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MIN12352
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codeparrot

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nodeA->rightmergeable = nodeB->rightmergeable;
break;
case MERGEABLE_RIGHTSIDE_A_EQUALS_B:
/* ...-------
...------- */
if (!nodeA->rightmergeable || !nodeB->rightmergeable)
nodeA->rightmergeable = false;
break;
case MERGEABLE_RIGHTSIDE_A_AFTER_B:
/* ...-------
...-----[
nothing to do */
break;
case NON_MERGEABLE_RIGHTSIDE:
default: gt_assert(0);
}
}
/*
The following function merges the exon nodes <nodeA> and
<nodeB>. That is, <nodeA> is modified to the merged node and
<nodeB> stays the same.
*/
static void mergenodes(Exonnode *nodeA, Exonnode *nodeB)
{
unsigned long i;
gt_assert(nodesaremergeable(nodeA, nodeB));
/* merge nodes */
mergeleftside(nodeA, nodeB);
mergerightside(nodeA, nodeB);
/* merge successor introns */
if (nodeA->successorintron == NULL && nodeB->successorintron != NULL) {
/* save successor intron of node B in node A */
nodeA->successorintron = nodeB->successorintron;
}
/* in the cases that (nodeA==NULL && nodeB==NULL) and that
(nodeA!=NULL && nodeB==NULL) nothing has to be done */
/* merge the exonscores */
for (i = 0; i < gt_array_size(nodeB->exonscores); i++) {
gt_array_add(nodeA->exonscores,
*(Exonscoreinfo*) gt_array_get(nodeB->exonscores, i));
}
}
static GthDbl computeexonscore(Exonnode *node)
{
unsigned long i, maxlength = 0;
GthDbl maxscore = DBL_MIN;
Exonscoreinfo *exonscoreinfo;
/* compute maximal length */
for (i = 0; i < gt_array_size(node->exonscores); i++) {
exonscoreinfo = gt_array_get(node->exonscores, i);
if (exonscoreinfo->lengthofscoringexon > maxlength)
maxlength = exonscoreinfo->lengthofscoringexon;
}
/* save exonscore */
for (i = 0; i < gt_array_size(node->exonscores); i++) {
exonscoreinfo = gt_array_get(node->exonscores, i);
if ((exonscoreinfo->lengthofscoringexon
+ SAVE_EXONSCORE_ALLOWED_DIFFERENCE >= maxlength) &&
(exonscoreinfo->exonscore > maxscore)) {
maxscore = exonscoreinfo->exonscore;
}
}
return maxscore;
}
static void addSAtoAGS(GthAGS *ags, GthSACluster *sacluster, GtArray *nodes)
{
unsigned long i, currentnode = 0, currentexon = 0,
numofexons = gth_sa_num_of_exons(sacluster->representative);
Exonnode node;
/* genomic strands equal */
gt_assert(gth_ags_is_forward(ags) ==
gth_sa_gen_strand_forward(sacluster->representative));
/* set genomic id */
if (!ags->gen_id)
ags->gen_id = gt_str_ref(gth_sa_gen_id_str(sacluster->representative));
#ifndef NDEBUG
else {
/* genomic ids equal */
gt_assert(!gt_str_cmp(ags->gen_id,
gth_sa_gen_id_str(sacluster->representative)));
}
#endif
/* save SA pointers */
gt_array_add(ags->alignments, sacluster->representative);
for (i = 0; i < gt_array_size(sacluster->members); i++) {
gt_array_add(ags->alignments, *(GthSA**)