void getText(struct kgXref *kg, struct hash *refSeqHash,
struct sqlConnection *conn,
struct sqlConnection *spConn, struct sqlConnection *goConn,
FILE *f)
/* Get loads of text and write it out. */
{
char query[512];
struct hash *uniqHash = hashNew(0);
char *spAcc = spFindAcc(spConn, kg->spID);
subChar(kg->description, '\n', ' ');
fprintf(f, "%s\t%s\t%s\t%s", kg->kgID,
kg->geneSymbol, kg->kgID, kg->description);
hashAdd(uniqHash, kg->geneSymbol, NULL);
hashAdd(uniqHash, kg->kgID, NULL);
addSimple(kg->kgID, "kgAlias", "kgID", "alias", conn, uniqHash, f);
addSimple(kg->kgID, "kgProtAlias", "kgID", "alias", conn, uniqHash, f);
if (refSeqHash != NULL)
{
char *s = hashFindVal(refSeqHash, kg->refseq);
if (s == NULL && strchr(kg->refseq, '.') != NULL)
{
char *accOnly = cloneString(kg->refseq);
chopSuffix(accOnly);
s = hashFindVal(refSeqHash, accOnly);
freeMem(accOnly);
}
if (s == NULL)
s = "";
fprintf(f, "\t%s", s);
}
sqlSafef(query, sizeof(query),
"select commentVal.val from comment,commentVal "
"where comment.acc='%s' and comment.commentVal=commentVal.id"
, spAcc);
addText(query, spConn, f);
sqlSafef(query, sizeof(query),
"select term.name from goaPart,term "
"where goaPart.dbObjectId='%s' "
"and goaPart.goId=term.acc"
, spAcc);
addText(query, goConn, f);
fprintf(f, "\n");
hashFree(&uniqHash);
freeMem(spAcc);
}
void Text::addSdata(const InternalEntity *entity,
const ConstPtr<Origin> &origin)
{
addSimple(TextItem::sdata, Location(origin, 0));
chars_.append(entity->string().data(), entity->string().size());
}