static void blackListFilter(struct cDnaQuery *cdna)
/* filter for black list */
{
struct cDnaAlign *aln;
for (aln = cdna->alns; aln != NULL; aln = aln->next)
{
if (!aln->drop && genbankBlackListFail(aln->psl->qName, gBlackListRanges))
cDnaAlignDrop(aln, FALSE, &cdna->stats->blackListCnts, "black listed");
}
}
static boolean keepGbEntry(boolean isEst)
/* should the current entry in the kvt be kept? */
{
char *acc = gbAccessionField->val->string;
char *cat = kvtGet(kvt, "cat")->val;
char *org = kvtGet(kvt, "org")->val;
if (genbankBlackListFail(acc, blackListRanges))
return FALSE;
else if (gbOrg && (differentString(org, gbOrg)))
return FALSE;
else if (gbGuessSrcDb(acc) == GB_REFSEQ)
{
return (startsWith("NM_", acc) || startsWith("NR_", acc)
|| ((startsWith("XM_", acc) && inclXMs)));
}
else if ((sameString(cat, "GSS") ||
sameString(cat, "HTG") ||
sameString(cat, "STS") ||
sameString(cat, "CON")) && !(gbType & GB_DNA))
return FALSE; // division to ignore
else
{
if (sameString(cat, "EST")) {
return (gbType & GB_EST) != 0;
}
else if (gbType & GB_MRNA)
{
// not an EST, keep any type of RNA
return containsStringNoCase(kvtGet(kvt, "mol")->val, "RNA") != NULL;
}
else if (gbType & GB_DNA)
{
// keep any type of DNA if DNA filter set
return containsStringNoCase(kvtGet(kvt, "mol")->val, "DNA") != NULL;
}
else
return FALSE;
}
}
