ff9313091f342ffe62a124427b5c9d6a516faaea hiram Thu Oct 15 15:03:07 2015 -0700 fixup gcc warnings for -Wunused-but-set-variable refs #16121 diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c index e89235c..8f0d449 100644 --- src/hg/hgc/hgc.c +++ src/hg/hgc/hgc.c @@ -1334,41 +1334,30 @@ atomStaticLoad(row, &ret); //atomOutput(&ret, stdout, '\t', '\n'); linkToOtherBrowser(ret.species, ret.chrom, ret.start, ret.end); if (sameString(ret.chrom, seqName) && (start == ret.start) && sameString(ret.species, database)) printf("* "); else printf(" "); printf( "%4d %-10s %-5s %12d %12d %10d %c %-10s %-10s\n", ret.instance, ret.species,ret.chrom, ret.start + 1, ret.end, ret.end - ret.start + 1, ret.strand[0],ret.fivePrime,ret.threePrime); } printf("</A>"); sqlFreeResult(&sr); -#if 0 -//struct tempName launchFile; -char *fileName = "../trash/braney.launch"; -FILE *launchF; -//trashDirFile(&launchFile, "braney", "launch", ".txt"); -//printf("writing %s\n",fileName); -launchF = mustOpen(fileName, "w"); -fprintf(launchF, "%s\n", item); -fclose(launchF); -#endif - if (!sameString("atom20080226d", table)) return; printf("<TABLE>"); printf("<THEAD>"); printf("<TBODY>"); printf("<TR><TH>"); printf("Suh Trees<BR>\n"); printf("<IMG src=http://hgwdev.cse.ucsc.edu/~braney/suhTrees/%s.tt.png><BR>",item); printf("<TD><IMG src=http://hgwdev.cse.ucsc.edu/~braney/suhTrees/%s.gt.png><BR>",item); printf("<TR><TH>"); printf("NJ Trees<BR>\n"); printf("<IMG src=http://hgwdev.cse.ucsc.edu/~braney/njTrees/%s.tt.png><BR>",item); printf("<TD><IMG src=http://hgwdev.cse.ucsc.edu/~braney/njTrees/%s.gt.png><BR>",item); printf("<TR><TH>"); @@ -2298,31 +2287,31 @@ freeDyString(&dyT); freeDyString(&dyQ); freeDyString(&dyQprot); freeDyString(&dyTprot); } } } struct axt *getAxtListForGene(struct genePred *gp, char *nib, char *fromDb, char *toDb, struct lineFile *lf) /* get all axts for a gene */ { struct axt *axt, *axtGap; struct axt *axtList = NULL; int prevEnd = gp->txStart; -int prevStart = gp->txEnd; +// int prevStart = gp->txEnd; unused variable int tmp; while ((axt = axtRead(lf)) != NULL) { if (sameString(gp->chrom, axt->tName) && ( ( (axt->tStart <= gp->cdsStart && axt->tEnd >= gp->cdsStart) || (axt->tStart <= gp->cdsEnd && axt->tEnd >= gp->cdsEnd ) ) || ( axt->tStart < gp->cdsEnd && axt->tEnd > gp->cdsStart ) ) ) { if (gp->strand[0] == '-') { reverseComplement(axt->qSym, axt->symCount); reverseComplement(axt->tSym, axt->symCount); tmp = hChromSize(fromDb, axt->qName) - axt->qStart; axt->qStart = hChromSize(fromDb, axt->qName) - axt->qEnd; @@ -2330,31 +2319,31 @@ if (prevEnd < (axt->tStart)-1) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,(axt->tStart),gp->strand[0]); reverseComplement(axtGap->qSym, axtGap->symCount); reverseComplement(axtGap->tSym, axtGap->symCount); slAddHead(&axtList, axtGap); } } else if (prevEnd < (axt->tStart)) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,(axt->tStart),gp->strand[0]); slAddHead(&axtList, axtGap); } slAddHead(&axtList, axt); prevEnd = axt->tEnd; - prevStart = axt->tStart; + // prevStart = axt->tStart; unused variable } if (sameString(gp->chrom, axt->tName) && (axt->tStart > gp->txEnd)) { if ((prevEnd < axt->tStart) && prevEnd < min(gp->txEnd, axt->tStart)) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,min(axt->tStart,gp->txEnd),gp->strand[0]); if (gp->strand[0] == '-') { reverseComplement(axtGap->qSym, axtGap->symCount); reverseComplement(axtGap->tSym, axtGap->symCount); } slAddHead(&axtList, axtGap); } else if (axtList == NULL) @@ -2371,31 +2360,31 @@ } } if (gp->strand[0] == '+') slReverse(&axtList); return axtList ; } struct axt *getAxtListForRange(struct genePred *gp, char *nib, char *fromDb, char *toDb, char *alignment, char *qChrom, int qStart, int qEnd) /* get all axts for a chain */ { struct lineFile *lf ; struct axt *axt, *axtGap; struct axt *axtList = NULL; int prevEnd = gp->txStart; -int prevStart = gp->txEnd; +// int prevStart = gp->txEnd; unused variable int tmp; lf = lineFileOpen(getAxtFileName(gp->chrom, toDb, alignment, fromDb), TRUE); printf("file %s\n",lf->fileName); while ((axt = axtRead(lf)) != NULL) { /* if (sameString(gp->chrom , axt->tName)) * printf("axt %s qstart %d axt tStart %d\n",axt->qName, axt->qStart,axt->tStart); */ if ( sameString(gp->chrom, axt->tName) && sameString( qChrom, axt->qName) && positiveRangeIntersection( qStart, qEnd, axt->qStart, axt->qEnd) && positiveRangeIntersection(gp->txStart, gp->txEnd, axt->tStart, axt->tEnd) ) { if (gp->strand[0] == '-') { @@ -2407,31 +2396,31 @@ if (prevEnd < (axt->tStart)-1) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,(axt->tStart)-1,gp->strand[0]); reverseComplement(axtGap->qSym, axtGap->symCount); reverseComplement(axtGap->tSym, axtGap->symCount); slAddHead(&axtList, axtGap); } } else if (prevEnd < (axt->tStart)-1) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,(axt->tStart)-1,gp->strand[0]); slAddHead(&axtList, axtGap); } slAddHead(&axtList, axt); prevEnd = axt->tEnd; - prevStart = axt->tStart; + // prevStart = axt->tStart; unused variable } if (sameString(gp->chrom, axt->tName) && (axt->tStart > gp->txEnd+20000)) { if (axt->tStart > prevEnd) { axtGap = createAxtGap(nib,gp->chrom,prevEnd+1,(axt->tStart)-1,gp->strand[0]); if (gp->strand[0] == '-') { reverseComplement(axtGap->qSym, axtGap->symCount); reverseComplement(axtGap->tSym, axtGap->symCount); } slAddHead(&axtList, axtGap); } break; } @@ -3478,49 +3467,45 @@ if (net->qNewR >= 0) printLabeledPercent(otherOrg, "new repeat bases", net->qOldR, qSize); if (net->tEnd >= net->tStart) printLabeledNumber(org, "size", net->tEnd - net->tStart); if (net->qEnd >= net->qStart) printLabeledNumber(otherOrg, "size", net->qEnd - net->qStart); printf("<BR>Fields above refer to entire chain or gap, not just the part inside the window.<BR>\n"); netAlignFree(&net); } void tfbsConsSites(struct trackDb *tdb, char *item) /* detail page for tfbsConsSites track */ { boolean printedPlus = FALSE; boolean printedMinus = FALSE; -char *dupe, *words[16]; -int wordCount; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); char table[64]; boolean hasBin; char query[512]; struct sqlResult *sr; char **row; struct tfbsConsSites *tfbsConsSites; struct tfbsConsSites *tfbsConsSitesList = NULL; struct tfbsConsFactors *tfbsConsFactor; struct tfbsConsFactors *tfbsConsFactorList = NULL; boolean firstTime = TRUE; char *mappedId = NULL; -dupe = cloneString(tdb->type); genericHeader(tdb, item); -wordCount = chopLine(dupe, words); hFindSplitTable(database, seqName, tdb->table, table, &hasBin); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { tfbsConsSites = tfbsConsSitesLoad(row+hasBin); slAddHead(&tfbsConsSitesList, tfbsConsSites); } sqlFreeResult(&sr); slReverse(&tfbsConsSitesList); hFindSplitTable(database, seqName, "tfbsConsFactors", table, &hasBin); @@ -3565,58 +3550,53 @@ { htmlHorizontalLine(); printf("<B style='font-size:large;'>Transcription Factors known to bind to this site:</B><BR><BR>"); for(tfbsConsFactor =tfbsConsFactorList ; tfbsConsFactor != NULL ; tfbsConsFactor = tfbsConsFactor ->next) { if (!sameString(tfbsConsFactor->species, "N")) { printf("<BR><B>Factor:</B> %s<BR>\n", tfbsConsFactor->factor); printf("<B>Species:</B> %s<BR>\n", tfbsConsFactor->species); printf("<B>SwissProt