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);
}
}
static void updateGeneEntries(struct sqlConnection *conn,
struct gbGeneTblSet *ggts,
struct gbStatus* status,
boolean hasVersion)
/* update gene table entries when annotation have changed */
{
if (status->srcDb == GB_REFSEQ)
{
struct gbGeneTbl *geneTbl = (status->orgCat == GB_NATIVE)
? gbGeneTblSetRefGeneGet(ggts, hasVersion, conn)
: gbGeneTblSetXenoRefGeneGet(ggts, hasVersion, conn);
gbGeneTblRebuild(geneTbl, status, conn);
}
else
{
// can be both MGC and orfeome
if (status->isMgcFull)
gbGeneTblRebuild(gbGeneTblSetMgcGenesGet(ggts, hasVersion, conn), status, conn);
if (status->isOrfeome)
gbGeneTblRebuild(gbGeneTblSetOrfeomeGenesGet(ggts, hasVersion, conn), status, conn);
}
}
