static void refSeqPepUpdate(struct sqlConnection *conn, HGID pepFaId)
/* Make or update a seq table entry for a RefSeq peptide sequence
* referenced a refLink table. */
{
/* done for all stateChg values */
if (raProtFaOff >= 0)
{
HGID gbSeqId = seqTblGetId(seqTbl, conn, raProtAcc);
if (gbSeqId == 0)
seqTblAdd(seqTbl, raProtAcc, raProtVersion, SEQ_PEP, SEQ_REFSEQ,
pepFaId, raProtSize, raProtFaOff, raProtFaSize);
else
seqTblMod(seqTbl, gbSeqId, raProtVersion, pepFaId, raProtSize,
raProtFaOff, raProtFaSize);
}
}
static void refPepRepairOne(struct sqlConnection *conn,
struct brokenRefPep *brp,
struct seqTbl* seqTbl,
struct extFileTbl* extFileTbl,
boolean dryRun)
/* repair a refPep */
{
gbVerbPrStart(2, "%s\t%s\trepair", sqlGetDatabase(conn), brp->protAcc);
gbVerbPrMore(3, "\tsz: %d\toff: %lld\trecSz: %d\tfid: %d\t%s",
brp->newSeqSize, (long long)brp->newFaOff, brp->newRecSize,
brp->newFaId, brp->newFaPath);
gbVerbPrMore(2, "\n");
if (!dryRun)
seqTblMod(seqTbl, brp->protSeqId, -1, brp->newFaId,
brp->newSeqSize, brp->newFaOff, brp->newRecSize);
}
static void seqUpdate(struct gbStatus* status, HGID faFileId)
/* Update the seq table for the current entry */
{
assert((status->stateChg & GB_NEW) || (status->gbSeqId != 0));
if (status->stateChg & GB_NEW)
{
char* seqType = (status->type == GB_MRNA) ? SEQ_MRNA : SEQ_EST;
char* seqSrcDb = (gSrcDb == GB_GENBANK) ? SEQ_GENBANK : SEQ_REFSEQ;
assert(status->gbSeqId == 0);
status->gbSeqId = seqTblAdd(seqTbl, raAcc, raVersion, seqType, seqSrcDb,
faFileId, raDnaSize, raFaOff, raFaSize);
}
else if (status->stateChg & (GB_SEQ_CHG|GB_EXT_CHG))
{
/* Update only the columns that need to change */
HGID fileId = (status->stateChg & (GB_SEQ_CHG|GB_EXT_CHG))
? faFileId : 0;
short version = (status->stateChg & GB_SEQ_CHG)
? raVersion : -1;
seqTblMod(seqTbl, status->gbSeqId, version, fileId, raDnaSize, raFaOff,
raFaSize);
}
}
