aedbaca2593e2adea277d6f5c91f57c65e54b7fc braney Mon Jan 14 11:10:16 2013 -0800 remove Stanford SOURCE link from refGene and few other places #9962 diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c index f032074..cb3081c 100644 --- src/hg/hgc/hgc.c +++ src/hg/hgc/hgc.c @@ -5222,55 +5222,30 @@ snprintf(qry, sizeof(qry), "select comment from rikenseq where id='%s';", seqid); sqlFreeResult(&sr); sr = sqlMustGetResult(conn, qry); row = sqlNextRow(sr); if (row != NULL) { comment = row[0]; printf("<B>Riken/comment:</B> %s<BR>\n",comment); } } } -void printStanSource(char *acc, char *type) -/* Print out a link (Human/Mouse/Rat only) to Stanford's SOURCE web resource. - Types known are: est,mrna,unigene,locusLink. */ -{ -if (startsWith("Human", organism) || startsWith("Mouse", organism) || - startsWith("Rat", organism)) - { - char *stanSourceLink = "http://smd.stanford.edu/cgi-bin/source/sourceResult?"; - if(sameWord(type, "est")) - { - printf("<B>Stanford SOURCE:</B> %s <A HREF=\"%soption=Number&criteria=%s&choice=Gene\" TARGET=_blank>[Gene Info]</A> ",acc,stanSourceLink,acc); - printf("<A HREF=\"%soption=Number&criteria=%s&choice=cDNA\" TARGET=_blank>[Clone Info]</A><BR>\n",stanSourceLink,acc); - } - else if(sameWord(type,"unigene")) - { - printf("<B>Stanford SOURCE:</B> %s <A HREF=\"%soption=CLUSTER&criteria=%s&choice=Gene\" TARGET=_blank>[Gene Info]</A> ",acc,stanSourceLink,acc); - printf("<A HREF=\"%soption=CLUSTER&criteria=%s&choice=cDNA\" TARGET=_blank>[Clone Info]</A><BR>\n",stanSourceLink,acc); - } - else if(sameWord(type,"mrna")) - printf("<B>Stanford SOURCE:</B> <A HREF=\"%soption=Number&criteria=%s&choice=Gene\" TARGET=_blank>%s</A><BR>\n",stanSourceLink,acc,acc); - else if(sameWord(type,"locusLink")) - printf("<B>Stanford SOURCE Locus Link:</B> <A HREF=\"%soption=LLID&criteria=%s&choice=Gene\" TARGET=_blank>%s</A><BR>\n",stanSourceLink,acc,acc); - } -} - void printGeneCards(char *geneName) /* Print out a link to GeneCards (Human only). */ { if (startsWith("hg", database) && isNotEmpty(geneName)) { printf("<B>GeneCards:</B> " "<A HREF = \"http://www.genecards.org/cgi-bin/cardsearch.pl?" "search=%s\" TARGET=_blank>%s</A><BR>\n", geneName, geneName); } } int getImageId(struct sqlConnection *conn, char *acc) /* get the image id for a clone, or 0 if none */ { @@ -5492,31 +5467,30 @@ if (sameWord(organism, "Rat")) { if (hTableExists(database, "rgdEstLink")) { snprintf(query, sizeof(query), "select id from %s.rgdEstLink where name = '%s';", database, acc); if (sqlQuickQuery(conn2, query, rgdEstId, sizeof(rgdEstId)) != NULL) { tdbRgdEst = hashFindVal(trackHash, "rgdEst"); printf("<B>RGD EST Report: "); printf("<A HREF=\"%s%s\" target=_blank>", tdbRgdEst->url, rgdEstId); printf("RGD:%s</B></A><BR>\n", rgdEstId); } } } - printStanSource(acc, type); if (isEst && hTableExists(database, "estOrientInfo") && (psl != NULL)) { int estOrient = getEstTranscriptionDir(conn2, psl); if (estOrient != 0) printf("<B>EST transcribed from %c strand </B>(supported by %d splice sites).