/*
# _store_type
*/
IDType AttributeAdaptor_storeType(AttributeAdaptor *ata, Attribute *attrib) {
char qStr[1024];
sprintf(qStr,"INSERT IGNORE INTO attrib_type set code = '%s', name = '%s', description = '%s'",
Attribute_getCode(attrib),
Attribute_getName(attrib),
Attribute_getDescription(attrib));
StatementHandle *sth1 = ata->prepare((BaseAdaptor *)ata,qStr,strlen(qStr));
// Not sure if this returns the num rows!
int rowsInserted = sth1->execute(sth1);
IDType atId = sth1->getInsertId(sth1);
if (rowsInserted == 0) {
// the insert failed because the code is already stored
sprintf(qStr,"SELECT attrib_type_id FROM attrib_type WHERE code = '%s'", Attribute_getCode(attrib));
StatementHandle *sth2 = ata->prepare((BaseAdaptor *)ata,qStr,strlen(qStr));
sth2->execute(sth2);
if (sth2->numRows(sth2) == 0) {
atId = 0;
} else {
ResultRow *row = sth2->fetchRow(sth2);
atId = row->getLongLongAt(row, 0);
}
if (!atId) {
fprintf(stderr, "Could not store or fetch attrib_type code [%s]\n"
"Wrong database user/permissions?\n", Attribute_getCode(attrib));
return 0;
}
sth2->finish(sth2);
}
sth1->finish(sth1);
// fprintf(stderr, "atId in end is "IDFMTSTR"\n", atId);
return atId;
}
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;
}