ID:</B> %s<BR>\n", sameString(tfbsConsFactor->id, "N")? "unknown": tfbsConsFactor->id); } } } printTrackHtml(tdb); -freez(&dupe); hFreeConn(&conn); } void tfbsCons(struct trackDb *tdb, char *item) /* detail page for tfbsCons track */ { boolean printFactors = FALSE; boolean printedPlus = FALSE; boolean printedMinus = FALSE; -char *dupe, *words[16]; -int wordCount; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); char table[64]; boolean hasBin; char query[512]; struct sqlResult *sr; char **row; struct tfbsCons *tfbs; struct tfbsCons *tfbsConsList = NULL; struct tfbsConsMap tfbsConsMap; boolean firstTime = TRUE; char *mappedId = NULL; -dupe = cloneString(tdb->type); genericHeader(tdb, item); -wordCount = chopLine(dupe, words); hFindSplitTable(database, seqName, tdb->table, table, &hasBin); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { tfbs = tfbsConsLoad(row+hasBin); slAddHead(&tfbsConsList, tfbs); } sqlFreeResult(&sr); slReverse(&tfbsConsList); if (hTableExists(database, "tfbsConsMap")) @@ -3665,74 +3645,68 @@ /* print only the positive strand when factors are on both strands */ if ((tfbs->strand[0] == '-') && printedPlus) continue; if (!sameString(tfbs->species, "N")) { printf("<BR><B>Factor:</B> %s<BR>\n", tfbs->factor); printf("<B>Species:</B> %s<BR>\n", tfbs->species); printf("<B>SwissProt ID:</B> %s<BR>\n", sameString(tfbs->id, "N")? "unknown": tfbs->id); } } } printTrackHtml(tdb); -freez(&dupe); hFreeConn(&conn); } void firstEF(struct trackDb *tdb, char *item) { -char *dupe, *words[16]; -int wordCount; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); char table[64]; boolean hasBin; struct bed *bed; char query[512]; struct sqlResult *sr; char **row; boolean firstTime = TRUE; /* itemForUrl = item; */ -dupe = cloneString(tdb->type); genericHeader(tdb, item); -wordCount = chopLine(dupe, words); printCustomUrl(tdb, item, FALSE); /* printCustomUrl(tdb, itemForUrl, item == itemForUrl); */ hFindSplitTable(database, seqName, tdb->table, table, &hasBin); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); bed = bedLoadN(row+hasBin, 6); printf("<B>Item:</B> %s<BR>\n", bed->name); printf("<B>Probability:</B> %g<BR>\n", bed->score / 1000.0); printf("<B>Strand:</B> %s<BR>\n", bed->strand); printPos(bed->chrom, bed->chromStart, bed->chromEnd, NULL, TRUE, bed->name); } printTrackHtml(tdb); -freez(&dupe); hFreeConn(&conn); } void doBed5FloatScore(struct trackDb *tdb, char *item) /* Handle click in BED 5+ track: BED 5 with 0-1000 score (for useScore * shading in hgTracks) plus real score for display in details page. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char table[64]; boolean hasBin; struct bed5FloatScore *b5; struct dyString *query = newDyString(512); char **row; boolean firstTime = TRUE; @@ -5287,58 +5261,58 @@ if ((s = skipLeadingSpaces(s)) != NULL && s[0] != 0) { int len = strlen(s); appendAuthor(dy, s, len); } } /* --- !!! Riken code is under development Fan. 4/16/02 */ void printRikenInfo(char *acc, struct sqlConnection *conn ) /* Print Riken annotation info */ { struct sqlResult *sr; char **row; char query[512]; char *seqid, *accession, *comment; -char *qualifier, *anntext, *datasrc, *srckey, *href, *evidence; +// char *qualifier, *anntext, *datasrc, *srckey, *href, *evidence; accession = acc; sqlSafef(query, sizeof(query), "select seqid from rikenaltid where altid='%s';", accession); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { seqid=cloneString(row[0]); sqlSafef(query, sizeof(query), "select Qualifier, Anntext, Datasrc, Srckey, Href, Evidence " "from rikenann where seqid='%s';", seqid); sqlFreeResult(&sr); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); while (row !