void cartMain(struct cart *theCart)
/* We got the persistent/CGI variable cart. Now
* set up the globals and make a web page. */
{
hgBotDelay();
cart = theCart;
getDbAndGenome(cart, &database, &genome, oldVars);
initGenbankTableNames(database);
getGenomeSettings();
if (cartVarExists(cart, hggDoKgMethod))
doKgMethod();
else if (cartVarExists(cart, hggDoTxInfoDescription))
doTxInfoDescription();
else
{
struct sqlConnection *conn = NULL;
char *geneName = cartUsualString(cart, hggGene, NULL);
if (isEmpty(geneName))
{
// Silly googlebots.
hUserAbort("Error: the hgg_gene parameter is missing from the cart and the CGI params.");
}
/* if kgProtMap2 table exists, this means we are doing KG III */
if (hTableExists(database, "kgProtMap2")) kgVersion = KG_III;
conn = hAllocConn(database);
curGeneId = findGeneId(conn, geneName);
getGenePosition(conn);
curGenePred = getCurGenePred(conn);
curGeneName = getGeneName(curGeneId, conn);
spConn = hAllocConn(UNIPROT_DB_NAME);
swissProtAcc = getSwissProtAcc(conn, spConn, curGeneId);
if (isRgdGene(conn)) swissProtAcc=getRgdGeneUniProtAcc(curGeneId, conn);
/* Check command variables, and do the ones that
* don't want to put up the hot link bar etc. */
if (cartVarExists(cart, hggDoGetMrnaSeq))
doGetMrnaSeq(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoWikiTrack))
doWikiTrack(conn);
else if (cartVarExists(cart, hggDoGetProteinSeq))
doGetProteinSeq(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoRnaFoldDisplay))
doRnaFoldDisplay(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoOtherProteinSeq))
doOtherProteinSeq(conn, curGeneName);
else if (cartVarExists(cart, hggDoOtherProteinAli))
doOtherProteinAli(conn, curGeneId, curGeneName);
else
{
/* Default case - start fancy web page. */
measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming"));
struct trackDb *tdb = hTrackDbForTrack(database, genomeSetting("knownGene"));
isGencode = trackDbSettingOn(tdb, "isGencode");
isGencode2 = trackDbSettingOn(tdb, "isGencode2");
cartWebStart(cart, database, "%s Gene %s (%s) Description and Page Index",
genome, curGeneName, isGencode2 ? curGeneId : curAlignId);
webMain(conn, tdb);
cartWebEnd();
}
hFreeConn(&spConn);
hFreeConn(&conn);
}
cartRemovePrefix(cart, hggDoPrefix);
}
static void synonymPrint(struct section *section,
struct sqlConnection *conn, char *id)
/* Print out SwissProt comments - looking up typeId/commentVal. */
{
char *protAcc = getSwissProtAcc(conn, spConn, id);
char *spDisplayId;
char *refSeqAcc = "";
char *mrnaAcc = "";
char *oldDisplayId;
char condStr[255];
char *kgProteinID;
char *parAcc; /* parent accession of a variant splice protein */
char *chp;
if (isRgdGene(conn))
{
rgdGene2SynonymPrint(section,conn, id);
return;
}
if (sqlTablesExist(conn, "kgAlias"))
printAlias(id, conn);
if (sameWord(genome, "Zebrafish"))
{
char *xrefTable = "ensXRefZfish";
char *geneIdCol = "ensGeneId";
/* get Gene Symbol and RefSeq accession from Zebrafish-specific */
/* cross-reference table */
printGeneSymbol(id, xrefTable, geneIdCol, conn);
