int DBEntryAdaptor_fetchAllByTranscript(DBEntryAdaptor *dbea, Transcript *trans) {
char qStr[512];
StatementHandle *sth;
ResultRow *row;
Vector *transLinks;
int i;
sprintf(qStr,
"SELECT t.canonical_translation_id"
" FROM transcript t"
" WHERE t.transcript_id = " IDFMTSTR,
Transcript_getDbID(trans));
sth = dbea->prepare((BaseAdaptor *)dbea,qStr,strlen(qStr));
sth->execute(sth);
//
// Did this to be consistent with fetch_by_Gene, but don't like
// it (filling in the object). I think returning the array would
// be better. Oh well. EB
//
while ((row = sth->fetchRow(sth))) {
IDType translationId = row->getLongLongAt(row,0);
Vector *translatLinks = DBEntryAdaptor_fetchByObjectType(dbea, translationId,"Translation");
for (i=0;i<Vector_getNumElement(translatLinks); i++) {
Transcript_addDBLink(trans,Vector_getElementAt(translatLinks,i));
}
Vector_free(translatLinks);
}
sth->finish(sth);
transLinks = DBEntryAdaptor_fetchByObjectType(dbea, Transcript_getDbID(trans),"Transcript");
fprintf(stderr,"transLinks\n");
for (i=0;i<Vector_getNumElement(transLinks); i++) {
Transcript_addDBLink(trans,Vector_getElementAt(transLinks,i));
}
Vector_free(transLinks);
return 1;
}
Vector *AttributeAdaptor_fetchAllByTranscript(AttributeAdaptor *ata, Transcript *transcript, char *code) {
Vector *result = NULL;
if (transcript == NULL) {
fprintf(stderr,"Error: NULL Transcript in AttributeAdaptor_fetchAllByTranscript\n");
} else {
char *type = "transcript";
char *table = "transcript";
IDType id = Transcript_getDbID(transcript);
result = AttributeAdaptor_doFetchAllByTypeAndTableAndID(ata, type, table, id, code);
}
return result;
}
/*
=head2 store_transcript_linkage
Arg[1] : Bio::EnsEMBL::IntronSupportingEvidence Evidence to link
Arg[2] : Bio::EnsEMBL::Transcript Transcript to link
Arg[3] : Integer an optional ID to give if the Transcript's own ID is possibly incorrect
Example : $isea->store_transcript_linkage($ise, $transcript);
$isea->store_transcript_linkage($ise, $transcript, $tid);
Description : Links a Transcript to a portion of Intron evidence
Returntype : None
Exceptions : Thrown if the given object is not a Transcript, if the
transcript is not stored, if the supporting evidence is not
stored and for any DB exception.
=cut
*/
void IntronSupportingEvidenceAdaptor_storeTranscriptLinkage(IntronSupportingEvidenceAdaptor *isea,
IntronSupportingEvidence *sf,
Transcript *transcript,
IDType transcriptId) {
if (sf == NULL || transcript == NULL) {
fprintf(stderr,"sf or transcript is NULL in IntronSupportingEvidenceAdaptor_storeTranscriptLinkage\n");
exit(1);
}
Class_assertType(CLASS_INTRONSUPPORTINGEVIDENCE, sf->objectType);
Class_assertType(CLASS_TRANSCRIPT, transcript->objectType);
if (! IntronSupportingEvidence_isStored(sf, isea->dba)) {
fprintf(stderr,"Cannot perform the link. The IntronSupportingEvidence must be persisted first\n");
exit(1);
}
// Moved up so can use in sprintf
Intron *intron = IntronSupportingEvidence_getIntron(sf, transcript);
Exon *prevExon = Intron_getPrevExon(intron);
Exon *nextExon = Intron_getNextExon(intron);
if (!transcriptId) {
transcriptId = Transcript_getDbID(transcript);
}
char qStr[1024];
sprintf(qStr, "INSERT IGNORE INTO transcript_intron_supporting_evidence "
"(transcript_id, intron_supporting_evidence_id, previous_exon_id, next_exon_id) "
"VALUES ("IDFMTSTR","IDFMTSTR","IDFMTSTR","IDFMTSTR")",
transcriptId, IntronSupportingEvidence_getDbID(sf), Exon_getDbID(prevExon), Exon_getDbID(nextExon));
StatementHandle *sth = isea->prepare((BaseAdaptor *)isea,qStr,strlen(qStr));
sth->execute(sth);
sth->finish(sth);
Intron_free(intron);
return;
}
/*
=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;
}
// Switch to passing two element array to fill in as an argument, so don't have to allocate it
IDType *IntronSupportingEvidenceAdaptor_fetchFlankingExonIds(IntronSupportingEvidenceAdaptor *isea, IntronSupportingEvidence *ise, Transcript *transcript, IDType *flanks) {
char qStr[1024];
sprintf(qStr,"SELECT previous_exon_id, next_exon_id "
"FROM transcript_intron_supporting_evidence "
"WHERE transcript_id ="IDFMTSTR" and intron_supporting_evidence_id ="IDFMTSTR,
Transcript_getDbID(transcript), IntronSupportingEvidence_getDbID(ise));
StatementHandle *sth = isea->prepare((BaseAdaptor *)isea,qStr,strlen(qStr));
sth->execute(sth);
if (sth->numRows(sth) == 0) {
return NULL;
}
ResultRow *row = sth->fetchRow(sth);
flanks[0] = row->getLongLongAt(row, 0);
flanks[1] = row->getLongLongAt(row, 1);
sth->finish(sth);
return flanks;
}