<BR>\n", (estOrient > 0 ? '+' : '-' ), abs(estOrient)); } if (hGenBankHaveSeq(database, acc, NULL)) { printf("<B>%s sequence:</B> ", type); hgcAnchorSomewhere("htcDisplayMrna", acc, tdb->track, seqName); printf("%s</A><BR>\n", acc); } } else @@ -10469,31 +10443,30 @@ puts("<BR>"); if (rl->omimId != 0) { printf("<B>OMIM:</B> <A HREF=\""); printEntrezOMIMUrl(stdout, rl->omimId); printf("\" TARGET=_blank>%d</A><BR>\n", rl->omimId); } if (rl->locusLinkId != 0) { printf("<B>Entrez Gene:</B> "); printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%d\" TARGET=_blank>", rl->locusLinkId); printf("%d</A><BR>\n", rl->locusLinkId); } -printStanSource(rl->mrnaAcc, "mrna"); htmlHorizontalLine(); /* print alignments that track was based on */ { char *aliTbl = (sameString(tdb->table, "rgdGene") ? "refSeqAli" : "xenoRGDAli"); struct psl *pslList = getAlignments(conn, aliTbl, rl->mrnaAcc); printf("<H3>mRNA/Genomic Alignments</H3>"); printAlignments(pslList, start, "htcCdnaAli", aliTbl, rl->mrnaAcc); } htmlHorizontalLine(); geneShowPosAndLinks(rl->mrnaAcc, rl->protAcc, tdb, "refPep", "htcTranslatedProtein", "htcRefMrna", "htcGeneInGenome", "mRNA Sequence"); @@ -10897,31 +10870,30 @@ jaxOrthologStaticLoad(row, &jo); printf("<B>MGI Mouse Ortholog:</B> "); printf("<A HREF=\"http://www.informatics.jax.org/searches/accession_report.cgi?id=%s\" target=_BLANK>", jo.mgiId); printf("%s</A><BR>\n", jo.mouseSymbol); } sqlFreeResult(&sr); } if (startsWith("hg", database)) { printf("\n"); printf("<B>AceView:</B> "); printf("<A HREF = \"http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&l=%s\" TARGET=_blank>", rl->name); printf("%s</A><BR>\n", rl->name); } -printStanSource(rl->mrnaAcc, "mrna"); prGRShortRefGene(rl->name); } void prKnownGeneInfo(struct sqlConnection *conn, char *rnaName, char *sqlRnaName, struct refLink *rl) /* print basic details information and links for a Known Gene */ { struct sqlResult *sr; char **row; char query[256]; int ver = gbCdnaGetVersion(conn, rl->mrnaAcc); char *cdsCmpl = NULL; printf("<td valign=top nowrap>\n"); @@ -10976,31 +10948,30 @@ printf("<B>Mouse Genome Informatics:</B> "); mgiID = cloneString(row[0]); printf("<A HREF=\"http://www.informatics.jax.org/searches/accession_report.cgi?id=%s\" TARGET=_BLANK>%s</A><BR>\n",mgiID, mgiID); } else { /* per Carol Bult from Jackson Lab 4/12/02, JAX do not always agree * with Locuslink on seq to gene association. * Thus, not finding a MGIid even if a LocusLink ID * exists is always a possibility. */ } sqlFreeResult(&sr); } } -printStanSource(rl->mrnaAcc, "mrna"); } void doKnownGene(struct trackDb *tdb, char *rnaName) /* Process click on a known gene. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; char *kgId = cartString(cart, "i"); char *sqlRnaName = rnaName; char *summary = NULL; struct refLink rlR; struct refLink *rl; int start = cartInt(cart, "o"); @@ -19422,31 +19393,30 @@ int featureCount; int count=0; seList=loadSageExps("sageExp",bedList); sgList = loadSageData("sage", bedList); slSort(&sgList,sortSageByBedOrder); printSageReference(sgList, tdb); /* temporarily disable this link until debugged and fixed. Fan printSageGraphUrl(sgList); */ printf("<BR>\n"); for(sg=sgList; sg != NULL; sg = sg->next) { char buff[256]; sprintf(buff,"Hs.%d",sg->uni); - printStanSource(buff, "unigene"); } featureCount= slCount(sgList); printf("<basefont size=-1>\n"); printf("<table cellspacing=0 style='border:1px solid black;'>\n"); printf("<tr>\n"); printf("<th align=center>Sage Experiment</th>\n"); printf("<th align=center>Tissue</th>\n"); printf("<th align=center colspan=%d valign=top>Uni-Gene Clusters<br>(<b>Median</b> [Ave ± Stdev])</th>\n",featureCount); printf("</tr>\n<tr><td> </td><td> </td>\n"); for(sg = sgList; sg != NULL; sg = sg->next) { char buff[32]; char url[256]; sprintf(buff,"Hs.%d",sg->uni); printf("<td valign=top align=center>\n");