void doGenePredPal(struct sqlConnection *conn)
/* Output genePred protein alignment. */
{
if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery))
{
sendParamsToGalaxy(hgtaDoPalOut, "submit");
return;
}
/* get rid of pesky cookies that would bring us back here */
cartRemove(cart, hgtaDoPal);
cartRemove(cart, hgtaDoPalOut);
if (anyIntersection() && intersectionIsBpWise())
errAbort("Can't do CDS FASTA output when bit-wise intersection is on. "
"Please go back and select another output type, or clear the intersection.");
checkNoGenomeDisabled(database, curTable);
struct lm *lm = lmInit(64*1024);
int fieldCount;
struct bed *bedList = cookedBedsOnRegions(conn, curTable, getRegions(),
lm, &fieldCount);
//lmCleanup(&lm);
textOpen();
int outCount = palOutPredsInBeds(conn, cart, bedList, curTable);
/* Do some error diagnostics for user. */
if (outCount == 0)
explainWhyNoResults(NULL);
}
void doGenePredSequence(struct sqlConnection *conn)
/* Output genePred sequence. */
{
char *type = cartString(cart, hgtaGeneSeqType);
if (sameWord(type, "protein"))
{
if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery))
sendParamsToGalaxy(hgtaDoGenePredSequence, "submit");
else
doGenePredNongenomic(conn, 1);
}
else if (sameWord(type, "mRNA"))
{
if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery))
sendParamsToGalaxy(hgtaDoGenePredSequence, "submit");
else
doGenePredNongenomic(conn, 2);
}
else
genomicFormatPage(conn);
}
