// This method was a mess - tidied and rearranged
IDType IntronSupportingEvidenceAdaptor_store(IntronSupportingEvidenceAdaptor *isea, IntronSupportingEvidence *sf) {
if (sf == NULL) {
fprintf(stderr,"sf is NULL in IntronSupportingEvidenceAdaptor_store\n");
exit(1);
}
Class_assertType(CLASS_INTRONSUPPORTINGEVIDENCE, sf->objectType);
DBAdaptor *db = isea->dba;
AnalysisAdaptor *analysisAdaptor = DBAdaptor_getAnalysisAdaptor(db);
if (IntronSupportingEvidence_isStored(sf, db)) {
fprintf(stderr,"ISE already stored\n");
return IntronSupportingEvidence_getDbID(sf);
}
Analysis *analysis = IntronSupportingEvidence_getAnalysis(sf);
if (!Analysis_isStored(analysis, db)) {
AnalysisAdaptor_store(analysisAdaptor, analysis);
}
IDType analysisId = Analysis_getDbID(analysis);
// Think the above is equivalent to this horror
//my $analysis_id = $analysis->is_stored($db) ? $analysis->dbID() : $db->get_AnalysisAdaptor()->store($analysis);
/* No transfer (see GeneAdaptor for why)
my $seq_region_id;
($sf, $seq_region_id) = $self->_pre_store($sf);
*/
IDType seqRegionId = BaseFeatureAdaptor_preStore((BaseFeatureAdaptor *)isea, (SeqFeature*)sf);
char qStr[1024];
sprintf(qStr, "INSERT IGNORE INTO intron_supporting_evidence "
"(analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_name, score, score_type, is_splice_canonical) "
"VALUES ("IDFMTSTR","IDFMTSTR",%ld,%ld,%d,'%s',%f,'%s',%d)",
analysisId,
seqRegionId,
IntronSupportingEvidence_getSeqRegionStart((SeqFeature*)sf),
IntronSupportingEvidence_getSeqRegionEnd((SeqFeature*)sf),
IntronSupportingEvidence_getSeqRegionStrand((SeqFeature*)sf),
IntronSupportingEvidence_getHitName(sf),
IntronSupportingEvidence_getScore(sf),
IntronSupportingEvidence_getScoreType(sf),
IntronSupportingEvidence_getIsSpliceCanonical(sf));
StatementHandle *sth = isea->prepare((BaseAdaptor *)isea,qStr,strlen(qStr));
sth->execute(sth);
IDType sfId = sth->getInsertId(sth);
sth->finish(sth);
if (!sfId) {
sprintf(qStr,"SELECT intron_supporting_evidence_id "
"FROM intron_supporting_evidence "
"WHERE analysis_id = "IDFMTSTR
" AND seq_region_id = "IDFMTSTR
" AND seq_region_start = %ld"
" AND seq_region_end = %ld"
" AND seq_region_strand = %d"
" AND hit_name = '%s'",
analysisId,
seqRegionId,
IntronSupportingEvidence_getSeqRegionStart((SeqFeature*)sf),
IntronSupportingEvidence_getSeqRegionEnd((SeqFeature*)sf),
IntronSupportingEvidence_getSeqRegionStrand((SeqFeature*)sf),
IntronSupportingEvidence_getHitName(sf));
sth = isea->prepare((BaseAdaptor *)isea,qStr,strlen(qStr));
sth->execute(sth);
if (sth->numRows(sth) > 0) {
ResultRow *row = sth->fetchRow(sth);
sfId = row->getLongLongAt(row, 0);
}
sth->finish(sth);
}
IntronSupportingEvidence_setAdaptor((SeqFeature*)sf, (BaseAdaptor*)isea);
IntronSupportingEvidence_setDbID(sf, sfId);
return IntronSupportingEvidence_getDbID(sf);
}
int dumpGenes(Vector *genes, int withSupport) {
FILE *fp = stderr;
int i;
int failed = 0;
for (i=0;i<Vector_getNumElement(genes) && !failed;i++) {
Gene *g = Vector_getElementAt(genes,i);
fprintf(fp,"Gene %s (%s) coords: %ld %ld %d\n",Gene_getStableId(g),(Gene_getDisplayXref(g) ? DBEntry_getDisplayId(Gene_getDisplayXref(g)) : ""),Gene_getStart(g),Gene_getEnd(g),Gene_getStrand(g));
int j;
for (j=0;j<Gene_getTranscriptCount(g);j++) {
Transcript *t = Gene_getTranscriptAt(g,j);
int k;
fprintf(fp," Trans %s coords: %ld %ld %d biotype: %s\n",Transcript_getStableId(t), Transcript_getStart(t),Transcript_getEnd(t),Transcript_getStrand(t),Transcript_getBiotype(t));
if (withSupport) {
Vector *support = Transcript_getAllSupportingFeatures(t);
for (k=0; k<Vector_getNumElement(support); k++) {
BaseAlignFeature *baf = Vector_getElementAt(support, k);
fprintf(fp," support %s coords: %ld %ld %d\n", BaseAlignFeature_getHitSeqName(baf), BaseAlignFeature_getStart(baf), BaseAlignFeature_getEnd(baf), BaseAlignFeature_getStrand(baf));
}
Vector *intronSupport = Transcript_getAllIntronSupportingEvidence(t);
for (k=0; k<Vector_getNumElement(intronSupport); k++) {
IntronSupportingEvidence *ise = Vector_getElementAt(intronSupport, k);
fprintf(fp," intron support %s coords: %ld %ld %d\n", IntronSupportingEvidence_getHitName(ise), IntronSupportingEvidence_getStart(ise), IntronSupportingEvidence_getEnd(ise), IntronSupportingEvidence_getStrand(ise));
}
}
for (k=0;k<Transcript_getExonCount(t);k++) {
Exon *e = Transcript_getExonAt(t,k);
fprintf(fp," exon %s (%p) coords: %ld %ld %d\n",Exon_getStableId(e), e, Exon_getStart(e), Exon_getEnd(e), Exon_getStrand(e));
if (withSupport) {
Vector *support = Exon_getAllSupportingFeatures(e);
int m;
for (m=0; m<Vector_getNumElement(support); m++) {
BaseAlignFeature *baf = Vector_getElementAt(support, m);
fprintf(fp," support %s coords: %ld %ld %d\n", BaseAlignFeature_getHitSeqName(baf), BaseAlignFeature_getStart(baf), BaseAlignFeature_getEnd(baf), BaseAlignFeature_getStrand(baf));
}
}
}
Translation *tln = Transcript_getTranslation(t);
if (tln) {
fprintf(fp," translation id: %s %s %d %s %d\n",Translation_getStableId(tln),
Exon_getStableId(Translation_getStartExon(tln)), Translation_getStart(tln),
Exon_getStableId(Translation_getEndExon(tln)), Translation_getEnd(tln));
char *tSeq = Transcript_translate(t);
fprintf(fp," translation: %s\n",tSeq);
free(tSeq);
Vector *tlnAttribs = Translation_getAllAttributes(tln, NULL);
if (Vector_getNumElement(tlnAttribs)) {
fprintf(fp, " translation attributes:\n");
int n;
for (n=0; n<Vector_getNumElement(tlnAttribs); n++) {
Attribute *attrib = Vector_getElementAt(tlnAttribs, n);
fprintf(fp, " code %s name %s desc %s value %s\n",
Attribute_getCode(attrib),
Attribute_getName(attrib),
Attribute_getDescription(attrib),
Attribute_getValue(attrib));
}
}
}
}
}
return failed;
}