static void processSelectedPsl(struct sqlConnection *conn, struct gbSelect* select,
struct gbStatus* status, struct psl* psl)
/* Process the next PSL that is selected for load */
{
struct gbAlignTbl *gat = gbAlignTblSetGet(alignTblSet, status);
gbAlignTblWrite(gat, psl, conn);
if (status->srcDb == GB_REFSEQ)
{
/* create refSeq genePred */
struct gbGeneTbl *ggt = (status->orgCat == GB_NATIVE)
? gbGeneTblSetRefGeneGet(geneTblSet, select->hasVersion, conn)
: gbGeneTblSetXenoRefGeneGet(geneTblSet, select->hasVersion, conn);
gbGeneTblWrite(ggt, status, psl, conn);
}
if (status->isMgcFull)
{
/* create MGC genePred and psl */
struct gbGeneTbl *ggt = gbGeneTblSetMgcGenesGet(geneTblSet, select->hasVersion, conn);
gbGeneTblWrite(ggt, status, psl, conn);
struct gbAlignTbl *mgat = gbAlignTblSetGetMgc(alignTblSet);
gbAlignTblWrite(mgat, psl, conn);
}
if (status->isOrfeome)
{
/* create ORFeome genePred and psl */
struct gbGeneTbl *ggt = gbGeneTblSetOrfeomeGenesGet(geneTblSet, select->hasVersion, conn);
gbGeneTblWrite(ggt, status, psl, conn);
struct gbAlignTbl *ogat = gbAlignTblSetOrfeomeGet(alignTblSet);
gbAlignTblWrite(ogat, psl, conn);
}
}
void gbGeneTblRebuild(struct gbGeneTbl *ggt, struct gbStatus* status,
struct sqlConnection *conn)
/* rebuild a gene from an alignment that is already loaded in a table */
{
char where[128];
sqlSafefFrag(where, sizeof(where), "qName = \"%s\"", status->acc);
struct psl *psls = pslReaderLoadQuery(conn, ggt->alnTbl, where);
struct psl *psl;
for (psl = psls; psl != NULL; psl = psl->next)
gbGeneTblWrite(ggt, status, psl, conn);
pslFreeList(&psls);
}
