Vector *IntronSupportingEvidenceAdaptor_listLinkedTranscriptIds(IntronSupportingEvidenceAdaptor *isea, IntronSupportingEvidence *ise) {
char qStr[1024];
sprintf(qStr,"SELECT transcript_id from transcript_intron_supporting_evidence "
"WHERE intron_supporting_evidence_id = "IDFMTSTR, IntronSupportingEvidence_getDbID(ise));
StatementHandle *sth = isea->prepare((BaseAdaptor *)isea,qStr,strlen(qStr));
sth->execute(sth);
Vector *idVec = Vector_new();
ResultRow *row;
while ((row = sth->fetchRow(sth))) {
IDType id = row->getLongLongAt(row, 0);
IDType *idP;
if ((idP = calloc(1,sizeof(IDType))) == NULL) {
fprintf(stderr, "Failed allocating space for a id\n");
exit(1);
}
*idP = id;
Vector_addElement(idVec, idP);
}
sth->finish(sth);
Vector_setFreeFunc(idVec, free);
return idVec;
}
/*
=head2 fetch_all_by_Transcript
Arg[1] : Bio::EnsEMBL::Transcript Transcript to search with
Example : my $ises = $isea->fetch_all_by_Transcript($transcript);
Description : Uses the given Transcript to search for all instances of
IntronSupportingEvidence linked to the transcript in the
database
Returntype : ArrayRef of IntronSupportingEvidence objects
Exceptions : Thrown if arguments are not as stated and for DB errors
=cut
*/
Vector *IntronSupportingEvidenceAdaptor_fetchAllByTranscript(IntronSupportingEvidenceAdaptor *isea, Transcript *transcript) {
char qStr[1024];
sprintf(qStr,"SELECT intron_supporting_evidence_id "
"FROM transcript_intron_supporting_evidence "
"WHERE transcript_id = "IDFMTSTR, Transcript_getDbID(transcript));
StatementHandle *sth = isea->prepare((BaseAdaptor *)isea,qStr,strlen(qStr));
sth->execute(sth);
Vector *idVec = Vector_new();
ResultRow *row;
while ((row = sth->fetchRow(sth))) {
IDType id = row->getLongLongAt(row, 0);
IDType *idP;
if ((idP = calloc(1,sizeof(IDType))) == NULL) {
fprintf(stderr, "Failed allocating space for a id\n");
exit(1);
}
*idP = id;
Vector_addElement(idVec, idP);
}
sth->finish(sth);
Vector *out;
if (Vector_getNumElement(idVec) > 0) {
out = IntronSupportingEvidenceAdaptor_fetchAllByDbIDList(isea, idVec, NULL);
} else {
out = Vector_new();
}
// Free ids vector
Vector_setFreeFunc(idVec, free);
Vector_free(idVec);
return out;
}
Vector *PredictionTranscriptAdaptor_fetchAllBySlice(PredictionTranscriptAdaptor *pta, Slice *slice, char *logicName, int loadExons) {
//my $transcripts = $self->SUPER::fetch_all_by_Slice($slice,$logic_name);
Vector *transcripts = BaseFeatureAdaptor_fetchAllBySlice((BaseFeatureAdaptor *)pta, slice, logicName);
// if there are 0 or 1 transcripts still do lazy-loading
if ( ! loadExons || Vector_getNumElement(transcripts) < 2 ) {
return transcripts;
}
// preload all of the exons now, instead of lazy loading later
// faster than 1 query per transcript
// get extent of region spanned by transcripts
long minStart = 2000000000;
long maxEnd = -2000000000;
int i;
for (i=0; i<Vector_getNumElement(transcripts); i++) {
PredictionTranscript *t = Vector_getElementAt(transcripts, i);
if (PredictionTranscript_getSeqRegionStart((SeqFeature*)t) < minStart) {
minStart = PredictionTranscript_getSeqRegionStart((SeqFeature*)t);
}
if (PredictionTranscript_getSeqRegionEnd((SeqFeature*)t) > maxEnd) {
maxEnd = PredictionTranscript_getSeqRegionEnd((SeqFeature*)t);