=NULL) { - qualifier = row[0]; - anntext = row[1]; - datasrc = row[2]; - srckey = row[3]; - href = row[4]; - evidence = row[5]; + // qualifier = row[0]; unused variable + // anntext = row[1]; unused variable + // datasrc = row[2]; unused variable + // srckey = row[3]; unused variable + // href = row[4]; unused variable + // evidence = row[5]; unused variable row = sqlNextRow(sr); } sqlSafef(query, sizeof(query), "select comment from rikenseq where id='%s';", seqid); sqlFreeResult(&sr); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { comment = row[0]; printf("<B>Riken/comment:</B> %s<BR>\n",comment); } } @@ -5435,36 +5409,37 @@ assert(msg != NULL); char *msg2= "Care should be taken in using alignments of this sequence as evidence of transcription."; printf("<B>Warning:<span style='color:red;'> %s %s %s</span></B><BR>\n", acc, msg, msg2); } static void printRnaSpecs(struct trackDb *tdb, char *acc, struct psl *psl) /* Print auxiliarry info on RNA. */ { struct dyString *dy = newDyString(1024); struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2= hAllocConn(database); struct sqlResult *sr; char **row; char rgdEstId[512]; char query[256]; -char *type,*direction,*source,*orgFullName,*library,*clone,*sex,*tissue, +char *type,*direction,*orgFullName,*library,*clone,*sex,*tissue, *development,*cell,*cds,*description, *author,*geneName, *date,*productName; -int seqSize,fileSize; -long fileOffset; -char *ext_file; +// char *source; unused variable +// int seqSize,fileSize; unused variables +// long fileOffset; unused variable +// char *extFile; unused variable boolean hasVersion = hHasField(database, "gbCdnaInfo", "version"); boolean haveGbSeq = sqlTableExists(conn, "gbSeq"); char *seqTbl = haveGbSeq ? "gbSeq" : "seq"; char *version = NULL; struct trackDb *tdbRgdEst; char *chrom = cartString(cart, "c"); int start = cartInt(cart, "o"); int end = cartUsualInt(cart, "t",0); struct gbWarn *gbWarn = checkGbWarn(conn, acc); /* This sort of query and having to keep things in sync between * the first clause of the select, the from clause, the where * clause, and the results in the row ... is really tedious. * One of my main motivations for going to a more object * based rather than pure relational approach in general, @@ -5501,38 +5476,40 @@ " where gbCdnaInfo.acc = '%s' and gbCdnaInfo.id = %s.id ", seqTbl, acc, seqTbl); dyStringAppend(dy, "and gbCdnaInfo.source = source.id and gbCdnaInfo.organism = organism.id " "and gbCdnaInfo.library = library.id and gbCdnaInfo.mrnaClone = mrnaClone.id " "and gbCdnaInfo.sex = sex.id and gbCdnaInfo.tissue = tissue.id " "and gbCdnaInfo.development = development.id and gbCdnaInfo.cell = cell.id " "and gbCdnaInfo.cds = cds.id and gbCdnaInfo.description = description.id " "and gbCdnaInfo.author = author.id and gbCdnaInfo.geneName = geneName.id " "and gbCdnaInfo.productName = productName.id"); sr = sqlMustGetResult(conn, dy->string); row = sqlNextRow(sr); if (row != NULL) { - type=row[0];direction=row[1];source=row[2];orgFullName=row[3];library=row[4];clone=row[5]; + type=row[0];direction=row[1]; + // source=row[2]; unused variable + orgFullName=row[3];library=row[4];clone=row[5]; sex=row[6];tissue=row[7];development=row[8];cell=row[9];cds=row[10];description=row[11]; author=row[12];geneName=row[13];productName=row[14]; - seqSize = sqlUnsigned(row[15]); + // seqSize = sqlUnsigned(row[15]); unused variable date = row[16]; - ext_file = row[17]; - fileOffset=sqlUnsigned(row[18]); - fileSize=sqlUnsigned(row[19]); + // ext_file = row[17]; unused variable + // fileOffset=sqlUnsigned(row[18]); unused variable + // fileSize=sqlUnsigned(row[19]); unused variable boolean isEst = sameWord(type, "est"); if (hasVersion) { version = row[20]; } /* Now we have all the info out of the database and into nicely named * local variables. There's still a few hoops to jump through to * format this prettily on the web with hyperlinks to NCBI. */ printf("<H2>Information on %s <A HREF=\"", type); if (isEst) printEntrezEstUrl(stdout, acc); else @@ -6351,32 +6328,33 @@ char query[256]; struct sqlResult *sr; char **row; char query2[256]; struct sqlResult *sr2; char **row2; char query3[256]; struct sqlResult *sr3; char **row3; struct agpFrag frag; struct contigAcc contigAcc; int start = cartInt(cart, "o"); boolean hasBin; char splitTable[64]; char *chp; -char *accession1, *accession2, *spanner, *evaluation, *variation, *varEvidence, +char *accession1, *accession2, *spanner, *variation, *varEvidence, *contact, *remark, *comment; +// char *evaluation; unused variable char *secondAcc, *secondAccVer; char *tmpString; int first; cartWebStart(cart, database, "%s", fragName); hFindSplitTable(database, seqName, tdb->table, splitTable, &hasBin); sqlSafef(query, sizeof query, "select * from %s where frag = '%s' and chromStart = %d", splitTable, fragName, start); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); agpFragStaticLoad(row+hasBin, &frag); printf("<B>Clone Fragment ID:</B> %s<BR>\n", frag.frag); printf("<B>Clone Fragment Type:</B> %s<BR>\n", frag.type); printf("<B>Clone Bases:</B> %d-%d<BR>\n", frag.fragStart+1, frag.fragEnd); @@ -6412,31 +6390,31 @@ { sqlSafef(query2, sizeof query2, "select * from certificate where accession1='%s';", tmpString); } else { sqlSafef(query2, sizeof query2, "select * from certificate where accession2='%s';", tmpString); } sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); while (row2 != NULL) { printf("<HR>"); accession1 = row2[0]; accession2 = row2[1]; spanner = row2[2]; - evaluation = row2[3]; + // evaluation = row2[3]; unused variable variation = row2[4]; varEvidence = row2[5]; contact = row2[6]; remark = row2[7]; comment = row2[8]; if (first) { secondAcc = accession2; } else { secondAcc = accession1; } @@ -8584,31 +8562,31 @@ pslList->misMatch, pslList->nCount, pslList->tBaseInsert, hOrganism(database), pslList->qBaseInsert, item, pslScore(pslList)); printTrackHtml(tdb); hFreeConn(&conn); } void printEnsemblCustomUrl(struct trackDb *tdb, char *itemName, boolean encode, char *archive) /* Print Ensembl Gene URL. */ { char *shortItemName; -char *genomeStr = ""; +// char *genomeStr = ""; unused variable char *genomeStrEnsembl = ""; struct sqlConnection *conn = hAllocConn(database); char cond_str[256], cond_str2[256], cond_str3[256]; char *proteinID = NULL; char *ensPep; char *chp; char ensUrl[256]; char *ensemblIdUrl = trackDbSettingOrDefault(tdb, "ensemblIdUrl", "http://www.ensembl.org"); /* shortItemName is the name without the "." + version */ shortItemName = cloneString(itemName); /* ensembl gene names are different from their usual naming scheme on ce6 */ if (! startsWith("ce6", database)) { chp = strstr(shortItemName, "."); @@ -8631,37 +8609,34 @@ char query[512]; char *geneName = NULL; if (hTableExists(database, "ensemblToGeneName")) { sqlSafef(query, sizeof(query), "select value from ensemblToGeneName where name='%s'", itemName); geneName = sqlQuickString(conn, query); } char *ensemblSource = NULL; if (hTableExists(database, "ensemblSource")) { sqlSafef(query, sizeof(query), "select source from ensemblSource where