refSeqAcc = getRefSeqAcc(id, xrefTable, geneIdCol, conn);
hPrintf("<B>ENSEMBL ID:</B> %s", id);
}
else
{
char query[256];
char *toRefTable = genomeOptionalSetting("knownToRef");
if (toRefTable != NULL && sqlTableExists(conn, toRefTable))
{
safef(query, sizeof(query), "select value from %s where name='%s'", toRefTable,
id);
refSeqAcc = emptyForNull(sqlQuickString(conn, query));
}
if (sqlTableExists(conn, "kgXref"))
{
safef(query, sizeof(query), "select mRNA from kgXref where kgID='%s'", id);
mrnaAcc = emptyForNull(sqlQuickString(conn, query));
}
if (sameWord(genome, "C. elegans"))
hPrintf("<B>WormBase ID:</B> %s<BR>", id);
else
hPrintf("<B>UCSC ID:</B> %s<BR>", id);
}
if (refSeqAcc[0] != 0)
{
hPrintf("<B>RefSeq Accession: </B> <A HREF=\"");
printOurRefseqUrl(stdout, refSeqAcc);
hPrintf("\">%s</A><BR>\n", refSeqAcc);
}
else if (mrnaAcc[0] != 0)
{
safef(condStr, sizeof(condStr), "acc = '%s'", mrnaAcc);
if (sqlGetField(database, "gbCdnaInfo", "acc", condStr) != NULL)
{
hPrintf("<B>Representative RNA: </B> <A HREF=\"");
printOurMrnaUrl(stdout, mrnaAcc);
hPrintf("\">%s</A><BR>\n", mrnaAcc);
}
else
/* do not show URL link if it is not found in gbCdnaInfo */
{
hPrintf("<B>Representative RNA: %s </B>", mrnaAcc);
}
}
if (protAcc != NULL)
{
kgProteinID = cloneString("");
if (hTableExists(sqlGetDatabase(conn), "knownGene")
&& (isNotEmpty(cartOptionalString(cart, hggChrom)) &&
differentWord(cartOptionalString(cart, hggChrom),"none")))
{
safef(condStr, sizeof(condStr), "name = '%s' and chrom = '%s' and txStart=%s and txEnd=%s",
id, cartOptionalString(cart, hggChrom),
cartOptionalString(cart, hggStart),
cartOptionalString(cart, hggEnd));
kgProteinID = sqlGetField(database, "knownGene", "proteinID", condStr);
}
hPrintf("<B>Protein: ");
if (strstr(kgProteinID, "-") != NULL)
{
parAcc = cloneString(kgProteinID);
chp = strstr(parAcc, "-");
*chp = '\0';
/* show variant splice protein and the UniProt link here */
hPrintf("<A HREF=\"http://www.uniprot.org/uniprot%s\" "
"TARGET=_blank>%s</A></B>, splice isoform of ",
kgProteinID, kgProteinID);
hPrintf("<A HREF=\"http://www.uniprot.org/uniprot/%s\" "
"TARGET=_blank>%s</A></B>\n",
parAcc, parAcc);
}
else
{
hPrintf("<A HREF=\"http://www.uniprot.org/uniprot/%s\" "
"TARGET=_blank>%s</A></B>\n",
protAcc, protAcc);
}
/* show SWISS-PROT display ID if it is different than the accession ID */
/* but, if display name is like: Q03399 | Q03399_HUMAN, then don't show display name */
spDisplayId = spAnyAccToId(spConn, protAcc);
if (spDisplayId == NULL)
{
errAbort("<br>%s seems to no longer be a valid protein ID in our latest UniProtKB DB.", protAcc);
}
if (strstr(spDisplayId, protAcc) == NULL)
{
hPrintf(" (aka %s", spDisplayId);
/* show once if the new and old displayId are the same */
oldDisplayId = oldSpDisplayId(spDisplayId);
if (oldDisplayId != NULL)
{
if (!sameWord(spDisplayId, oldDisplayId)
&& !sameWord(protAcc, oldDisplayId))
{
hPrintf(" or %s", oldDisplayId);
}
}
hPrintf(")<BR>\n");
}
}
printCcds(id, conn);
}
