taxId >= 0) { float[] values = taxId2counts.get(taxId); size += values[0]; } } } if (size == 0) { for (String classificationName : dataTable.getClassification2Class2Counts().keySet()) { if (!classificationName.equals(ClassificationType.Taxonomy.toString())) { final Map<Integer, float[]> id2counts = tarClassification2class2counts.get(classificationName); if (id2counts != null) { for (Integer ids : id2counts.keySet()) { final float[] values = id2counts.get(ids); if (ids >= 0) size += values[0]; } if (size > 0) break; } } } } } return size; } /** * determines the number of counts necessary for a taxon to be considered detected, for each sample * * @return thresholds */ static int[] computeDetectionThreshold(String classificationName, int numberOfSamples, Map<Integer, float[]> srcClass2counts, float detectionThresholdPercent) { final int[] array = new int[numberOfSamples]; if (detectionThresholdPercent > 0) { for (Integer id : srcClass2counts.keySet()) { if (id > 0) { final float[] counts = srcClass2counts.get(id); if (counts != null) { for (int i = 0; i < counts.length; i++) { array[i] += counts[i]; } } } } for (int i = 0; i < array.length; i++) { array[i] *= detectionThresholdPercent / 100.0; } System.err.println("Read detection thresholds for " + classificationName + ":"); for (float value : array) { System.err.printf(" %,12.0f", value); } System.err.println(); } for (int i = 0; i < array.length; i++) { // need at least 1 to detect array[i] = Math.max(1, array[i]); } return array; } /** * recursively compute the core biome * */ static float[] computeCoreBiomeRec(BitSet sampleIds, boolean asUpperBound, int numberOfSamples, int samplesThreshold, int[] detectionThreshold, Node v, Map<Integer, float[]> srcClass2counts, Map<Integer, float[]> tarClass2counts, ProgressListener progress) throws CanceledException { final float[] summarized = new float[numberOfSamples]; final int classId = (Integer) v.getInfo(); if (classId == -1 || classId == -2 || classId == -3) return summarized; // ignore unassigned etc final float[] countsV = srcClass2counts.get(classId); if (countsV != null) { for (int i = 0; i < countsV.length; i++) { if (sampleIds.get(i)) summarized[i] = countsV[i]; } } for (Edge e = v.getFirstOutEdge(); e != null; e = v.getNextOutEdge(e)) { final Node w = e.getTarget(); final float[] countsBelow = computeCoreBiomeRec(sampleIds, asUpperBound, numberOfSamples, samplesThreshold, detectionThreshold, w, srcClass2counts, tarClass2counts, progress); for (int i = 0; i < numberOfSamples; i++) { if (sampleIds.get(i)) { summarized[i] += countsBelow[i]; } } } int numberOfSamplesWithClass = 0; int value = 0; for (int i = 0; i < numberOfSamples; i++) { if (sampleIds.get(i)) { if (summarized[i] >= detectionThreshold[i]) numberOfSamplesWithClass++; if (countsV != null && i < countsV.length && sampleIds.get(i)) value += countsV[i]; } } if (countsV != null && numberOfSamplesWithClass > 0 && ((!asUpperBound && numberOfSamplesWithClass >= samplesThreshold) || (asUpperBound && numberOfSamplesWithClass <= samplesThreshold))) { tarClass2counts.put(classId, new float[]{value}); } progress.checkForCancel(); return summarized; } }
8,408
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ComputeBiomeCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/algorithms/ComputeBiomeCommand.java
/* * ComputeBiomeCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.algorithms; import jloda.seq.BlastMode; import jloda.swing.commands.ICommand; import jloda.swing.util.ProgramProperties; import jloda.swing.window.NotificationsInSwing; import jloda.util.FileUtils; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.core.Director; import megan.core.Document; import megan.core.MeganFile; import megan.main.MeganProperties; import megan.viewer.gui.NodeDrawer; import javax.swing.*; import java.awt.event.ActionEvent; import java.util.HashMap; import java.util.HashSet; import java.util.Map; import java.util.Set; /** * compute biome * Daniel Huson, 2.2013 */ public class ComputeBiomeCommand extends CommandBase implements ICommand { private Director newDir; public String getSyntax() { return "compute biome={core|total|rare} [classThreshold=<percentage>] [sampleThreshold=<percentage>] samples=<name name...>;"; } public void apply(NexusStreamParser np) throws Exception { final Director dir = getDir(); final Document doc = dir.getDocument(); np.matchIgnoreCase("compute biome="); final String what = np.getWordMatchesIgnoringCase("core total rare"); final float classThreshold; if (np.peekMatchIgnoreCase("classThreshold")) { np.matchIgnoreCase("classThreshold="); classThreshold = (float) np.getDouble(0, 100); } else classThreshold = 1; final float samplesThreshold; if (np.peekMatchIgnoreCase("sampleThreshold")) { np.matchIgnoreCase("sampleThreshold="); samplesThreshold = (float) np.getDouble(0, 100); } else samplesThreshold = 50; final String legalSampleNames = "'" + StringUtils.toString(doc.getSampleNames(), "' '") + "' ALL"; final Set<String> selectedSamples = new HashSet<>(); np.matchIgnoreCase("samples="); while (!np.peekMatchIgnoreCase(";")) { selectedSamples.add(np.getWordMatchesRespectingCase(legalSampleNames)); } np.matchIgnoreCase(";"); if (selectedSamples.contains("ALL")) { selectedSamples.addAll(doc.getSampleNames()); } System.err.println("Number of samples: " + selectedSamples.size()); newDir = Director.newProject(false); if (dir.getMainViewer() != null) { newDir.getMainViewer().getFrame().setVisible(true); newDir.getMainViewer().setDoReInduce(true); newDir.getMainViewer().setDoReset(true); } final Document newDocument = newDir.getDocument(); final Map<String, Map<Integer, float[]>> classification2class2counts = new HashMap<>(); int sampleSize = 0; String title = null; if (what.equalsIgnoreCase("core")) { int minSamplesToHave = (int) Math.ceil((samplesThreshold / 100.0) * selectedSamples.size()); sampleSize = ComputeCoreOrRareBiome.apply(doc, selectedSamples, false, minSamplesToHave, classThreshold, classification2class2counts, doc.getProgressListener()); title = "CoreBiome-%s-%s".formatted(StringUtils.removeTrailingZerosAfterDot(samplesThreshold), StringUtils.removeTrailingZerosAfterDot(classThreshold)); } else if (what.equalsIgnoreCase("rare")) { int minSamplesNotToHave = (int) Math.ceil((samplesThreshold / 100.0) * selectedSamples.size()); sampleSize = ComputeCoreOrRareBiome.apply(doc, selectedSamples, true, minSamplesNotToHave, classThreshold, classification2class2counts, doc.getProgressListener()); title = "RareBiome-%s-%s".formatted(StringUtils.removeTrailingZerosAfterDot(samplesThreshold), StringUtils.removeTrailingZerosAfterDot(classThreshold)); } else if (what.equalsIgnoreCase("total")) { sampleSize = ComputeCoreOrRareBiome.apply(doc, selectedSamples, false, 0, classThreshold, classification2class2counts, doc.getProgressListener()); title = "TotalBiome"; } if (classification2class2counts.size() > 0) { newDocument.addSample(title, sampleSize, 0, BlastMode.Unknown, classification2class2counts); newDocument.setNumberReads(newDocument.getDataTable().getTotalReads()); String fileName = FileUtils.replaceFileSuffix(doc.getMeganFile().getFileName(), "-" + title + ".megan"); newDocument.getMeganFile().setFile(fileName, MeganFile.Type.MEGAN_SUMMARY_FILE); System.err.println("Number of reads: " + newDocument.getNumberOfReads()); newDocument.processReadHits(); newDocument.setTopPercent(100); newDocument.setMinScore(0); newDocument.setMaxExpected(10000); newDocument.setMinSupport(1); newDocument.setMinSupportPercent(0); newDocument.setDirty(true); for (String classificationName : newDocument.getDataTable().getClassification2Class2Counts().keySet()) { newDocument.getActiveViewers().add(classificationName); } newDocument.getSampleAttributeTable().addTable(doc.getSampleAttributeTable().mergeSamples(selectedSamples, newDocument.getSampleNames().get(0)), false, true); if (newDocument.getNumberOfSamples() > 1) { newDir.getMainViewer().getNodeDrawer().setStyle(ProgramProperties.get(MeganProperties.COMPARISON_STYLE, ""), NodeDrawer.Style.PieChart); } NotificationsInSwing.showInformation(String.format(StringUtils.capitalizeFirstLetter(what) + " biome has %,d reads", newDocument.getNumberOfReads())); newDir.execute("update reprocess=true reinduce=true;", newDir.getMainViewer().getCommandManager()); } } public boolean isApplicable() { return false; } public boolean isCritical() { return true; } public void actionPerformed(ActionEvent event) { } public String getName() { return "Compute Core Biome..."; } public ImageIcon getIcon() { return null; } public String getDescription() { return "Compute the core biome for a set of samples"; } /** * gets the new director created by running this command * * @return new dir */ public Director getNewDir() { return newDir; } }
7,189
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SetFirstWordIsAccessionCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/preferences/SetFirstWordIsAccessionCommand.java
/* * SetFirstWordIsAccessionCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.preferences; import jloda.swing.commands.ICheckBoxCommand; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.classification.IdParser; import megan.commands.CommandBase; import javax.swing.*; import java.awt.event.ActionEvent; public class SetFirstWordIsAccessionCommand extends CommandBase implements ICheckBoxCommand { @Override public boolean isSelected() { return ProgramProperties.get(IdParser.PROPERTIES_FIRST_WORD_IS_ACCESSION, true); } public String getSyntax() { return "set firstWordIsAccession={true|false};"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("set firstWordIsAccession="); boolean state = np.getBoolean(); np.matchIgnoreCase(";"); ProgramProperties.put(IdParser.PROPERTIES_FIRST_WORD_IS_ACCESSION, state); } public void actionPerformed(ActionEvent event) { executeImmediately("set firstWordIsAccession=" + (!isSelected()) + ";"); } public boolean isApplicable() { return true; } public String getName() { return "First Word Is Accession"; } public String getDescription() { return "Parse first word of reference header-line as accession number in accordance with 2016 NCBI formatting"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Preferences16.gif"); } public boolean isCritical() { return true; } }
2,403
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
FullScreenModeCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/preferences/FullScreenModeCommand.java
/* * FullScreenModeCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.preferences; import jloda.swing.commands.ICheckBoxCommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; public class FullScreenModeCommand extends CommandBase implements ICheckBoxCommand { private static final GraphicsDevice device = GraphicsEnvironment.getLocalGraphicsEnvironment().getScreenDevices()[0]; @Override public boolean isSelected() { return isApplicable() && device.getFullScreenWindow() == getViewer().getFrame(); } public String getSyntax() { return "set fullScreen={false|true};"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("set fullScreen="); boolean state = np.getBoolean(); np.matchIgnoreCase(";"); JFrame frame = (state ? getViewer().getFrame() : null); device.setFullScreenWindow(frame); } public void actionPerformed(ActionEvent event) { executeImmediately("set fullScreen=" + (!isSelected()) + ";"); } public boolean isApplicable() { return getViewer() != null && device.isFullScreenSupported(); } public String getName() { return "Full Screen Mode"; } public String getDescription() { return "Full Screen Mode"; } public ImageIcon getIcon() { return ResourceManager.getIcon("FullScreen16.gif"); } public boolean isCritical() { return false; } }
2,392
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ShowNotificationsCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/preferences/ShowNotificationsCommand.java
/* * ShowNotificationsCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.preferences; import jloda.swing.commands.ICheckBoxCommand; import jloda.swing.util.ResourceManager; import jloda.swing.window.NotificationsInSwing; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; public class ShowNotificationsCommand extends CommandBase implements ICheckBoxCommand { private static final GraphicsDevice device = GraphicsEnvironment.getLocalGraphicsEnvironment().getScreenDevices()[0]; @Override public boolean isSelected() { return NotificationsInSwing.isShowNotifications(); } public String getSyntax() { return "set showNotifications={true|false};"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("set showNotifications="); boolean state = np.getBoolean(); np.matchIgnoreCase(";"); NotificationsInSwing.setShowNotifications(state); } public void actionPerformed(ActionEvent event) { executeImmediately("set showNotifications=" + (!NotificationsInSwing.isShowNotifications()) + ";"); } public boolean isApplicable() { return getViewer() != null && device.isFullScreenSupported(); } public String getName() { return "Show Notifications"; } public String getDescription() { return "Show notifications"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Preferences16.gif"); } public boolean isCritical() { return false; } }
2,428
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SetAccessionTagsCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/preferences/SetAccessionTagsCommand.java
/* * SetAccessionTagsCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.preferences; import jloda.swing.commands.ICommand; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.classification.IdParser; import megan.commands.CommandBase; import javax.swing.*; import java.awt.event.ActionEvent; public class SetAccessionTagsCommand extends CommandBase implements ICommand { public String getSyntax() { return "set accessionTags=<word ...>;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("set accessionTags="); String[] tags = np.getWordRespectCase().split("\\s+"); np.matchIgnoreCase(";"); ProgramProperties.put(IdParser.PROPERTIES_ACCESSION_TAGS, tags); } public void actionPerformed(ActionEvent event) { String[] tags = ProgramProperties.get(IdParser.PROPERTIES_ACCESSION_TAGS, IdParser.ACCESSION_TAGS); String result = JOptionPane.showInputDialog(getViewer().getFrame(), "Enter tag(s) for identifying accession numbers (separated by spaces):", StringUtils.toString(tags, " ")); if (result != null) executeImmediately("set accessionTags='" + result + "';"); } public boolean isApplicable() { return true; } public String getName() { return "Set Accession Tags"; } public String getDescription() { return "Set tags used to identify accession numbers"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Preferences16.gif"); } public boolean isCritical() { return true; } }
2,489
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ZoomToFullCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/zoom/ZoomToFullCommand.java
/* * ZoomToFullCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.zoom; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.event.ActionEvent; /** * zoom to full * Daniel Huson, 2005 */ public class ZoomToFullCommand extends CommandBase implements ICommand { public String getSyntax() { return "zoom what={fit|full|selection}"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("zoom what="); final String what = np.getWordMatchesIgnoringCase("fit full selected"); np.matchIgnoreCase(";"); if (getViewer() instanceof ViewerBase) { final ViewerBase viewer = (ViewerBase) getViewer(); if (what.equalsIgnoreCase("fit")) { viewer.fitGraphToWindow(); //viewer.trans.setScaleY(0.14); // no idea why this was here... } else if (what.equalsIgnoreCase("full")) { viewer.fitGraphToWindow(); viewer.trans.setScaleY(1); } else { // selection viewer.zoomToSelection(); } } } public void actionPerformed(ActionEvent event) { executeImmediately("zoom what=full;"); } public String getName() { return "Fully Expand"; } public String getDescription() { return "Expand tree"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/AlignJustifyVertical16.gif"); } public boolean isApplicable() { return getViewer() instanceof ViewerBase; } public boolean isCritical() { return true; } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } }
2,753
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ZoomToSelectionCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/zoom/ZoomToSelectionCommand.java
/* * ZoomToSelectionCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.zoom; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.event.ActionEvent; /** * zoom to selection * Daniel Huson, 2005 */ public class ZoomToSelectionCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } @Override public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { executeImmediately("zoom what=selected;"); } public boolean isApplicable() { return getViewer() instanceof ViewerBase && ((ViewerBase) getViewer()).getSelectedNodes().size() > 0; } public String getName() { return "Zoom To Selection"; } public String getDescription() { return "Zoom to the selection"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/AlignCenter16.gif"); } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } @Override public boolean isCritical() { return true; } }
2,140
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ZoomToFitCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/zoom/ZoomToFitCommand.java
/* * ZoomToFitCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.zoom; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.event.ActionEvent; /** * zoom to fit * Daniel Huson, 2005 */ public class ZoomToFitCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } @Override public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { executeImmediately("zoom what=fit;"); } public String getName() { return "Fully Contract"; } public String getDescription() { return "Contract tree vertically"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/AlignJustifyHorizontal16.gif"); } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } @Override public boolean isCritical() { return true; } @Override public boolean isApplicable() { return getViewer() instanceof ViewerBase; } }
2,082
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
RunBlastOnNCBICommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/additional/RunBlastOnNCBICommand.java
/* * RunBlastOnNCBICommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.additional; import javafx.application.Platform; import javafx.beans.value.ChangeListener; import jloda.seq.FastAFileIterator; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.director.IDirector; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.ProgressDialog; import jloda.swing.window.NotificationsInSwing; import jloda.util.*; import jloda.util.parse.NexusStreamParser; import megan.blastclient.BlastService; import megan.blastclient.RemoteBlastClient; import megan.blastclient.RemoteBlastDialog; import megan.core.Director; import megan.core.Document; import megan.importblast.ImportBlastDialog; import megan.util.IReadsProvider; import megan.util.MeganFileFilter; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; import java.io.BufferedWriter; import java.io.File; import java.io.FileWriter; import java.util.ArrayList; /** * analyse a sequence on NCBI * Daniel Huson, 3/2017 */ public class RunBlastOnNCBICommand extends CommandBase implements ICommand { private static BlastService blastService; private static boolean serviceIsRunning = false; public String getSyntax() { return "remoteBlastNCBI readsFile=<file-name> [longReads={false|true}] [blastMode={blastn|blastx|blastp}] [blastDB={nr|<name>}];"; } /** * apply the command */ public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("remoteBlastNCBI readsFile="); final File readsFile = new File(np.getWordFileNamePunctuation()); final boolean longReads; if (np.peekMatchIgnoreCase("longReads")) { np.matchIgnoreCase("longReads="); longReads = np.getBoolean(); } else longReads = false; final String blastMode; if (np.peekMatchIgnoreCase("blastMode")) { np.matchIgnoreCase("blastMode="); blastMode = np.getWordMatchesIgnoringCase(StringUtils.toString(RemoteBlastClient.BlastProgram.values(), " ")); } else blastMode = "blastn"; final String blastDB; if (np.peekMatchIgnoreCase("blastDB")) { np.matchIgnoreCase("blastDB="); blastDB = np.getWordMatchesIgnoringCase(StringUtils.toString(RemoteBlastClient.getDatabaseNames(blastMode), " ")); } else blastDB = "nr"; np.matchIgnoreCase(";"); getDir().notifyLockInput(); if (blastService == null) { blastService = new BlastService(); } if (serviceIsRunning && ProgramProperties.isUseGUI()) { if (JOptionPane.showConfirmDialog(getViewer().getFrame(), "A remote BLAST is currently running, kill it?", "Kill current remote job?", JOptionPane.YES_NO_CANCEL_OPTION) != JOptionPane.YES_OPTION) { getDir().executeImmediately("close what=current;", ((Director) getDir()).getCommandManager()); return; } } blastService.setProgram(RemoteBlastClient.BlastProgram.valueOf(blastMode)); final ArrayList<Pair<String, String>> queries = new ArrayList<>(); try (FastAFileIterator it = new FastAFileIterator(readsFile.getPath())) { while (it.hasNext()) { queries.add(it.next()); } } blastService.setQueries(queries); blastService.setDatabase(blastDB); final Document doc = ((Director) getDir()).getDocument(); doc.setProgressListener(new ProgressDialog("Blasting at NCBI", "Running", getViewer().getFrame())); doc.getProgressListener().setMaximum(1000); final ChangeListener<Number> progressChangeListener = (observable, oldValue, newValue) -> { try { if (doc.getProgressListener() != null) doc.getProgressListener().setProgress(Math.round(1000 * newValue.doubleValue())); } catch (CanceledException e) { blastService.cancel(); } }; final ChangeListener<String> messageChangeListener = (observable, oldValue, newValue) -> { System.err.println(newValue); if (doc.getProgressListener() != null) doc.getProgressListener().setSubtask(newValue); }; // if user cancels progress listener, cancels service final Thread thread = new Thread(() -> { while (serviceIsRunning) { if (doc.getProgressListener().isUserCancelled()) { Platform.runLater(() -> { if (blastService.isRunning()) blastService.cancel(); }); } try { Thread.sleep(100); } catch (InterruptedException ignored) { } } }); thread.start(); Platform.runLater(() -> { blastService.setOnRunning(event -> SwingUtilities.invokeLater(() -> { serviceIsRunning = true; getCommandManager().updateEnableState(NAME); })); blastService.messageProperty().addListener(messageChangeListener); blastService.progressProperty().addListener(progressChangeListener); blastService.restart(); blastService.setOnSucceeded(event -> { blastService.progressProperty().removeListener(progressChangeListener); blastService.messageProperty().removeListener(messageChangeListener); final String result = blastService.getValue(); SwingUtilities.invokeLater(() -> { try { if (result != null && result.length() > 0) { try { final File blastFile = ChooseFileDialog.chooseFileToSave(getViewer().getFrame(), FileUtils.replaceFileSuffix(readsFile, "." + blastMode), new MeganFileFilter(), new MeganFileFilter(), null, "Save BLAST file", "." + blastMode); if (blastFile != null) { try (BufferedWriter w = new BufferedWriter(new FileWriter(blastFile))) { w.write(result); } System.err.println("Alignments written to: " + blastFile.getPath()); if (ProgramProperties.isUseGUI()) { final int result1 = JOptionPane.showConfirmDialog(null, "Import remotely BLASTED file into MEGAN?", "Import - MEGAN", JOptionPane.YES_NO_CANCEL_OPTION); getDir().notifyUnlockInput(); if (result1 == JOptionPane.YES_OPTION) { final ImportBlastDialog importBlastDialog = new ImportBlastDialog(getViewer().getFrame(), (Director) getDir(), "Import Blast File"); importBlastDialog.getBlastFileNameField().setText(blastFile.getPath()); importBlastDialog.getReadFileNameField().setText(readsFile.getPath()); importBlastDialog.setLongReads(longReads); importBlastDialog.getMeganFileNameField().setText(FileUtils.replaceFileSuffix(blastFile.getPath(), "-" + blastMode + ".rma6")); importBlastDialog.updateView(IDirector.ALL); final String command = importBlastDialog.showAndGetCommand(); if (command != null) { getDir().notifyUnlockInput(); getDir().execute(command, getViewer().getCommandManager()); } } } } } catch (Exception ex) { NotificationsInSwing.showError("Create RMA file failed: " + ex.getMessage()); getDir().notifyUnlockInput(); getDir().executeImmediately("close what=current;", ((Director) getDir()).getCommandManager()); } } else { NotificationsInSwing.showInformation("No hits found"); getDir().notifyUnlockInput(); getDir().executeImmediately("close what=current;", ((Director) getDir()).getCommandManager()); } } finally { serviceIsRunning = false; if (doc.getProgressListener() != null) doc.getProgressListener().close(); } }); }); blastService.setOnFailed(event -> { blastService.progressProperty().removeListener(progressChangeListener); blastService.messageProperty().removeListener(messageChangeListener); NotificationsInSwing.showError("Remote blast failed: " + blastService.getException()); SwingUtilities.invokeLater(() -> { try { doc.getProgressListener().close(); getDir().notifyUnlockInput(); getDir().executeImmediately("close what=current;", ((Director) getDir()).getCommandManager()); } finally { serviceIsRunning = false; } }); }); blastService.setOnCancelled(event -> { blastService.progressProperty().removeListener(progressChangeListener); blastService.messageProperty().removeListener(messageChangeListener); if (serviceIsRunning) NotificationsInSwing.showWarning("Remote blast canceled"); SwingUtilities.invokeLater(() -> { if (serviceIsRunning) { try { getDir().notifyUnlockInput(); getDir().executeImmediately("close what=current;", ((Director) getDir()).getCommandManager()); } finally { serviceIsRunning = false; if (doc.getProgressListener() != null) doc.getProgressListener().close(); } } }); }); }); } public void actionPerformed(ActionEvent event) { if (isApplicable()) { final IReadsProvider readProvider = ((IReadsProvider) getViewer()); if (readProvider.isReadsAvailable()) { final Pair<String, String> first = readProvider.getReads(1).iterator().next(); final String commandString = RemoteBlastDialog.apply(getViewer(), (Director) getDir(), readProvider, null, StringUtils.toCleanName(first.getFirst())); if (commandString != null) { final Director newDir = Director.newProject(); newDir.getMainViewer().getFrame().setVisible(true); newDir.getMainViewer().setDoReInduce(true); newDir.getMainViewer().setDoReset(true); newDir.executeImmediately(commandString, newDir.getMainViewer().getCommandManager()); getCommandManager().updateEnableState(NAME); } } } } public boolean isApplicable() { return getViewer() instanceof IReadsProvider && (blastService == null || !serviceIsRunning) && ((IReadsProvider) getViewer()).isReadsAvailable(); } private static final String NAME = "BLAST on NCBI..."; public String getName() { return NAME; } public String getDescription() { return "Remotely BLAST sequence on NCBI website"; } public ImageIcon getIcon() { return null; } public boolean isCritical() { return true; } @Override public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_B, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()); } }
