DBEntry *DBEntryAdaptor_fetchByDbID(DBEntryAdaptor *dbea, IDType dbID) {
char qStr[512];
StatementHandle *sth;
ResultRow *row;
DBEntry *dbe = NULL;
sprintf(qStr,
"SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label,"
" xref.version, xref.description,"
" exDB.db_name, exDB.db_release, es.synonym"
" FROM (xref, external_db exDB)"
" LEFT JOIN external_synonym es on es.xref_id = xref.xref_id"
" WHERE xref.xref_id = " IDFMTSTR
" AND xref.external_db_id = exDB.external_db_id",
dbID);
sth = dbea->prepare((BaseAdaptor *)dbea,qStr,strlen(qStr));
sth->execute(sth);
// Why???? my %duplicate;
while ((row = sth->fetchRow(sth))){
if (!row->col(row,0)) {
fprintf(stderr,"WARNING: Got xref with no refID\n");
return NULL;
}
if (!dbe) {
dbe = DBEntry_new();
DBEntry_setAdaptor(dbe,(BaseAdaptor *)dbea);
DBEntry_setDbID(dbe, dbID);
DBEntry_setPrimaryId(dbe, row->getStringAt(row,1));
DBEntry_setDisplayId(dbe, row->getStringAt(row,2));
DBEntry_setVersion(dbe, row->getStringAt(row,3));
DBEntry_setRelease(dbe, row->getStringAt(row,6));
DBEntry_setDbName(dbe, row->getStringAt(row,5));
if (row->col(row,4)) DBEntry_setDescription(dbe, row->getStringAt(row,4));
}
if (row->col(row,7)) DBEntry_addSynonym(dbe, row->getStringAt(row,7));
}
sth->finish(sth);
return dbe;
}
int DBEntryAdaptor_fetchAllByGene(DBEntryAdaptor *dbea, Gene *gene) {
char qStr[512];
StatementHandle *sth;
ResultRow *row;
sprintf(qStr,
"SELECT t.transcript_id, t.canonical_translation_id"
" FROM transcript t"
" WHERE t.gene_id = " IDFMTSTR,
Gene_getDbID(gene));
sth = dbea->prepare((BaseAdaptor *)dbea,qStr,strlen(qStr));
sth->execute(sth);
while ((row = sth->fetchRow(sth))) {
IDType transcriptId = row->getLongLongAt(row,0);
int i;
Vector *transLinks;
if (row->col(row,1)) {
IDType translationId = row->getLongLongAt(row,1);
Vector *translatLinks = DBEntryAdaptor_fetchByObjectType(dbea, translationId,"Translation");
for (i=0;i<Vector_getNumElement(translatLinks); i++) {
Gene_addDBLink(gene,Vector_getElementAt(translatLinks,i));
}
Vector_free(translatLinks);
}
transLinks = DBEntryAdaptor_fetchByObjectType(dbea, transcriptId,"Transcript");
for (i=0;i<Vector_getNumElement(transLinks); i++) {
Gene_addDBLink(gene, Vector_getElementAt(transLinks,i));
}
Vector_free(transLinks);
}
/* NIY This is wrong so I'm not going to implement it!
if($gene->stable_id){
my $genelinks = $self->_fetch_by_object_type( $gene->stable_id, 'Gene' );
foreach my $genelink ( @$genelinks ) {
$gene->add_DBLink( $genelink );
}
}
*/
return 1;
}
Vector *DBEntryAdaptor_fetchByObjectType(DBEntryAdaptor *dbea, IDType ensObj, char *ensType) {
Vector *out;
char qStr[1024];
StatementHandle *sth;
ResultRow *row;
IDHash *seen;
if (!ensObj) {
fprintf(stderr,"Error: Can't fetchByObjectType without an object\n");
exit(1);
}
if (!ensType) {
fprintf(stderr,"Error: Can't fetchByObjectType without a type\n");
exit(1);
}
// Not sure if idt identities are right way round
sprintf(qStr,
"SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label, xref.version,"
" xref.description,"
" exDB.db_name, exDB.db_release, exDB.status,"
" oxr.object_xref_id,"
" es.synonym,"
" idt.xref_identity, idt.ensembl_identity"
" FROM (external_db exDB, object_xref oxr, xref xref)"
" LEFT JOIN external_synonym es on es.xref_id = xref.xref_id"
" LEFT JOIN identity_xref idt on idt.object_xref_id = oxr.object_xref_id"
" WHERE xref.xref_id = oxr.xref_id"
" AND xref.external_db_id = exDB.external_db_id"
" AND oxr.ensembl_id = " IDFMTSTR
" AND oxr.ensembl_object_type = '%s'",
ensObj,
ensType);
sth = dbea->prepare((BaseAdaptor *)dbea,qStr,strlen(qStr));
sth->execute(sth);
seen = IDHash_new(IDHASH_SMALL);
out = Vector_new();
while ((row = sth->fetchRow(sth))) {
DBEntry *exDB;
IDType refID = row->getLongLongAt(row,0);
// using an outer join on the synonyms as well as on identity_xref, we
// now have to filter out the duplicates (see v.1.18 for
// original). Since there is at most one identity_xref row per xref,
// this is easy enough; all the 'extra' bits are synonyms
if (!IDHash_contains(seen,refID)) {
exDB = DBEntry_new();
DBEntry_setAdaptor(exDB,(BaseAdaptor *)dbea);
DBEntry_setDbID(exDB, refID);
DBEntry_setPrimaryId(exDB, row->getStringAt(row,1));
DBEntry_setDisplayId(exDB, row->getStringAt(row,2));
DBEntry_setVersion(exDB, row->getStringAt(row,3));
DBEntry_setDbName(exDB, row->getStringAt(row,5));
DBEntry_setRelease(exDB, row->getStringAt(row,6));
if (row->col(row,10)) {
IdentityXref *idx = IdentityXref_new();
DBEntry_setIdentityXref(exDB,idx);
IdentityXref_setQueryIdentity(idx, row->getDoubleAt(row,10));
IdentityXref_setTargetIdentity(idx, row->getDoubleAt(row,11));
}
if (row->col(row,4)) DBEntry_setDescription(exDB, row->getStringAt(row,4));
if (row->col(row,7)) DBEntry_setStatus(exDB, row->getStringAt(row,7));
Vector_addElement(out, exDB);
IDHash_add(seen, refID, exDB);
}
exDB = IDHash_getValue(seen, refID);
if (row->col(row,9)) {
DBEntry_addSynonym(exDB,row->getStringAt(row,9));
}
}
IDHash_free(seen, NULL);
sth->finish(sth);
return out;
}