}
}
Slice *extSlice;
if (minStart >= Slice_getStart(slice) && maxEnd <= Slice_getEnd(slice)) {
extSlice = slice;
} else {
SliceAdaptor *sa = DBAdaptor_getSliceAdaptor(pta->dba);
extSlice = SliceAdaptor_fetchByRegion(sa, Slice_getCoordSystemName(slice), Slice_getSeqRegionName(slice),
minStart, maxEnd, Slice_getStrand(slice), CoordSystem_getVersion(Slice_getCoordSystem(slice)), 0);
}
// associate exon identifiers with transcripts
IDHash *trHash = IDHash_new(IDHASH_MEDIUM);
for (i=0; i<Vector_getNumElement(transcripts); i++) {
PredictionTranscript *t = Vector_getElementAt(transcripts, i);
if ( ! IDHash_contains(trHash, PredictionTranscript_getDbID(t))) {
IDHash_add(trHash, PredictionTranscript_getDbID(t), t);
}
}
IDType *uniqueIds = IDHash_getKeys(trHash);
char tmpStr[1024];
char *qStr = NULL;
if ((qStr = (char *)calloc(655500,sizeof(char))) == NULL) {
fprintf(stderr,"Failed allocating qStr\n");
return transcripts;
}
int lenNum;
int endPoint = sprintf(qStr, "SELECT prediction_transcript_id, prediction_exon_id, exon_rank FROM prediction_exon WHERE prediction_transcript_id IN (");
for (i=0; i<IDHash_getNumValues(trHash); i++) {
if (i!=0) {
qStr[endPoint++] = ',';
qStr[endPoint++] = ' ';
}
lenNum = sprintf(tmpStr,IDFMTSTR,uniqueIds[i]);
memcpy(&(qStr[endPoint]), tmpStr, lenNum);
endPoint+=lenNum;
}
qStr[endPoint++] = ')';
qStr[endPoint] = '\0';
free(uniqueIds);
StatementHandle *sth = pta->prepare((BaseAdaptor *)pta,qStr,strlen(qStr));
sth->execute(sth);
IDHash *exTrHash = IDHash_new(IDHASH_MEDIUM);
ResultRow *row;
while ((row = sth->fetchRow(sth))) {
IDType trId = row->getLongLongAt(row,0);
IDType exId = row->getLongLongAt(row,1);
int rank = row->getIntAt(row,2);
if (! IDHash_contains(exTrHash, exId)) {
Vector *vec = Vector_new();
Vector_setFreeFunc(vec, PredictionTranscriptRankPair_free);
IDHash_add(exTrHash, exId, vec);
}
Vector *exVec = IDHash_getValue(exTrHash, exId);
PredictionTranscriptRankPair *trp = PredictionTranscriptRankPair_new(IDHash_getValue(trHash, trId), rank);
Vector_addElement(exVec, trp);
}
IDHash_free(trHash, NULL);
sth->finish(sth);
PredictionExonAdaptor *pea = DBAdaptor_getPredictionExonAdaptor(pta->dba);
Vector *exons = PredictionExonAdaptor_fetchAllBySlice(pea, extSlice);
// move exons onto transcript slice, and add them to transcripts
for (i=0; i<Vector_getNumElement(exons); i++) {
PredictionExon *ex = Vector_getElementAt(exons, i);
// Perl didn't have this line - it was in GeneAdaptor version so I think I'm going to keep it
if (!IDHash_contains(exTrHash, PredictionExon_getDbID(ex))) continue;
PredictionExon *newEx;
if (slice != extSlice) {
newEx = (PredictionExon*)PredictionExon_transfer((SeqFeature*)ex, slice);
if (newEx == NULL) {
fprintf(stderr, "Unexpected. Exon could not be transferred onto PredictionTranscript slice.\n");
exit(1);
}
} else {
newEx = ex;
}
Vector *exVec = IDHash_getValue(exTrHash, PredictionExon_getDbID(newEx));
int j;
for (j=0; j<Vector_getNumElement(exVec); j++) {
PredictionTranscriptRankPair *trp = Vector_getElementAt(exVec, j);
PredictionTranscript_addExon(trp->transcript, newEx, &trp->rank);
}
}
IDHash_free(exTrHash, Vector_free);
free(qStr);
return transcripts;
}