13,241
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ProjectAssignmentsToRankCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/additional/ProjectAssignmentsToRankCommand.java
/* * ProjectAssignmentsToRankCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.additional; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.swing.window.NotificationsInSwing; import jloda.util.FileUtils; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.algorithms.NaiveProjectionProfile; import megan.classification.ClassificationManager; import megan.core.Director; import megan.core.Document; import megan.core.MeganFile; import megan.core.SampleAttributeTable; import megan.main.MeganProperties; import megan.util.CallBack; import megan.util.PopupChoice; import megan.viewer.ClassificationViewer; import megan.viewer.TaxonomicLevels; import megan.viewer.gui.NodeDrawer; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; import java.util.ArrayList; import java.util.HashMap; import java.util.Map; public class ProjectAssignmentsToRankCommand extends CommandBase implements ICommand { public String getSyntax() { return "project rank={" + StringUtils.toString(TaxonomicLevels.getAllMajorRanks(), "|") + "} [minPercent={number}];"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("project rank="); final String rank = np.getWordMatchesRespectingCase(StringUtils.toString(TaxonomicLevels.getAllNames(), " ")); final float minPercent; if (np.peekMatchIgnoreCase("minPercent")) { np.matchIgnoreCase("minPercent="); minPercent = (float) np.getDouble(0, 100); } else minPercent = 0f; np.matchIgnoreCase(";"); final Document doc = ((Director) getDir()).getDocument(); final int numberOfSamples = doc.getNumberOfSamples(); final String[] sampleNames = doc.getSampleNamesAsArray(); final String fileName = FileUtils.replaceFileSuffix(doc.getMeganFile().getFileName(), "-" + rank + "-projection.megan"); final SampleAttributeTable sampleAttributeTable = doc.getSampleAttributeTable().copy(); final long numberOfReads = doc.getNumberOfReads(); final int[] sampleSizes = new int[numberOfSamples]; for (int s = 0; s < numberOfSamples; s++) { sampleSizes[s] = Math.round(doc.getDataTable().getSampleSizes()[s]); } final Director newDir; final Document newDocument; if (ProgramProperties.isUseGUI()) { newDir = Director.newProject(false); newDir.getMainViewer().setDoReInduce(true); newDir.getMainViewer().setDoReset(true); newDocument = newDir.getDocument(); newDocument.setReadAssignmentMode(doc.getReadAssignmentMode()); } else { newDir = (Director) getDir(); newDocument = doc; newDocument.clearReads(); newDocument.getSampleAttributeTable().clear(); } newDocument.getMeganFile().setFile(fileName, MeganFile.Type.MEGAN_SUMMARY_FILE); newDocument.setNumberReads(numberOfReads); Map<String, Map<Integer, float[]>> classification2class2counts = new HashMap<>(); { var viewers = new ArrayList<ClassificationViewer>(); viewers.add(((Director) getDir()).getMainViewer()); if (doc.getClassificationNames().contains("GTDB")) { for (var viewer : ((Director) getDir()).getViewers()) { if (viewer instanceof ClassificationViewer && viewer.getClassName().equals("GTDB")) { viewers.add((ClassificationViewer) viewer); break; } } if (viewers.size() < 2) { System.err.println("Document has GTDB classification, open GTDB viewer to ensure that it gets projected, too"); } } for (var viewer : viewers) { final Map<Integer, float[]> taxonMap = NaiveProjectionProfile.compute(viewer, rank, minPercent); final Map<Integer, float[]>[] sample2taxonMap = sortBySample(numberOfSamples, taxonMap); for (int s = 0; s < numberOfSamples; s++) { classification2class2counts.put(viewer.getClassName(), sample2taxonMap[s]); // float sampleSize = computeSize(sample2taxonMap[s]); newDocument.addSample(sampleNames[s], sampleSizes[s], 0, doc.getBlastMode(), classification2class2counts); } } } System.err.printf("Number of reads: %,d%n",newDocument.getNumberOfReads()); newDocument.processReadHits(); newDocument.setTopPercent(100); newDocument.setMinScore(0); newDocument.setMaxExpected(10000); newDocument.setMinSupportPercent(0); newDocument.setMinSupport(1); newDocument.setDirty(true); newDocument.getDataTable().setParameters(doc.getDataTable().getParameters()); newDocument.getActiveViewers().addAll(newDocument.getDataTable().getClassification2Class2Counts().keySet()); newDocument.getSampleAttributeTable().addTable(sampleAttributeTable, true, true); NotificationsInSwing.showInformation(String.format("Computed taxonomic profile for %,d reads", newDocument.getNumberOfReads())); if (ProgramProperties.isUseGUI() && newDocument.getNumberOfReads() == 0) { newDocument.setDirty(false); newDir.close(); } else { newDir.getMainViewer().getFrame().setVisible(true); if (newDocument.getNumberOfSamples() > 1) { newDir.getMainViewer().getNodeDrawer().setStyle(ProgramProperties.get(MeganProperties.COMPARISON_STYLE, ""), NodeDrawer.Style.PieChart); } newDir.execute("update reprocess=true reInduce=true;collapse rank=" + rank + ";", newDir.getMainViewer().getCommandManager()); } } /** * compute the size of the classification * * @return size */ private float computeSize(Map<Integer, float[]> integerMap) { float size = 0; for (Integer taxonId : integerMap.keySet()) { size += integerMap.get(taxonId)[0]; } return size; } /** * split into single sample tables * * @return single sample tables */ private Map<Integer, float[]>[] sortBySample(int numberOfSamples, Map<Integer, float[]> taxonMap) { Map<Integer, float[]>[] sample2TaxonMap = new HashMap[numberOfSamples]; for (int i = 0; i < numberOfSamples; i++) { sample2TaxonMap[i] = new HashMap<>(); } for (Integer taxId : taxonMap.keySet()) { float[] counts = taxonMap.get(taxId); for (int i = 0; i < numberOfSamples; i++) { sample2TaxonMap[i].put(taxId, new float[]{counts[i]}); } } return sample2TaxonMap; } public void actionPerformed(ActionEvent event) { final String[] ranks = TaxonomicLevels.getAllMajorRanks().toArray(new String[0]); PopupChoice<String> popupChoice = new PopupChoice<>(ranks, null, new CallBack<>() { @Override public void call(String choice) { execute("collapse rank='" + choice + "';project rank='" + choice + "' minPercent=0;"); } }); popupChoice.showAtCurrentMouseLocation(getViewer().getFrame()); } public boolean isApplicable() { return ClassificationManager.isTaxonomy(getViewer().getClassName()) && ((Director) getDir()).getDocument().getNumberOfReads() > 0; } public String getName() { return "Project Assignments To Rank..."; } public String getDescription() { return "Projects all taxonomic assignments onto a given rank"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/New16.gif"); } public boolean isCritical() { return true; } @Override public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()); } }
9,050
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ComputeMatepairLCARanksCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/additional/ComputeMatepairLCARanksCommand.java
/* * ComputeMatepairLCARanksCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.additional; import jloda.graph.Node; import jloda.swing.commands.ICommand; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.viewer.TaxonomicLevels; import megan.viewer.TaxonomyData; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.BufferedReader; import java.io.BufferedWriter; import java.io.FileReader; import java.io.FileWriter; import java.util.HashSet; public class ComputeMatepairLCARanksCommand extends CommandBase implements ICommand { public String getSyntax() { return "mpAnalyzer what={lca-ranks|compare} infile=<filename> outfile=<filename>;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("mpAnalyzer what="); String what = np.getWordMatchesIgnoringCase("lca-ranks compare"); np.matchIgnoreCase("infile="); String infile = np.getWordFileNamePunctuation(); np.matchIgnoreCase("outfile="); String outfile = np.getWordFileNamePunctuation(); np.matchIgnoreCase(";"); int lines = 0; int warnings = 0; try (BufferedReader r = new BufferedReader(new FileReader(infile))) { BufferedWriter w = new BufferedWriter(new FileWriter(outfile)); try { String aLine; while ((aLine = r.readLine()) != null) { String[] tokens = aLine.split("\t"); if (tokens.length != 3) { if (warnings < 10) System.err.println("Skipping line: " + aLine); else if (warnings == 10) System.err.println("..."); warnings++; continue; } if (tokens[0].equals("ReadID")) continue; if (what.charAt(0) == 'l') { // lca-ranks int taxId1 = TaxonomyData.getName2IdMap().get(tokens[1].trim()); int taxId2 = TaxonomyData.getName2IdMap().get(tokens[2].trim()); if (taxId1 <= 0 || taxId2 <= 0) { w.write("NA\n"); lines++; } else { HashSet<Integer> taxIds = new HashSet<>(); taxIds.add(taxId1); taxIds.add(taxId2); Integer taxId = TaxonomyData.getLCA(taxIds, false); int level = 0; while (level == 0) { level = TaxonomyData.getTaxonomicRank(taxId); if (level == 0) { Node v = TaxonomyData.getTree().getANode(taxId); if (v == null || v.getInDegree() == 0) break; v = v.getFirstInEdge().getSource(); taxId = (Integer) v.getInfo(); } } if (level != 0) w.write(TaxonomicLevels.getName(level) + "\n"); else w.write("NA\n"); lines++; } } else // compare { String readId = tokens[0].trim(); String taxonName1 = tokens[1].trim(); String taxonName2 = tokens[2].trim(); int taxId1 = TaxonomyData.getName2IdMap().get(taxonName1); int taxId2 = TaxonomyData.getName2IdMap().get(taxonName2); if (taxId1 <= 0 || taxId2 <= 0) { w.write(readId + "\tNA\tNA\n"); lines++; } else { HashSet<Integer> taxIds = new HashSet<>(); taxIds.add(taxId1); taxIds.add(taxId2); int taxId = TaxonomyData.getLCA(taxIds, true); if (taxId == taxId1 || taxId == taxId2) { w.write(readId + "\t" + TaxonomyData.getName2IdMap().get(taxId) + "\t" + TaxonomyData.getName2IdMap().get(taxId) + "\n"); } else { w.write(readId + "\t" + taxonName1 + "\t" + taxonName2 + "\n"); } lines++; } } } } finally { w.flush(); w.close(); System.err.println("lines wrote: " + lines); } } } public void actionPerformed(ActionEvent event) { } public boolean isApplicable() { return true; } public String getName() { return "MP-Compute"; } public String getDescription() { return "Compute the rank at which the LCA is found for each mate-pair, or preprocess comparison"; } public ImageIcon getIcon() { return null; } public boolean isCritical() { return false; } }
6,241
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
SplitByAttributeCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/additional/SplitByAttributeCommand.java
/* * SplitByAttributeCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.additional; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.FileUtils; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.core.Director; import megan.core.Document; import megan.core.SampleAttributeTable; import javax.swing.*; import java.awt.event.ActionEvent; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; /** * * split by command * * Daniel Huson, 11.2020 */ public class SplitByAttributeCommand extends CommandBase implements ICommand { public String getSyntax() { return "splitBy attribute=<name> [samples=<names>];"; } /** * parses the given command and executes it */ public void apply(NexusStreamParser np) throws Exception { final Document doc = ((Director) getDir()).getDocument(); np.matchIgnoreCase("splitBy attribute="); String attribute = np.getWordRespectCase(); final ArrayList<String> srcSamples = new ArrayList<>(); if (np.peekMatchIgnoreCase("samples")) { srcSamples.addAll(np.getTokensRespectCase("samples=", ";")); } else { srcSamples.addAll(doc.getSampleNames()); np.matchIgnoreCase(";"); } final Map<String, List<String>> tarSample2SrcSamples = new HashMap<>(); for (String sample : srcSamples) { final Object obj = doc.getSampleAttributeTable().get(sample, attribute); if (obj != null) { final String value = StringUtils.toCleanName(obj.toString()); if (value.length() > 0) { final String tarSample =attribute.equals(SampleAttributeTable.SAMPLE_ID) ? value : attribute + "-" + value; tarSample2SrcSamples.computeIfAbsent(tarSample, k -> new ArrayList<>()); tarSample2SrcSamples.get(tarSample).add(sample); } } } final List<String> commands=new ArrayList<>(); if (tarSample2SrcSamples.size() > 0) { for(String tarName:tarSample2SrcSamples.keySet()) { final String fileName = FileUtils.replaceFileSuffix(FileUtils.getFileNameWithoutPath(doc.getMeganFile().getFileName()), "-" + tarName + ".megan"); final List<String> samples = tarSample2SrcSamples.get(tarName); if(samples.size()>0) commands.add(String.format("extract samples='%s' file='%s';", StringUtils.toString(samples, "' '"), fileName)); } } executeImmediately(StringUtils.toString(commands, "\n")); } public void actionPerformed(ActionEvent event) { } public boolean isApplicable() { return true; } public String getName() { return null; } public String getDescription() { return "Splits samples by this attribute and show in new documents"; } public ImageIcon getIcon() { return ResourceManager.getIcon("Compare16.gif"); } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return null; } }
4,021
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
OpenDecontamCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/additional/OpenDecontamCommand.java
/* * OpenDecontamCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.additional; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.util.parse.NexusStreamParser; import megan.core.Director; import megan.fx.dialogs.decontam.DecontamDialog; import megan.util.WindowUtilities; import javax.swing.*; import java.awt.event.ActionEvent; /** * open the decontam viewer * Daniel Huson, 8/2020 */ public class OpenDecontamCommand extends CommandBase implements ICommand { public String getSyntax() { return "open decontam;"; } /** * apply the command */ public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase(getSyntax()); final Director dir = (Director) getDir(); DecontamDialog viewer = (DecontamDialog) dir.getViewerByClass(DecontamDialog.class); if (viewer == null) { viewer = new DecontamDialog(getViewer().getFrame(), dir); dir.addViewer(viewer); } else { WindowUtilities.toFront(viewer); } } public boolean isApplicable() { return ((Director) getDir()).getDocument().getNumberOfReads() > 0; } @Override public void actionPerformed(ActionEvent ev) { execute(getSyntax()); } private static final String NAME = "Decontam..."; public String getName() { return NAME; } public String getDescription() { return "Open the Decontam dialog"; } public ImageIcon getIcon() { return null; } public boolean isCritical() { return true; } @Override public KeyStroke getAcceleratorKey() { return null; } }
2,485
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
CompareByAttributeCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/additional/CompareByAttributeCommand.java
/* * CompareByAttributeCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.additional; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.swing.window.NotificationsInSwing; import jloda.util.FileUtils; import jloda.util.parse.NexusStreamParser; import megan.commands.algorithms.ComputeCoreOrRareBiome; import megan.core.*; import megan.dialogs.compare.Comparer; import megan.main.MeganProperties; import megan.viewer.gui.NodeDrawer; import javax.swing.*; import java.awt.event.ActionEvent; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; /** * * compare by command * * Daniel Huson, 9.2015 */ public class CompareByAttributeCommand extends CommandBase implements ICommand { public String getSyntax() { return "compareBy attribute=<name> [mode={relative|absolute}] [samples=<names>];"; } /** * parses the given command and executes it */ public void apply(NexusStreamParser np) throws Exception { final Document doc = ((Director) getDir()).getDocument(); np.matchIgnoreCase("compareBy attribute="); String attribute = np.getWordRespectCase(); final Comparer.COMPARISON_MODE mode; if (np.peekMatchIgnoreCase("mode")) { np.matchIgnoreCase("mode="); mode = Comparer.COMPARISON_MODE.valueOfIgnoreCase(np.getWordMatchesIgnoringCase("relative absolute")); } else mode = Comparer.COMPARISON_MODE.ABSOLUTE; final ArrayList<String> srcSamples = new ArrayList<>(); if (np.peekMatchIgnoreCase("samples")) { srcSamples.addAll(np.getTokensRespectCase("samples=", ";")); } else { srcSamples.addAll(doc.getSampleNames()); np.matchIgnoreCase(";"); } final Map<String, List<String>> tarSample2SrcSamples = new HashMap<>(); final List<String> tarSamples = new ArrayList<>(); final Map<String, Object> tarSample2Value = new HashMap<>(); for (String sample : srcSamples) { final Object obj = doc.getSampleAttributeTable().get(sample, attribute); if (obj != null) { final String value = obj.toString().trim(); if (value.length() > 0) { final String tarSample = (attribute.equals(SampleAttributeTable.SAMPLE_ID) ? value : attribute + ":" + value); if (tarSample2SrcSamples.get(tarSample) == null) { tarSamples.add(tarSample); tarSample2SrcSamples.put(tarSample, new ArrayList<>()); } tarSample2SrcSamples.get(tarSample).add(sample); tarSample2Value.put(tarSample, value); } } } if (tarSample2SrcSamples.size() > 0) { final String fileName = FileUtils.replaceFileSuffix(doc.getMeganFile().getFileName(), "-" + attribute + ".megan"); final Director newDir = Director.newProject(false); final Document newDocument = newDir.getDocument(); newDocument.getMeganFile().setFile(fileName, MeganFile.Type.MEGAN_SUMMARY_FILE); doc.getProgressListener().setMaximum(srcSamples.size()); doc.getProgressListener().setProgress(0); for (String tarSample : tarSamples) { doc.getProgressListener().setTasks("Comparing samples", tarSample); final List<String> samples = tarSample2SrcSamples.get(tarSample); Map<String, Map<Integer, float[]>> classification2class2counts = new HashMap<>(); final int sampleSize = ComputeCoreOrRareBiome.apply(doc, samples, false, 0, 0, classification2class2counts, doc.getProgressListener()); if (classification2class2counts.size() > 0) { newDocument.addSample(tarSample, sampleSize, 0, doc.getBlastMode(), classification2class2counts); } doc.getProgressListener().incrementProgress(); } // normalize: if (mode == Comparer.COMPARISON_MODE.RELATIVE) { float newSize = Float.MAX_VALUE; float maxSize = 0; for (String tarSample : tarSamples) { newSize = Math.min(newSize, newDocument.getNumberOfReads(tarSample)); maxSize = Math.max(maxSize, newDocument.getNumberOfReads(tarSample)); } if (newSize < maxSize) { double[] factor = new double[tarSamples.size()]; for (int i = 0; i < tarSamples.size(); i++) { String tarSample = tarSamples.get(i); factor[i] = (newSize > 0 ? (double) newSize / (double) newDocument.getNumberOfReads(tarSample) : 0); } final DataTable dataTable = newDocument.getDataTable(); for (String classificationName : dataTable.getClassification2Class2Counts().keySet()) { Map<Integer, float[]> class2counts = dataTable.getClass2Counts(classificationName); for (Integer classId : class2counts.keySet()) { float[] counts = class2counts.get(classId); for (int i = 0; i < counts.length; i++) { counts[i] = (int) Math.round(factor[i] * counts[i]); } } } } newDocument.getDataTable().setParameters("mode=" + Comparer.COMPARISON_MODE.RELATIVE + " normalizedTo=" + newSize); } else newDocument.getDataTable().setParameters("mode=" + Comparer.COMPARISON_MODE.ABSOLUTE); newDocument.getSampleAttributeTable().addAttribute(attribute, tarSample2Value, true); newDocument.setNumberReads(newDocument.getDataTable().getTotalReads()); newDocument.setDirty(true); if (newDocument.getNumberOfSamples() > 1) { newDir.getMainViewer().getNodeDrawer().setStyle(ProgramProperties.get(MeganProperties.COMPARISON_STYLE, ""), NodeDrawer.Style.PieChart); } NotificationsInSwing.showInformation(String.format("Wrote %,d reads to file '%s'", newDocument.getNumberOfReads(), fileName)); newDir.getMainViewer().getFrame().setVisible(true); newDir.getMainViewer().setDoReInduce(true); newDir.getMainViewer().setDoReset(true); newDir.execute("update reprocess=true reinduce=true;", newDir.getMainViewer().getCommandManager()); } } public void actionPerformed(ActionEvent event) { } public boolean isApplicable() { return true; } public String getName() { return null; } public String getDescription() { return "Aggregate samples by this attribute and show comparison in new document"; } public ImageIcon getIcon() { return ResourceManager.getIcon("Compare16.gif"); } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return null; } }
8,114
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportGeneCentricAssemblyCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/additional/ExportGeneCentricAssemblyCommand.java
/* * ExportGeneCentricAssemblyCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.additional; import jloda.fx.util.ProgramExecutorService; import jloda.seq.BlastMode; import jloda.swing.commands.ICommand; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.FastaFileFilter; import jloda.swing.util.ResourceManager; import jloda.swing.window.NotificationsInSwing; import jloda.util.*; import jloda.util.parse.NexusStreamParser; import jloda.util.progress.ProgressListener; import jloda.util.progress.ProgressPercentage; import megan.alignment.AlignmentViewer; import megan.assembly.ReadAssembler; import megan.assembly.ReadDataCollector; import megan.assembly.alignment.AlignmentAssembler; import megan.blastclient.RemoteBlastDialog; import megan.commands.CommandBase; import megan.core.Director; import megan.core.Document; import megan.data.ReadBlockIteratorMaxCount; import megan.viewer.ClassificationViewer; import megan.viewer.ViewerBase; import javax.swing.*; import javax.swing.event.DocumentEvent; import javax.swing.event.DocumentListener; import java.awt.*; import java.awt.event.ActionEvent; import java.io.*; import java.util.HashSet; import java.util.Set; /** * assemble all reads associated with a selected node * Daniel Huson, 5.2015 */ public class ExportGeneCentricAssemblyCommand extends CommandBase implements ICommand { public String getSyntax() { return "export assembly file=<name> [minOverlap=<number>] [minReads=<number>] [minLength=<number>] [minAvCoverage=<number>] [minPercentIdentity=<number>] [maxNumberOfReads=<number>] [showGraph={false|true}];"; } // nt minReads, double minCoverage, int minLength, public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("export assembly"); np.matchIgnoreCase("file="); final String outputFile = np.getWordFileNamePunctuation(); final int minOverlap; if (np.peekMatchIgnoreCase("minOverlap")) { np.matchIgnoreCase("minOverlap="); minOverlap = np.getInt(1, 1000000); } else minOverlap = 20; final int minReads; if (np.peekMatchIgnoreCase("minReads")) { np.matchIgnoreCase("minReads="); minReads = np.getInt(1, 1000000); } else minReads = 2; final int minLength; if (np.peekMatchIgnoreCase("minLength")) { np.matchIgnoreCase("minLength="); minLength = np.getInt(1, 1000000); } else minLength = 0; final float minAvCoverage; if (np.peekMatchIgnoreCase("minAvCoverage") || np.peekMatchIgnoreCase("minCoverage")) { // allow minCoverage for legacy np.matchAnyTokenIgnoreCase("minAvCoverage minCoverage"); np.matchIgnoreCase("="); minAvCoverage = (float) np.getDouble(0, 1000000); } else minAvCoverage = 0; final boolean doOverlapContigs; if (np.peekMatchIgnoreCase("doOverlapContigs")) { np.matchIgnoreCase("doOverlapContigs="); doOverlapContigs = np.getBoolean(); } else doOverlapContigs = true; final int minContigOverlap; if (np.peekMatchIgnoreCase("minContigOverlap")) { np.matchIgnoreCase("minContigOverlap="); minContigOverlap = np.getInt(1, 1000000); } else minContigOverlap = 20; final float maxPercentIdentity; if (np.peekMatchIgnoreCase("minPercentIdentity")) { np.matchIgnoreCase("minPercentIdentity="); maxPercentIdentity = (float) np.getDouble(0, 100); } else maxPercentIdentity = 100; final int maxNumberOfReads; if (np.peekMatchIgnoreCase("maxNumberOfReads")) { np.matchIgnoreCase("maxNumberOfReads="); maxNumberOfReads = np.getInt(-1, Integer.MAX_VALUE); } else maxNumberOfReads = -1; final boolean showGraph; if (np.peekMatchIgnoreCase("showGraph")) { np.matchIgnoreCase("showGraph="); showGraph = np.getBoolean(); } else showGraph = false; np.matchIgnoreCase(";"); // test whether we can write the output file: try (FileWriter w = new FileWriter(outputFile)) { w.write(""); } final Director dir = getDir(); final Document doc = dir.getDocument(); if (doc.getNumberOfReads() == 0 || doc.getMeganFile().isMeganSummaryFile()) throw new IOException("No reads available for assembly"); final ProgressListener progress = (ProgramProperties.isUseGUI() ? doc.getProgressListener() : new ProgressPercentage()); progress.setTasks("Gene-centric assembly", "Initializing"); String message = ""; if (getViewer() instanceof final AlignmentViewer viewer) { final var alignmentAssembler = new AlignmentAssembler(); alignmentAssembler.computeOverlapGraph(minOverlap, viewer.getAlignment(), progress); var count = alignmentAssembler.computeContigs(0, minReads, minAvCoverage, minLength, false, progress); System.err.printf("Number of contigs:%6d%n", count); if (doOverlapContigs) { final int numberOfThreads = ProgramExecutorService.getNumberOfCoresToUse(); count = ReadAssembler.mergeOverlappingContigs(numberOfThreads, progress, maxPercentIdentity, minContigOverlap, alignmentAssembler.getContigs(), true); System.err.printf("Remaining contigs:%6d%n", count); } try (Writer w = new BufferedWriter(new FileWriter(outputFile))) { alignmentAssembler.writeContigs(w, progress); System.err.println("Contigs written to: " + outputFile); message += "Wrote " + count + " contigs\n"; } if (ProgramProperties.isUseGUI()) { if (JOptionPane.showConfirmDialog(null, "BLAST contigs on NCBI?", "Remote BLAST - MEGAN", JOptionPane.YES_NO_CANCEL_OPTION) == JOptionPane.YES_OPTION) { final String commandString = RemoteBlastDialog.apply(getViewer(), getDir(), null, outputFile, "contig"); if (commandString != null) { final Director newDir = Director.newProject(); newDir.getMainViewer().getFrame().setVisible(true); newDir.getMainViewer().setDoReInduce(true); newDir.getMainViewer().setDoReset(true); newDir.executeImmediately(commandString, newDir.getMainViewer().getCommandManager()); } } } if (showGraph) alignmentAssembler.showOverlapGraph(dir, dir.getDocument().getProgressListener()); } else { final ViewerBase viewer = (ViewerBase) getViewer(); if (viewer.getSelectedNodeIds().size() > 0) { final ReadAssembler readAssembler = new ReadAssembler(true); final var it0 = doc.getConnector().getReadsIteratorForListOfClassIds(viewer.getClassName(), viewer.getSelectedNodeIds(), 0, 10, true, true); try (var it = (maxNumberOfReads > 0 ? new ReadBlockIteratorMaxCount(it0, maxNumberOfReads) : it0)) { final var label = viewer.getClassName() + ". Id(s): " + StringUtils.toString(viewer.getSelectedNodeIds(), ", "); final var readData = ReadDataCollector.apply(it, progress); readAssembler.computeOverlapGraph(label, minOverlap, readData, progress); var count = readAssembler.computeContigs(minReads, minAvCoverage, minLength, progress); System.err.printf("Number of contigs:%6d%n", count); if (count == 0) { message = "Could not assemble reads, 0 contigs created."; } else { if (doOverlapContigs) { final int numberOfThreads = ProgramExecutorService.getNumberOfCoresToUse(); count = ReadAssembler.mergeOverlappingContigs(numberOfThreads, progress, maxPercentIdentity, minContigOverlap, readAssembler.getContigs(), true); System.err.printf("Remaining contigs:%6d%n", count); } if (ProgramProperties.get("verbose-assembly", false)) { for (Pair<String, String> contig : readAssembler.getContigs()) { System.err.println(contig.getFirst()); } } try (Writer w = new BufferedWriter(new FileWriter(outputFile))) { readAssembler.writeContigs(w, progress); System.err.println("Contigs written to: " + outputFile); readAssembler.reportContigStats(); message += "Wrote " + count + " contigs\n"; } if (showGraph) readAssembler.showOverlapGraph(dir, progress); if (ProgramProperties.isUseGUI()) { if (JOptionPane.showConfirmDialog(null, "BLAST contigs on NCBI?", "Remote BLAST - MEGAN", JOptionPane.YES_NO_CANCEL_OPTION) == JOptionPane.YES_OPTION) { final String commandString = RemoteBlastDialog.apply(getViewer(), getDir(), null, outputFile, "contig"); if (commandString != null) { final Director newDir = Director.newProject(); newDir.getMainViewer().setDoReInduce(true); newDir.getMainViewer().setDoReset(true); newDir.executeImmediately(commandString, newDir.getMainViewer().getCommandManager()); } } } } } } else { NotificationsInSwing.showWarning(getViewer().getFrame(), "Nothing selected"); } } if (message.length() > 0) NotificationsInSwing.showInformation(getViewer().getFrame(), message); } public void actionPerformed(final ActionEvent event) { final Single<Boolean> askedToOverwrite = new Single<>(false); final Document doc = getDir().getDocument(); final String classificationName = getViewer().getClassName(); final JDialog dialog = new JDialog(getViewer().getFrame()); dialog.setModal(true); dialog.setLocationRelativeTo(getViewer().getFrame()); dialog.setSize(400, 400); dialog.getContentPane().setLayout(new BorderLayout()); final JPanel mainPanel = new JPanel(); mainPanel.setLayout(new BorderLayout()); mainPanel.setBorder(BorderFactory.createEmptyBorder(2, 2, 2, 2)); dialog.getContentPane().add(mainPanel, BorderLayout.CENTER); dialog.setTitle("Assembly for " + classificationName + " - " + ProgramProperties.getProgramName()); final JPanel middlePanel = new JPanel(); middlePanel.setLayout(new BoxLayout(middlePanel, BoxLayout.Y_AXIS)); { final String message; if (getViewer() instanceof AlignmentViewer) message = "Run 'gene-centric assembly' on current alignment"; else message = "Run 'gene-centric assembly' on selected node(s)"; final JPanel messagePanel = newSingleLine(new JLabel(message), Box.createHorizontalGlue()); messagePanel.setBorder(BorderFactory.createEmptyBorder(4, 6, 4, 6)); middlePanel.add(messagePanel); } File lastOpenFile = ProgramProperties.getFile("AssemblyFile"); String fileName = FileUtils.replaceFileSuffix(doc.getMeganFile().getName(), ""); String addOn = null; if (getViewer() instanceof AlignmentViewer) { addOn = StringUtils.toCleanName(((AlignmentViewer) getViewer()).getAlignment().getName()).replaceAll("[_]+", "_"); } else if (getViewer() instanceof ViewerBase) { addOn = getViewer().getClassName().toLowerCase(); final Set<String> labels = new HashSet<>(((ViewerBase) getViewer()).getSelectedNodeLabels(false)); if (labels.size() == 1) addOn += "-" + StringUtils.toCleanName(labels.iterator().next()).replaceAll("[_]+", "_"); } if (addOn != null) { final File file = new File(fileName); final String name = file.getName(); fileName = FileUtils.getFilePath(file.getParent(), FileUtils.replaceFileSuffix(name, "-" + addOn)); } if (lastOpenFile != null) { fileName = new File(lastOpenFile.getParent(), fileName).getPath(); } fileName += "-contigs.fasta"; final JTextField outfile = new JTextField(); outfile.setText(fileName); final JPanel m1 = new JPanel(); m1.setLayout(new BorderLayout()); m1.setBorder(BorderFactory.createEmptyBorder(2, 4, 20, 4)); m1.add(new JLabel("Output file:"), BorderLayout.WEST); m1.add(outfile, BorderLayout.CENTER); outfile.setToolTipText("Set file to save to"); m1.add(new JButton(new AbstractAction("Browse...") { public void actionPerformed(ActionEvent actionEvent) { File file = ChooseFileDialog.chooseFileToSave(getViewer().getFrame(), new File(outfile.getText()), new FastaFileFilter(), new FastaFileFilter(), event, "Save assembly file", ".fasta"); if (file != null) { askedToOverwrite.set(true); outfile.setText(file.getPath()); } } }), BorderLayout.EAST); middlePanel.add(m1); final JPanel parametersPanel = new JPanel(); parametersPanel.setLayout(new BoxLayout(parametersPanel, BoxLayout.Y_AXIS)); mainPanel.add(parametersPanel, BorderLayout.CENTER); final JPanel firstPanel = new JPanel(); firstPanel.setBorder(BorderFactory.createTitledBorder("Read overlapping: ")); firstPanel.setLayout(new GridLayout(4, 2)); parametersPanel.add(firstPanel); final JTextField minOverlapTextField = new JTextField(6); minOverlapTextField.setMaximumSize(new Dimension(100, 20)); minOverlapTextField.setText("" + ProgramProperties.get("AssemblyMinOverlap", 20)); firstPanel.add(newSingleLine(Box.createHorizontalGlue(), new JLabel("Mininum overlap: "))); firstPanel.add(newSingleLine(minOverlapTextField, Box.createHorizontalGlue())); minOverlapTextField.setToolTipText("Minimum length of exact overlap between two reads"); final JTextField minReadsTextField = new JTextField(6); minReadsTextField.setMaximumSize(new Dimension(100, 20)); minReadsTextField.setText("" + ProgramProperties.get("AssemblyMinReads", 5)); firstPanel.add(newSingleLine(Box.createHorizontalGlue(), new JLabel("Minimum reads: "))); firstPanel.add(newSingleLine(minReadsTextField, Box.createHorizontalGlue())); minReadsTextField.setToolTipText("Minimum number of reads in a contig"); final JTextField minLengthTextField = new JTextField(6); minLengthTextField.setMaximumSize(new Dimension(100, 20)); minLengthTextField.setText("" + ProgramProperties.get("AssemblyMinLength", 200)); firstPanel.add(newSingleLine(Box.createHorizontalGlue(), new JLabel("Minimum length: "))); firstPanel.add(newSingleLine(minLengthTextField, Box.createHorizontalGlue())); minLengthTextField.setToolTipText("Minimum contig length"); final JTextField minAvCoverageTextField = new JTextField(6); minAvCoverageTextField.setMaximumSize(new Dimension(100, 20)); minAvCoverageTextField.setText("" + ProgramProperties.get("AssemblyMinAvCoverage", 2)); firstPanel.add(newSingleLine(Box.createHorizontalGlue(), new JLabel("Min average coverage: "))); firstPanel.add(newSingleLine(minAvCoverageTextField, Box.createHorizontalGlue())); minAvCoverageTextField.setToolTipText("Minimum average coverage of a contig"); final JPanel secondPanel = new JPanel(); secondPanel.setBorder(BorderFactory.createTitledBorder("Contig overlapping: ")); secondPanel.setLayout(new GridLayout(3, 2)); parametersPanel.add(secondPanel); final JCheckBox doContigOverlappingCBOX = new JCheckBox(); doContigOverlappingCBOX.setToolTipText("Perform all pairwise alignments of contigs to detect overlaps"); doContigOverlappingCBOX.setSelected(ProgramProperties.get("AssemblyDoOverlapContigs", true)); secondPanel.add(newSingleLine(Box.createHorizontalGlue(), new JLabel("Contig Overlapping:"))); secondPanel.add(newSingleLine(doContigOverlappingCBOX, Box.createHorizontalGlue())); final JTextField minContigOverlapTextField = new JTextField(6); minContigOverlapTextField.setMaximumSize(new Dimension(100, 20)); minContigOverlapTextField.setText("" + ProgramProperties.get("AssemblyMinContigOverlap", 20)); secondPanel.add(newSingleLine(Box.createHorizontalGlue(), new JLabel("Min contig overlap:"))); secondPanel.add(newSingleLine(minContigOverlapTextField, Box.createHorizontalGlue())); minContigOverlapTextField.setToolTipText("Minimum length overlap between two contigs"); final JTextField minPercentIdentityTextField = new JTextField(6); minPercentIdentityTextField.setMaximumSize(new Dimension(100, 20)); minPercentIdentityTextField.setText("" + ProgramProperties.get("AssemblyMinPercentIdentity", 99)); secondPanel.add(newSingleLine(Box.createHorizontalGlue(), new JLabel("Min percent identity:"))); secondPanel.add(newSingleLine(minPercentIdentityTextField, Box.createHorizontalGlue())); minPercentIdentityTextField.setToolTipText("Minimum percent identity to overlap two contigs"); middlePanel.add(parametersPanel); mainPanel.add(middlePanel, BorderLayout.NORTH); JPanel bottomPanel = new JPanel(); bottomPanel.setBorder(BorderFactory.createEtchedBorder()); bottomPanel.setLayout(new BorderLayout()); JPanel b1 = new JPanel(); b1.setLayout(new BoxLayout(b1, BoxLayout.X_AXIS)); b1.add(new JButton(new AbstractAction("Cancel") { public void actionPerformed(ActionEvent actionEvent) { dialog.setVisible(false); } })); final JButton applyButton = new JButton(new AbstractAction("Apply") { public void actionPerformed(ActionEvent actionEvent) { String fileName = (new File(outfile.getText().trim())).getPath(); if (fileName.length() > 0) { if (FileUtils.getFileSuffix(fileName) == null) fileName = FileUtils.replaceFileSuffix(fileName, ".fasta"); if (!askedToOverwrite.get() && (new File(fileName)).exists()) { switch (JOptionPane.showConfirmDialog(getViewer().getFrame(), "File already exists, do you want to replace it?", "File exists", JOptionPane.YES_NO_CANCEL_OPTION)) { case JOptionPane.CANCEL_OPTION: // close and abort dialog.setVisible(false); return; case JOptionPane.NO_OPTION: // don't close return; default: // close and continue } } dialog.setVisible(false); ProgramProperties.put("AssemblyFile", fileName); ProgramProperties.put("AssemblyMinOverlap", minOverlapTextField.getText()); ProgramProperties.put("AssemblyMinReads", minReadsTextField.getText()); ProgramProperties.put("AssemblyMinLength", minLengthTextField.getText()); ProgramProperties.put("AssemblyMinAvCoverage", minAvCoverageTextField.getText()); ProgramProperties.put("AssemblyDoOverlapContigs", doContigOverlappingCBOX.isSelected()); ProgramProperties.put("AssemblyMinContigOverlap", minContigOverlapTextField.getText()); ProgramProperties.put("AssemblyMinPercentIdentity", minPercentIdentityTextField.getText()); final String command = "export assembly file='" + fileName + "'" + " minOverlap=" + minOverlapTextField.getText() + " minReads=" + minReadsTextField.getText() + " minLength=" + minLengthTextField.getText() + " minAvCoverage=" + minAvCoverageTextField.getText() + " doOverlapContigs=" + doContigOverlappingCBOX.isSelected() + " minContigOverlap=" + minContigOverlapTextField.getText() + " minPercentIdentity=" + minPercentIdentityTextField.getText() + " showGraph=false;"; execute(command); } } }); b1.add(applyButton); dialog.getRootPane().setDefaultButton(applyButton); bottomPanel.add(b1, BorderLayout.EAST); mainPanel.add(bottomPanel, BorderLayout.SOUTH); dialog.getContentPane().setLayout(new BorderLayout()); dialog.getContentPane().add(mainPanel, BorderLayout.CENTER); dialog.validate(); outfile.getDocument().addDocumentListener(new DocumentListener() { @Override public void insertUpdate(DocumentEvent e) { applyButton.setEnabled(outfile.getText().trim().length() > 0); } @Override public void removeUpdate(DocumentEvent e) { insertUpdate(e); } @Override public void changedUpdate(DocumentEvent e) { insertUpdate(e); } }); dialog.setVisible(true); } private static JPanel newSingleLine(Component left, Component right) { final JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.X_AXIS)); panel.add(left); panel.add(right); return panel; } public boolean isApplicable() { final Document doc = getDir().getDocument(); return (getViewer() instanceof AlignmentViewer && ((AlignmentViewer) getViewer()).getAlignment().getLength() > 0) || (getViewer() instanceof ClassificationViewer && ((ClassificationViewer) getViewer()).getNumberSelectedNodes() > 0 && doc.getMeganFile().hasDataConnector() && doc.getBlastMode().equals(BlastMode.BlastX)); } public String getName() { return "Gene-Centric Assembly..."; } public String getDescription() { return "Compute and export 'gene-centric' assembly of reads for all selected nodes.\n" + "Huson et al, Protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads. J. Microbiome, 2017"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public boolean isCritical() { return true; } }
24,181
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ExportOverlapGraphCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/additional/ExportOverlapGraphCommand.java
/* * ExportOverlapGraphCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.additional; import jloda.seq.BlastMode; import jloda.swing.commands.ICommand; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.swing.util.TextFileFilter; import jloda.swing.window.NotificationsInSwing; import jloda.util.FileUtils; import jloda.util.Pair; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.assembly.ReadAssembler; import megan.assembly.ReadData; import megan.assembly.ReadDataCollector; import megan.commands.CommandBase; import megan.core.Director; import megan.core.Document; import megan.data.IReadBlockIterator; import megan.viewer.ClassificationViewer; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.BufferedWriter; import java.io.File; import java.io.FileWriter; import java.io.Writer; import java.util.List; /** * assemble all reads associated with a selected node * Daniel Huson, 5.2015 */ public class ExportOverlapGraphCommand extends CommandBase implements ICommand { public String getSyntax() { return "export overlapGraph file=<name> [minOverlap=<number>] [showGraph={false|true}];"; } // nt minReads, double minCoverage, int minLength, public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("export overlapGraph file="); final String overlapGraphFile = np.getWordFileNamePunctuation(); final int minOverlap; if (np.peekMatchIgnoreCase("minOverlap")) { np.matchIgnoreCase("minOverlap="); minOverlap = np.getInt(1, 1000000); } else minOverlap = ProgramProperties.get("AssemblyMinOverlap", 20); boolean showGraph = false; if (np.peekMatchIgnoreCase("showGraph")) { np.matchIgnoreCase("showGraph="); showGraph = np.getBoolean(); } np.matchIgnoreCase(";"); final Director dir = getDir(); final Document doc = dir.getDocument(); final ClassificationViewer viewer = (ClassificationViewer) getViewer(); String message = ""; if (viewer.getSelectedNodeIds().size() > 0) { final ReadAssembler readAssembler = new ReadAssembler(true); try (IReadBlockIterator it = doc.getConnector().getReadsIteratorForListOfClassIds(viewer.getClassName(), viewer.getSelectedNodeIds(), 0, 10, true, true)) { final String label = viewer.getClassName() + ". Id(s): " + StringUtils.toString(viewer.getSelectedNodeIds(), ", "); final List<ReadData> readData = ReadDataCollector.apply(it, doc.getProgressListener()); readAssembler.computeOverlapGraph(label, minOverlap, readData, doc.getProgressListener()); if (overlapGraphFile != null) { try (final Writer w = new BufferedWriter(new FileWriter(overlapGraphFile))) { Pair<Integer, Integer> counts = readAssembler.writeOverlapGraph(w); System.err.println("Graph written to: " + overlapGraphFile); message = "Wrote " + counts.getFirst() + " nodes and " + counts.getSecond() + " edges"; } } if (showGraph) readAssembler.showOverlapGraph(dir, doc.getProgressListener()); } } else message = "Nothing selected"; if (message.length() > 0) { NotificationsInSwing.showInformation(getViewer().getFrame(), message); } } public void actionPerformed(ActionEvent event) { final Document doc = getDir().getDocument(); File lastOpenFile = ProgramProperties.getFile("OverlapGraphFile"); String fileName = doc.getMeganFile().getName(); if (fileName == null) fileName = "Untitled"; else fileName = StringUtils.toCleanName(fileName); if (lastOpenFile != null) { fileName = new File(lastOpenFile.getParent(), fileName).getPath(); } fileName = FileUtils.replaceFileSuffix(fileName, "-overlap.gml"); File file = ChooseFileDialog.chooseFileToSave(getViewer().getFrame(), new File(fileName), new TextFileFilter(".gml"), new TextFileFilter(".gml"), event, "Save overlap graph", ".gml"); if (file != null) { if (FileUtils.getFileSuffix(file.getName()) == null) file = FileUtils.replaceFileSuffix(file, ".gml"); ProgramProperties.put("OverlapGraphFile", file); execute("export overlapGraph file='" + file.getPath() + "' minOverlap=" + ProgramProperties.get("AssemblyMinOverlap", 20) + " showGraph=false;"); } } public boolean isApplicable() { final Document doc = getDir().getDocument(); return getViewer() instanceof ClassificationViewer && ((ClassificationViewer) getViewer()).getNumberSelectedNodes() > 0 && doc.getMeganFile().hasDataConnector() && doc.getBlastMode().equals(BlastMode.BlastX); } public String getName() { return "Overlap Graph..."; } public String getDescription() { return "Build and export the overlap graph for selected nodes"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Export16.gif"); } public boolean isCritical() { return true; } }
6,147
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
CorrelateClassToAttributeCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/additional/CorrelateClassToAttributeCommand.java
/* * CorrelateClassToAttributeCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.additional; import jloda.graph.Node; import jloda.graph.NodeData; import jloda.swing.commands.ICommand; import jloda.swing.util.ProgramProperties; import jloda.util.NumberUtils; import jloda.util.parse.NexusStreamParser; import megan.classification.ClassificationManager; import megan.classification.data.Name2IdMap; import megan.commands.CommandBase; import megan.viewer.ClassificationViewer; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.IOException; import java.util.ArrayList; import java.util.Collection; public class CorrelateClassToAttributeCommand extends CommandBase implements ICommand { public String getSyntax() { return "correlate class={name|number ...} classification={name} attribute={name} ;"; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("correlate class="); ArrayList<String> labels = new ArrayList<>(); while (!np.peekMatchIgnoreCase("classification")) { labels.add(np.getWordRespectCase()); } np.matchIgnoreCase("classification="); String classificationName = np.getWordRespectCase(); np.matchIgnoreCase("attribute="); String attribute = np.getWordRespectCase(); np.matchIgnoreCase(";"); final ClassificationViewer viewer = (ClassificationViewer) getDir().getViewerByClassName(classificationName); final Name2IdMap name2IdMap = ClassificationManager.get(classificationName, false).getName2IdMap(); final String[] sampleNames = getDoc().getSampleNamesAsArray(); final int n = sampleNames.length; for (String label : labels) { final int id = (NumberUtils.isInteger(label) ? NumberUtils.parseInt(label) : name2IdMap.get(label)); final String name = (NumberUtils.isInteger(label) ? name2IdMap.get(id) : label); if (id != 0) { final Node v = viewer.getANode(id); final NodeData nodeData = (NodeData) v.getData(); final float[] x = (v.getOutDegree() == 0 ? nodeData.getSummarized() : nodeData.getAssigned()); final double[] y = new double[n]; for (int i = 0; i < n; i++) { Object obj = getDoc().getSampleAttributeTable().get(sampleNames[i], attribute); if (obj instanceof Number) y[i] = ((Number) obj).doubleValue(); else throw new IOException("Attribute '" + attribute + "': has non-numerical value: " + obj); } System.out.println("Sample\t'" + name + "'\t'" + attribute + "':"); for (int i = 0; i < n; i++) { System.err.printf("%s\t%f\t%f%n", sampleNames[i], x[i], y[i]); } System.err.println("Correlation coefficient: " + computeCorrelationCoefficient(x, y, n)); } } } /** * computes the correlation coefficient * */ private double computeCorrelationCoefficient(float[] x, double[] y, int n) { double sumX = 0; double sumY = 0; double sumXY = 0; double sumX2 = 0; double sumY2 = 0; for (int i = 0; i < n; i++) { sumX += x[i]; sumY += y[i]; sumXY += x[i] * y[i]; sumX2 += x[i] * x[i]; sumY2 += y[i] * y[i]; } final double bottom = Math.sqrt((n * sumX2 - sumX * sumX) * (n * sumY2 - sumY * sumY)); if (bottom == 0) return 0; final double top = n * sumXY - sumX * sumY; return top / bottom; } public void actionPerformed(ActionEvent event) { final Collection<String> list = getDoc().getSampleAttributeTable().getNumericalAttributes(); final ClassificationViewer viewer = (ClassificationViewer) getViewer(); final Collection<Integer> ids = viewer.getSelectedNodeIds(); if (ids.size() > 0 && list.size() > 0) { final String[] choices = list.toArray(new String[0]); String choice = ProgramProperties.get("CorrelateToAttribute", choices[0]); if (!list.contains(choice)) choice = choices[0]; choice = (String) JOptionPane.showInputDialog(getViewer().getFrame(), "Choose attribute to correlate to:", "Compute Correlation Coefficient", JOptionPane.QUESTION_MESSAGE, ProgramProperties.getProgramIcon(), choices, choice); if (choice != null) { ProgramProperties.put("CorrelateToAttribute", choice); StringBuilder buf = new StringBuilder(); buf.append("correlate class="); for (Integer id : ids) { buf.append(" ").append(id); } buf.append(" classification='").append(viewer.getClassName()).append("' attribute='").append(choice).append("';"); executeImmediately("show window=message;"); execute(buf.toString()); } } } public boolean isApplicable() { return getViewer() instanceof ClassificationViewer && ((ClassificationViewer) getViewer()).getNumberSelectedNodes() > 0 && getDoc().getNumberOfSamples() > 0 && getDoc().getSampleAttributeTable().getNumberOfAttributes() > 0; } public String getName() { return "Correlate To Attributes..."; } public String getDescription() { return "Correlate assigned (or summarized) counts for nodes with a selected attribute"; } public ImageIcon getIcon() { return null; } public boolean isCritical() { return true; } }
6,554
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
PasteCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/clipboard/PasteCommand.java
/* * PasteCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.clipboard; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import javax.swing.*; import javax.swing.text.DefaultEditorKit; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; public class PasteCommand extends ClipboardBase implements ICommand { public String getSyntax() { return null; } public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { Action action = findAction(DefaultEditorKit.pasteAction); if (action != null) action.actionPerformed(event); } public boolean isApplicable() { return true; } public String getName() { return "Paste"; } public String getDescription() { return "Paste"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Paste16.gif"); } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()); } }
2,013
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
CopyEdgeLabelCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/clipboard/CopyEdgeLabelCommand.java
/* * CopyEdgeLabelCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.clipboard; import jloda.graph.Edge; import jloda.swing.commands.ICommand; import jloda.swing.graphview.GraphView; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import javax.swing.*; import java.awt.*; import java.awt.datatransfer.StringSelection; import java.awt.event.ActionEvent; public class CopyEdgeLabelCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { GraphView viewer = (GraphView) getViewer(); StringBuilder buf = new StringBuilder(); boolean first = true; for (Edge e : viewer.getSelectedEdges()) { String label = viewer.getLabel(e); if (label != null) { if (first) first = false; else buf.append(" "); buf.append(label); } } if (buf.toString().length() > 0) { StringSelection selection = new StringSelection(buf.toString()); Toolkit.getDefaultToolkit().getSystemClipboard().setContents(selection, null); } } public boolean isApplicable() { return ((GraphView) getViewer()).getSelectedEdges().size() > 0; } public String getName() { return "Copy Edge Label"; } public String getDescription() { return "Copy the edge label"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Copy16.gif"); } public boolean isCritical() { return false; } }
2,539
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
ClipboardBase.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/clipboard/ClipboardBase.java
/* * ClipboardBase.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.clipboard; import jloda.swing.util.ResourceManager; import megan.commands.CommandBase; import javax.swing.*; import javax.swing.text.DefaultEditorKit; import java.awt.*; import java.awt.event.KeyEvent; /** * base for cut, copy and paste * Daniel Huson, 11.2010 */ public abstract class ClipboardBase extends CommandBase { // need an instance to get default textComponent Actions static private DefaultEditorKit kit; /** * find the action * * @return action */ static protected Action findAction(String name) { if (kit == null) kit = new DefaultEditorKit(); Action[] actions = kit.getActions(); for (int i = 0; i < kit.getActions().length; i++) { Action action = actions[i]; if (action.getValue(AbstractAction.NAME).equals(name)) return action; } return null; } static public Action getCutDefaultKit() { Action action = findAction(DefaultEditorKit.cutAction); if (action == null) return null; action.putValue(Action.ACCELERATOR_KEY, KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx())); action.putValue(Action.SHORT_DESCRIPTION, "Cut"); action.putValue(AbstractAction.SMALL_ICON, ResourceManager.getIcon("sun/Cut16.gif")); return action; } static public Action getCopyDefaultKit() { Action action = findAction(DefaultEditorKit.copyAction); if (action == null) return null; action.putValue(Action.ACCELERATOR_KEY, KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx())); action.putValue(Action.SHORT_DESCRIPTION, "Copy"); action.putValue(AbstractAction.SMALL_ICON, ResourceManager.getIcon("sun/Copy16.gif")); return action; } static public Action getPasteDefaultKit() { Action action = findAction(DefaultEditorKit.pasteAction); if (action == null) return null; action.putValue(Action.ACCELERATOR_KEY, KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx())); action.putValue(Action.SHORT_DESCRIPTION, "Paste"); action.putValue(AbstractAction.SMALL_ICON, ResourceManager.getIcon("sun/Paste16.gif")); return action; } static public Action getSelectAllDefaultEditorKit() { Action action = findAction(DefaultEditorKit.selectAllAction); if (action == null) return null; action.putValue(Action.ACCELERATOR_KEY, KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx())); action.putValue(Action.SHORT_DESCRIPTION, "Select All"); return action; } }
3,664
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
CopyCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/clipboard/CopyCommand.java
/* * CopyCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.clipboard; import jloda.swing.commands.ICommand; import jloda.swing.director.IDirectableViewer; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.viewer.ViewerBase; import javax.swing.*; import javax.swing.text.DefaultEditorKit; import java.awt.*; import java.awt.datatransfer.StringSelection; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; public class CopyCommand extends ClipboardBase implements ICommand { public String getSyntax() { return null; } public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { IDirectableViewer viewer = getViewer(); if (viewer instanceof ViewerBase) { ViewerBase graphView = (ViewerBase) viewer; if (graphView.getSelectedNodes().size() > 0) { StringBuilder buf = new StringBuilder(); boolean first = true; for (String label : graphView.getSelectedNodeLabels(true)) { if (label != null) { if (first) first = false; else buf.append("\n"); buf.append(label); } } if (buf.toString().length() > 0) { StringSelection selection = new StringSelection(buf.toString()); Toolkit.getDefaultToolkit().getSystemClipboard().setContents(selection, null); return; } } } Action action = findAction(DefaultEditorKit.copyAction); if (action != null) action.actionPerformed(event); } public boolean isApplicable() { return true; } public String getName() { return "Copy"; } public String getDescription() { return "Copy"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Copy16.gif"); } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()); } }
3,093
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
CutCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/clipboard/CutCommand.java
/* * CutCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.clipboard; import jloda.swing.commands.ICommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import javax.swing.*; import javax.swing.text.DefaultEditorKit; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; public class CutCommand extends ClipboardBase implements ICommand { public String getSyntax() { return null; } public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { Action action = findAction(DefaultEditorKit.cutAction); if (action != null) action.actionPerformed(event); } public boolean isApplicable() { return true; } public String getName() { return "Cut"; } public String getDescription() { return "Cut"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Cut16.gif"); } public boolean isCritical() { return true; } public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()); } }
2,001
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
CopyNodeLabelCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/clipboard/CopyNodeLabelCommand.java
/* * CopyNodeLabelCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.clipboard; import jloda.swing.commands.ICommand; import jloda.swing.graphview.GraphView; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.viewer.ViewerBase; import javax.swing.*; import java.awt.*; import java.awt.datatransfer.StringSelection; import java.awt.event.ActionEvent; public class CopyNodeLabelCommand extends CommandBase implements ICommand { public String getSyntax() { return null; } public void apply(NexusStreamParser np) { } public void actionPerformed(ActionEvent event) { ViewerBase viewer = (ViewerBase) getViewer(); StringBuilder buf = new StringBuilder(); boolean first = true; for (String label : viewer.getSelectedNodeLabels(true)) { if (label != null) { if (first) first = false; else buf.append(" "); buf.append(label); } } if (buf.toString().length() > 0) { StringSelection selection = new StringSelection(buf.toString()); Toolkit.getDefaultToolkit().getSystemClipboard().setContents(selection, null); } } public boolean isApplicable() { return getViewer() instanceof GraphView && ((GraphView) getViewer()).getSelectedNodes().size() > 0; } public String getName() { return "Copy Node Label"; } public String getDescription() { return "Copy the node label"; } public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Copy16.gif"); } public boolean isCritical() { return false; } }
2,553
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
FindCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/find/FindCommand.java
/* * FindCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.find; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICheckBoxCommand; import jloda.swing.director.IViewerWithFindToolBar; import jloda.swing.util.ResourceManager; import jloda.swing.window.NotificationsInSwing; import jloda.util.parse.NexusStreamParser; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; /** * Open the Find dialog * Daniel Huson, 7 2010 */ public class FindCommand extends CommandBase implements ICheckBoxCommand { public boolean isSelected() { return getViewer() instanceof IViewerWithFindToolBar && ((IViewerWithFindToolBar) getViewer()).isShowFindToolBar(); } /** * get the name to be used as a menu label * * @return name */ public String getName() { return "Find..."; } /** * get description to be used as a tooltip * * @return description */ public String getDescription() { return "Open the find toolbar"; } /** * get icon to be used in menu or button * * @return icon */ public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Find16.gif"); } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()); } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("show findToolbar="); boolean show = np.getBoolean(); np.matchIgnoreCase(";"); if (getViewer() instanceof IViewerWithFindToolBar) { IViewerWithFindToolBar viewer = (IViewerWithFindToolBar) getViewer(); if (show) { if (!viewer.getSearchManager().getFindDialogAsToolBar().isEnabled()) viewer.setShowFindToolBar(true); else viewer.getSearchManager().getFindDialogAsToolBar().setEnabled(true); // refocus } else viewer.setShowFindToolBar(false); } else { NotificationsInSwing.showWarning(getViewer().getFrame(), "Find not implemented for this type of window"); } } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * get command-line usage description * * @return usage */ @Override public String getSyntax() { return "show findToolbar={true|false};"; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return getViewer() instanceof IViewerWithFindToolBar; } /** * action to be performed * */ @Override public void actionPerformed(ActionEvent ev) { execute("show findToolbar=true;"); } }
4,034
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
FindAgainCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/find/FindAgainCommand.java
/* * FindAgainCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.find; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICommand; import jloda.swing.director.IViewerWithFindToolBar; import jloda.swing.find.SearchManager; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; /** * Find again * Daniel Huson, 7 2010 */ public class FindAgainCommand extends CommandBase implements ICommand { /** * get the name to be used as a menu label * * @return name */ public String getName() { return "Find Again"; } /** * get description to be used as a tooltip * * @return description */ public String getDescription() { return "Find the next occurrence"; } /** * get icon to be used in menu or button * * @return icon */ public ImageIcon getIcon() { return ResourceManager.getIcon("sun/FindAgain16.gif"); } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()); } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) { } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * get command-line usage description * * @return usage */ @Override public String getSyntax() { return null; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return getViewer() instanceof IViewerWithFindToolBar && ((IViewerWithFindToolBar) getViewer()).isShowFindToolBar(); } /** * action to be performed * */ @Override public void actionPerformed(ActionEvent ev) { SearchManager searchManager = ((IViewerWithFindToolBar) getViewer()).getSearchManager(); if (searchManager != null) searchManager.applyFindNext(); } }
3,238
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
DrawCirclesCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/compare/DrawCirclesCommand.java
/* * DrawCirclesCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.compare; import jloda.swing.commands.ICheckBoxCommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.viewer.ViewerBase; import megan.viewer.gui.NodeDrawer; import javax.swing.*; import java.awt.event.ActionEvent; public class DrawCirclesCommand extends CommandBase implements ICheckBoxCommand { public boolean isSelected() { ViewerBase viewer = (ViewerBase) getViewer(); return viewer != null && viewer.getNodeDrawer().getStyle() == NodeDrawer.Style.Circle; } public String getSyntax() { return null; } public void actionPerformed(ActionEvent event) { execute("set nodeDrawer=" + NodeDrawer.Style.Circle + ";"); } public String getName() { return "Draw Circles"; } public ImageIcon getIcon() { return ResourceManager.getIcon("Circle16.gif"); } public String getDescription() { return "Draw data as circles"; } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return getDoc().getNumberOfReads() > 0; } /** * parses the given command and executes it */ public void apply(NexusStreamParser np) { } }
2,420
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
DrawMetersCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/compare/DrawMetersCommand.java
/* * DrawMetersCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.compare; import jloda.swing.commands.ICheckBoxCommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.viewer.ViewerBase; import megan.viewer.gui.NodeDrawer; import javax.swing.*; import java.awt.event.ActionEvent; public class DrawMetersCommand extends CommandBase implements ICheckBoxCommand { public boolean isSelected() { ViewerBase viewer = (ViewerBase) getViewer(); return viewer != null && viewer.getNodeDrawer().getStyle() == NodeDrawer.Style.BarChart; } public String getSyntax() { return null; } public void actionPerformed(ActionEvent event) { execute("set nodeDrawer=" + NodeDrawer.Style.BarChart + ";"); } public String getName() { return "Draw Bars"; } public ImageIcon getIcon() { return ResourceManager.getIcon("Meters16.gif"); } public String getDescription() { return "Draw nodes as bars"; } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return getDoc().getNumberOfReads() > 0; } /** * parses the given command and executes it */ public void apply(NexusStreamParser np) { } }
2,416
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
DrawPieChartsCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/compare/DrawPieChartsCommand.java
/* * DrawPieChartsCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.compare; import jloda.swing.commands.ICheckBoxCommand; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.core.Document; import megan.main.MeganProperties; import megan.viewer.ViewerBase; import megan.viewer.gui.NodeDrawer; import javax.swing.*; import java.awt.event.ActionEvent; public class DrawPieChartsCommand extends CommandBase implements ICheckBoxCommand { public boolean isSelected() { ViewerBase viewer = (ViewerBase) getViewer(); return viewer != null && viewer.getNodeDrawer().getStyle() == NodeDrawer.Style.PieChart; } public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("set nodeDrawer="); final ViewerBase viewer = (ViewerBase) getViewer(); final Document doc = getDoc(); final String style = np.getWordMatchesIgnoringCase(StringUtils.toString(NodeDrawer.Style.values(), " ")); np.matchIgnoreCase(";"); viewer.getNodeDrawer().setStyle(style, NodeDrawer.Style.Circle); viewer.getLegendPanel().setStyle(viewer.getNodeDrawer().getStyle()); doc.setDirty(true); if (doc.getNumberOfSamples() > 1) ProgramProperties.put(MeganProperties.COMPARISON_STYLE, style); viewer.repaint(); } public String getSyntax() { return "set nodeDrawer={" + StringUtils.toString(NodeDrawer.ScaleBy.values(), "|") + "};"; } public void actionPerformed(ActionEvent event) { execute("set nodeDrawer=" + NodeDrawer.Style.PieChart + ";"); } public String getName() { return "Draw Pies"; } public ImageIcon getIcon() { return ResourceManager.getIcon("PieChart16.gif"); } public String getDescription() { return "Draw data as pie charts"; } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return getDoc().getNumberOfReads() > 0; } }
3,205
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
DrawHeatMapCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/compare/DrawHeatMapCommand.java
/* * DrawHeatMapCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.compare; import jloda.swing.commands.ICheckBoxCommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.viewer.ViewerBase; import megan.viewer.gui.NodeDrawer; import javax.swing.*; import java.awt.event.ActionEvent; public class DrawHeatMapCommand extends CommandBase implements ICheckBoxCommand { public boolean isSelected() { ViewerBase viewer = (ViewerBase) getViewer(); return viewer != null && viewer.getNodeDrawer().getStyle() == NodeDrawer.Style.HeatMap; } public String getSyntax() { return null; } public void actionPerformed(ActionEvent event) { execute("set nodeDrawer=" + NodeDrawer.Style.HeatMap + ";"); } public String getName() { return "Draw Heatmaps"; } public ImageIcon getIcon() { return ResourceManager.getIcon("HeatMap16.gif"); } public String getDescription() { return "Draw data as heat maps"; } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return getDoc().getNumberOfReads() > 0; } /** * parses the given command and executes it */ public void apply(NexusStreamParser np) { } }
2,424
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
DrawCoxCombsCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/compare/DrawCoxCombsCommand.java
/* * DrawCoxCombsCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.compare; import jloda.swing.commands.CommandBase; import jloda.swing.commands.ICheckBoxCommand; import jloda.swing.util.ResourceManager; import jloda.util.parse.NexusStreamParser; import megan.core.Director; import megan.viewer.ViewerBase; import megan.viewer.gui.NodeDrawer; import javax.swing.*; import java.awt.event.ActionEvent; public class DrawCoxCombsCommand extends CommandBase implements ICheckBoxCommand { public boolean isSelected() { ViewerBase viewer = (ViewerBase) getViewer(); return viewer != null && viewer.getNodeDrawer().getStyle() == NodeDrawer.Style.CoxComb; } public String getSyntax() { return null; } public void actionPerformed(ActionEvent event) { execute("set nodeDrawer=" + NodeDrawer.Style.CoxComb + ";"); } public String getName() { return "Draw Coxcombs"; } public ImageIcon getIcon() { return ResourceManager.getIcon("Coxcomb16.gif"); } public String getDescription() { return "Draw data as coxcombs"; } public boolean isApplicable() { return ((Director) getDir()).getDocument().getNumberOfReads() > 0 && ((Director) getDir()).getDocument().getNumberOfSamples() > 1; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) { } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } }
2,591
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
UseDefaultTaxonomyFileCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/load/UseDefaultTaxonomyFileCommand.java
/* * UseDefaultTaxonomyFileCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.load; import jloda.swing.commands.ICommand; import jloda.swing.director.ProjectManager; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.core.Director; import javax.swing.*; import java.awt.event.ActionEvent; /** * load command * Daniel Huson, 11.2010 */ public class UseDefaultTaxonomyFileCommand extends CommandBase implements ICommand { public static final String NAME="Use Default NCBI Taxonomy"; /** * get the name to be used as a menu label * * @return name */ public String getName() { return NAME; } /** * get description to be used as a tooltip * * @return description */ public String getDescription() { return "Open default NCBI taxonomy"; } /** * get icon to be used in menu or button * * @return icon */ public ImageIcon getIcon() { return null; } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) { } /** * action to be performed * */ public void actionPerformed(ActionEvent ev) { execute("load taxonomyFile=ncbi.tre mapfile=ncbi.map;collapse level=2;"); } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return ProjectManager.getNumberOfProjects() == 1 && ((Director) ProjectManager.getProjects().get(0)).getDocument().getNumberOfSamples() == 0; } /** * get command-line usage description * * @return usage */ @Override public String getSyntax() { return null; } }
2,997
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
LoadAlternativeTaxonomyFileCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/load/LoadAlternativeTaxonomyFileCommand.java
/* * LoadAlternativeTaxonomyFileCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.load; import jloda.swing.commands.ICommand; import jloda.swing.director.ProjectManager; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.swing.util.TextFileFilter; import jloda.util.FileUtils; import jloda.util.parse.NexusStreamParser; import megan.commands.CommandBase; import megan.core.Director; import megan.main.MeganProperties; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.File; /** * load command * Daniel Huson, 11.2010 */ public class LoadAlternativeTaxonomyFileCommand extends CommandBase implements ICommand { /** * get the name to be used as a menu label * * @return name */ public String getName() { return "Use Alternative Taxonomy..."; } /** * get description to be used as a tooltip * * @return description */ public String getDescription() { return "Open alternative taxonomy.tre and taxonomy.map files"; } /** * get icon to be used in menu or button * * @return icon */ public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Open16.gif"); } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) { } /** * action to be performed * */ public void actionPerformed(ActionEvent ev) { File lastOpenFile = ProgramProperties.getFile(MeganProperties.TAXONOMYFILE); getDir().notifyLockInput(); File file = ChooseFileDialog.chooseFileToOpen(getViewer().getFrame(), lastOpenFile, new TextFileFilter("tre"), new TextFileFilter("tre"), ev, "Open Tree File"); getDir().notifyUnlockInput(); if (file != null && file.exists() && file.canRead()) { ProgramProperties.put(MeganProperties.TAXONOMYFILE, file.getAbsolutePath()); String mappingFile = FileUtils.replaceFileSuffix(file.getPath(), ".map"); if (!(new File(mappingFile)).exists()) { mappingFile = null; } StringBuilder buf = new StringBuilder(); buf.append("load taxonomyFile='").append(file.getPath()).append("'"); if (mappingFile != null) buf.append(" mapFile='").append(mappingFile).append("';"); else buf.append(";"); buf.append("collapse level=2;"); execute(buf.toString()); } } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return ProjectManager.getNumberOfProjects() == 1 && ((Director) ProjectManager.getProjects().get(0)).getDocument().getNumberOfSamples() == 0; } /** * get command-line usage description * * @return usage */ @Override public String getSyntax() { return null; } }
4,251
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
AddClassificationCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/load/AddClassificationCommand.java
/* * AddClassificationCommand.java Copyright (C) 2022. Daniel H. Huson * * No usage, copying or distribution without explicit permission. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. * */ package megan.commands.load; import jloda.swing.commands.CommandBase; import jloda.swing.commands.CommandManager; import jloda.swing.commands.ICommand; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.swing.util.TextFileFilter; import jloda.swing.window.NotificationsInSwing; import jloda.util.FileUtils; import jloda.util.StringUtils; import jloda.util.parse.NexusStreamParser; import megan.main.MeganProperties; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; /** * add classification command * Daniel Huson, 4.2021 */ public class AddClassificationCommand extends CommandBase implements ICommand { public AddClassificationCommand() { } /** * constructor */ public AddClassificationCommand(CommandManager commandManager) { super(commandManager); } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("addClassification file="); var treeFileName = np.getWordFileNamePunctuation(); np.matchWordIgnoreCase(";"); if (!(treeFileName.endsWith(".tre"))) throw new IOException("addClassification: file must have suffix .tre"); if (!FileUtils.fileExistsAndIsNonEmpty(treeFileName)) throw new IOException("addClassification: specified .tre file does not exist or is empty"); var mapFile = FileUtils.replaceFileSuffixKeepGZ(treeFileName, ".map"); if (!FileUtils.fileExistsAndIsNonEmpty(mapFile)) throw new IOException("addClassification: corresponding .map file does not exist or is empty"); var addedClassificationFiles = Arrays.asList(ProgramProperties.get(MeganProperties.ADDITION_CLASSIFICATION_FILES, new String[0])); var treeFile = new File(treeFileName); var found = false; for (var other : addedClassificationFiles) { if (treeFile.equals(new File(other))) { found = true; NotificationsInSwing.showWarning("Classification has already been added, no action will be taken"); break; } } if (!found) { addedClassificationFiles = new ArrayList<>(addedClassificationFiles); addedClassificationFiles.add(0, treeFileName); ProgramProperties.put(MeganProperties.ADDITION_CLASSIFICATION_FILES, addedClassificationFiles.toArray(new String[0])); System.err.println("All added classification files: " + StringUtils.toString(addedClassificationFiles, ", ")); NotificationsInSwing.showInformation("Classification file has been added, restart MEGAN to use"); } } /** * get the name to be used as a menu label * * @return name */ public String getName() { return "Add Classification..."; } /** * get description to be used as a tooltip * * @return description */ public String getDescription() { return "Adds a classification to MEGAN"; } /** * get icon to be used in menu or button * * @return icon */ public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Import16.gif"); } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } /** * action to be performed * */ public void actionPerformed(ActionEvent ev) { var addedClassificationFiles = Arrays.asList(ProgramProperties.get(MeganProperties.ADDITION_CLASSIFICATION_FILES, new String[0])); var lastOpenFile = (addedClassificationFiles.size() > 0 ? new File(addedClassificationFiles.get(0)) : null); File file = ChooseFileDialog.chooseFileToOpen(getViewer().getFrame(), lastOpenFile, new TextFileFilter("tre", false), new TextFileFilter("tre", false), ev, "Open Classification Tree File"); if (file != null) { executeImmediately("addClassification file='" + file.getPath() + "';"); } } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return true; } /** * get command-line usage description * * @return usage */ @Override public String getSyntax() { return "addClassification file=<file-name>;"; } }
4,762
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z
LoadTaxonomyFileCommand.java
/FileExtraction/Java_unseen/husonlab_megan-ce/src/megan/commands/load/LoadTaxonomyFileCommand.java
/* * LoadTaxonomyFileCommand.java Copyright (C) 2024 Daniel H. Huson * * (Some files contain contributions from other authors, who are then mentioned separately.) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package megan.commands.load; import jloda.graph.Node; import jloda.swing.commands.ICommand; import jloda.swing.director.ProjectManager; import jloda.swing.util.ChooseFileDialog; import jloda.swing.util.ProgramProperties; import jloda.swing.util.ResourceManager; import jloda.swing.util.TextFileFilter; import jloda.util.FileUtils; import jloda.util.parse.NexusStreamParser; import megan.classification.Classification; import megan.classification.ClassificationManager; import megan.commands.CommandBase; import megan.core.Director; import megan.core.Document; import megan.main.MeganProperties; import megan.viewer.TaxonomyData; import javax.swing.*; import java.awt.event.ActionEvent; import java.io.File; /** * load command * Daniel Huson, 11.2010 */ public class LoadTaxonomyFileCommand extends CommandBase implements ICommand { /** * get the name to be used as a menu label * * @return name */ public String getName() { return "Load Taxonomy..."; } /** * get description to be used as a tooltip * * @return description */ public String getDescription() { return "Load taxonomy.tre and taxonomy.map files"; } /** * get icon to be used in menu or button * * @return icon */ public ImageIcon getIcon() { return ResourceManager.getIcon("sun/Open16.gif"); } /** * gets the accelerator key to be used in menu * * @return accelerator key */ public KeyStroke getAcceleratorKey() { return null; } /** * parses the given command and executes it */ @Override public void apply(NexusStreamParser np) throws Exception { np.matchIgnoreCase("load taxonomyFile="); String treeFile = np.getWordFileNamePunctuation(); String mapFile = null; if (np.peekMatchAnyTokenIgnoreCase("mapFile")) { np.matchIgnoreCase("mapFile="); mapFile = np.getWordFileNamePunctuation(); } np.matchIgnoreCase(";"); if (mapFile == null) mapFile = FileUtils.replaceFileSuffix(treeFile, ".map"); final Classification classification = ClassificationManager.load(Classification.Taxonomy, treeFile, mapFile, getDoc().getProgressListener()); TaxonomyData.ensureDisabledTaxaInitialized(); Node v = classification.getFullTree().getRoot(); if (v != null && (Integer) v.getInfo() == 0) { v.setInfo(1); classification.getFullTree().addId2Node(0, null); classification.getFullTree().addId2Node(1, v); classification.getIdMapper().getName2IdMap().put("Root", 1); } ProgramProperties.put(MeganProperties.TAXONOMYFILE, treeFile); Document.loadVersionInfo("Taxonomy", treeFile); } /** * action to be performed * */ public void actionPerformed(ActionEvent ev) { File lastOpenFile = ProgramProperties.getFile(MeganProperties.TAXONOMYFILE); getDir().notifyLockInput(); File file = ChooseFileDialog.chooseFileToOpen(getViewer().getFrame(), lastOpenFile, new TextFileFilter("tre"), new TextFileFilter("tre"), ev, "Open Tree File"); getDir().notifyUnlockInput(); if (file != null && file.exists() && file.canRead()) { ProgramProperties.put(MeganProperties.TAXONOMYFILE, file.getAbsolutePath()); String mappingFile = FileUtils.replaceFileSuffix(file.getPath(), ".map"); if (!(new File(mappingFile)).exists()) { mappingFile = null; } StringBuilder buf = new StringBuilder(); buf.append("load taxonomyFile='").append(file.getPath()).append("'"); if (mappingFile != null) buf.append(" mapFile='").append(mappingFile).append("';"); else buf.append(";"); buf.append("collapse level=2;"); execute(buf.toString()); } } /** * is this a critical command that can only be executed when no other command is running? * * @return true, if critical */ public boolean isCritical() { return true; } /** * is the command currently applicable? Used to set enable state of command * * @return true, if command can be applied */ public boolean isApplicable() { return ProjectManager.getNumberOfProjects() == 1 && ((Director) ProjectManager.getProjects().get(0)).getDocument().getNumberOfSamples() == 0; } /** * get command-line usage description * * @return usage */ @Override public String getSyntax() { return "load taxonomyFile=<filename> [mapFile=<filename>];"; } }
5,559
Java
.java
husonlab/megan-ce
62
21
18
2016-05-09T10:55:38Z
2024-02-22T23:23:42Z