name='%s'", itemName); ensemblSource = sqlQuickString(conn, query); } -boolean nonCoding = FALSE; sqlSafefFrag(query, sizeof(query), "name = \"%s\"", itemName); struct genePred *gpList = genePredReaderLoadQuery(conn, "ensGene", query); if (gpList && gpList->name2) { - if (gpList->cdsStart == gpList->cdsEnd) - nonCoding = TRUE; printf("<B>Ensembl Gene Link: </B>"); if ((strlen(gpList->name2) < 1) || sameString(gpList->name2, "noXref")) printf("none<BR>\n"); else printf("<A HREF=\"%s/geneview?gene=%s\" " "target=_blank>%s</A><BR>", ensUrl, gpList->name2, gpList->name2); } genePredFreeList(&gpList); printf("<B>Ensembl Transcript: </B>"); printf("<A HREF=\"%s/transview?transcript=%s\" " "target=_blank>", ensUrl, shortItemName); printf("%s</A><br>", itemName); if (hTableExists(database, "superfamily")) @@ -8697,30 +8672,31 @@ { if (hTableExists(database, "ensemblXref")) { proteinID=sqlGetField(database, "ensemblXref","translation_name",cond_str); } } } if (proteinID != NULL) { printf("<B>Ensembl Protein: </B>"); printf("<A HREF=\"%s/protview?peptide=%s\" target=_blank>", ensUrl, proteinID); printf("%s</A><BR>\n", proteinID); } +#ifdef NOT /* get genomeStr to be used in Superfamily URL */ if (sameWord(organism, "human")) { genomeStr = "hs"; } else { if (sameWord(organism, "mouse")) { genomeStr = "mm"; } else { if (sameWord(organism, "rat")) { @@ -8728,31 +8704,30 @@ } else { if (sameWord(organism, "dog")) { genomeStr = "dg"; } else { warn("Organism %s not found!", organism); return; } } } } -#ifdef NOT /* superfamily does not update with ensGene updates, stop printing an invalid URL */ sqlSafefFrag(cond_str, "name='%s'", shortItemName); char *ans = sqlGetField(conn, database, "superfamily", "name", cond_str); if (ans != NULL) { /* double check to make sure trackDb is also updated to be in sync with existence of supfamily table */ struct trackDb *tdbSf = hashFindVal(trackHash, "superfamily"); if (tdbSf != NULL) { char supfamURL[512]; printf("<B>Superfamily Link: </B>"); safef(supfamURL, sizeof(supfamURL), "<A HREF=\"%s%s;seqid=%s\" target=_blank>", tdbSf->url, genomeStr, proteinID); printf("%s%s</A><BR>\n", supfamURL, proteinID); @@ -9114,56 +9089,49 @@ printf("<HR>"); printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, TRUE, transcript); } sqlFreeResult(&sr); } printTrackHtml(tdb); } void doOmimAv(struct trackDb *tdb, char *avName) /* Process click on an OMIM AV. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; -char *chrom, *chromStart, *chromEnd; char *chp; char *omimId, *avSubFdId; char *avDescStartPos, *avDescLen; char *omimTitle = cloneString(""); char *geneSymbol = NULL; int iAvDescStartPos = 0; int iAvDescLen = 0; struct lineFile *lf; char *line; int lineSize; cartWebStart(cart, database, "%s (%s)", tdb->longLabel, avName); sqlSafef(query, sizeof(query), "select * from omimAv where name = '%s'", avName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find %s in omimAv table - database inconsistency.", avName); -else - { - chrom = cloneString(row[1]); - chromStart = cloneString(row[2]); - chromEnd = cloneString(row[3]); - } sqlFreeResult(&sr); omimId = strdup(avName); chp = strstr(omimId, "."); *chp = '\0'; chp++; avSubFdId = chp; sqlSafef(query, sizeof(query), "select title, geneSymbol from hgFixed.omimTitle where omimId = %s", omimId); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { omimTitle = cloneString(row[0]); @@ -9480,59 +9448,60 @@ /* Print details of a COSMIC entry. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2 = hAllocConn(database); char query[1024]; char query2[1024]; struct sqlResult *sr; struct sqlResult *sr2; char **row; char **row2; char *chp; char indent1[40] = {" "}; char indent2[40] = {""}; -char *source, *cosmic_mutation_id, *gene_name, *accession_number; +char *gene_name, *accession_number; +// char $source, *cosmic_mutation_id; unused variable char *mut_description, *mut_syntax_cds, *mut_syntax_aa; char *chromosome, *grch37_start, *grch37_stop, *mut_nt; char *mut_aa, *tumour_site, *mutated_samples, *examined_samples, *mut_freq; char *url = tdb->url; char *chrom, *chromStart, *chromEnd; chrom = cartOptionalString(cart, "c"); chromStart = cartOptionalString(cart, "o"); chromEnd = cartOptionalString(cart, "t"); sqlSafef(query, sizeof(query), "select source,cosmic_mutation_id,gene_name,accession_number,mut_description,mut_syntax_cds,mut_syntax_aa," "chromosome,grch37_start,grch37_stop,mut_nt,mut_aa,tumour_site,mutated_samples,examined_samples,mut_freq" " from cosmicRaw where cosmic_mutation_id='%s'", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { int ii; boolean multipleTumorSites; char *indentString; ii=0; - source = row[ii];ii++; - cosmic_mutation_id = row[ii];ii++; + ii++; // source = row[ii];ii++; unused variable + ii++; // cosmic_mutation_id = row[ii];ii++; unused variable gene_name = row[ii];ii++; accession_number = row[ii];ii++; mut_description = row[ii];ii++; mut_syntax_cds = row[ii];ii++; mut_syntax_aa = row[ii];ii++; chromosome = row[ii];ii++; grch37_start = row[ii];ii++; grch37_stop = row[ii];ii++; mut_nt = row[ii];ii++; mut_aa = row[ii];ii++; tumour_site = row[ii];ii++; mutated_samples = row[ii];ii++; examined_samples = row[ii];ii++; mut_freq = row[ii];ii++; @@ -10358,69 +10327,65 @@ printOmimLocationDetails(tdb, item, FALSE); printTrackHtml(tdb); } void printOmimAvSnpDetails(struct trackDb *tdb, char *itemName, boolean encode) /* Print details of an OMIM AvSnp entry. */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; char *url = tdb->url; char *title1 = NULL; char *title2 = NULL; char *chrom, *chromStart, *chromEnd; -char *omimId; char *avId; char *dbSnpId; char *chp; -char *seqId = NULL; char avString[255]; char *avDesc = NULL; chrom = cartOptionalString(cart, "c"); chromStart = cartOptionalString(cart, "o"); chromEnd = cartOptionalString(cart, "t"); avId = strdup(itemName); chp = strstr(avId, "-"); if (chp != NULL) *chp = '\0'; safef(avString, sizeof(avString), "%s", itemName); chp = strstr(itemName, "."); *chp = '\0'; -omimId = strdup(itemName); chp = avString; chp = strstr(avString, "."); *chp = '#'; if (url != NULL && url[0] != 0) { sqlSafef(query, sizeof(query), "select title1, title2, format(seqNo/10000,4), v.description" " from omimGeneMap m, omimAv v" " where m.omimId=%s and m.omimId=v.omimId and v.avId='%s';", itemName, avId); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { - seqId = strdup(row[2]); if (row[0] != NULL) { title1 = cloneString(row[0]); } if (row[1] != NULL) { title2 = cloneString(row[1]); } avDesc = cloneString(row[3]); } sqlFreeResult(&sr); printf("<B>OMIM Allelic Variant: "); printf("<A HREF=\"%s%s\" target=_blank>", url, avString); printf("%s</A></B>", avId); @@ -10748,51 +10713,50 @@ printTrackHtml(tdb); hFreeConn(&conn); } void doRgdGene2(struct trackDb *tdb, char *rgdGeneId) /* Process click on a RGD gene. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; char *sqlRnaName = rgdGeneId; char *rgdId = NULL; char *chp; char *GeneID, *Name, *note; -char *rgdPathwayId; char *rgdPathwayName; /* Make sure to escape single quotes for DB parseability */ if (strchr(rgdGeneId, '\'')) sqlRnaName = replaceChars(rgdGeneId, "'", "''"); cartWebStart(cart, database, "%s", tdb->longLabel); chp = strstr(rgdGeneId, ":"); if (chp != NULL) { chp++; rgdId = strdup(chp); } else { errAbort("Couldn't find %s.", rgdGeneId); } -sqlSafef(query, sizeof(query), "select GeneID, Name, note from rgdGeneXref where rgdGeneId = '%s'", rgdGeneId); +sqlSafef(query, sizeof(query), "select GeneID, Name, note from rgdGeneXref where rgdGeneId = '%s'", sqlRnaName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find %s in rgdGeneXref table - database inconsistency.", rgdGeneId); GeneID = cloneString(row[0]); Name = cloneString(row[1]); note = cloneString(row[2]); sqlFreeResult(&sr); printf("<H2>Gene %s</H2>\n", Name); printf("<B>RGD Gene Report: </B> <A HREF=\""); printf("%s%s", tdb->url, rgdId); printf("\" TARGET=_blank>RGD:%s</A>", rgdId); @@ -10844,31 +10808,30 @@ row = sqlNextRow(sr); } } sqlFreeResult(&sr); htmlHorizontalLine(); printf("<H3>RGD Pathway(s)</H3>\n"); sqlSafef(query, sizeof(query), "select p.rgdPathwayId, p.name from rgdGenePathway g, rgdPathway p where g.rgdGeneId = '%s' and g.rgdPathwayId=p.rgdPathwayId", rgdGeneId); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find %s in rgdGenePathway table - database inconsistency.", rgdGeneId); printf("<UL>"); while (row != NULL) { - rgdPathwayId = cloneString(row[0]); rgdPathwayName = cloneString(row[1]); printf("<LI><B>%s</B><BR>", rgdPathwayName); row = sqlNextRow(sr); } sqlFreeResult(&sr); printf("</UL>"); printf("<A HREF=\""); printf("%s%s%s", "http://rgd.mcw.edu/tools/genes/gene_ont_view.cgi?id=", rgdId, "#Pathway"); printf("\" TARGET=_blank> %s</A> </H3>", "Click here for more RGD pathway details related to this gene..."); htmlHorizontalLine(); printTrackHtml(tdb); hFreeConn(&conn); } @@ -12247,41 +12210,37 @@ void doSangerGene(struct trackDb *tdb, char *geneName, char *pepTable, char *mrnaTable, char *extraTable) /* Handle click on Sanger gene track. */ { genericHeader(tdb, geneName); showSangerExtra(geneName, extraTable); geneShowCommon(geneName, tdb, pepTable); printTrackHtml(tdb); } void doTrnaGenesGb(struct trackDb *tdb, char *trnaName) { struct tRNAs *trna; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; -char *dupe, *words[16]; char **row; -int wordCount; int rowOffset; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); genericHeader(tdb,trnaName); -dupe = cloneString(tdb->type); -wordCount = chopLine(dupe, words); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sqlSafef(query, ArraySize(query), "select * from %s where name = '%s' and chromStart=%d and chromEnd=%d", tdb->table, trnaName, start, end); sr = sqlGetResult(conn, query); /* use TABLE to align image with other info side by side */ printf("<TABLE>"); while ((row = sqlNextRow(sr)) != NULL) { char imgFileName[512]; char encodedName[255]; char *chp1, *chp2; @@ -13469,36 +13428,35 @@ if (hTableExists(database, chainTable_chrom) ) { /* lookup chain if not stored */ char **row; struct sqlResult *sr = NULL; sqlDyStringPrintf(dy, "select id, score, qStart, qEnd, qStrand, qSize from %s where ", chainTable_chrom); hAddBinToQuery(chromStart, chromEnd, dy); dyStringPrintf(dy, "tEnd > %d and tStart < %d ", chromStart,chromEnd); dyStringAppend(dy, " order by qStart"); sr = sqlGetResult(conn, dy->string); while ((row = sqlNextRow(sr)) != NULL) { - int chainId = 0, score; + int chainId = 0; unsigned int qStart, qEnd, qSize; struct chain *chain = NULL; char qStrand; chainId = sqlUnsigned(row[0]); - score = sqlUnsigned(row[1]); qStart = sqlUnsigned(row[2]); qEnd = sqlUnsigned(row[3]); qStrand =row[4][0]; qSize = sqlUnsigned(row[5]); if (qStrand == '-') { unsigned int tmp = qSize - qEnd; qEnd = qSize - qStart; qStart = tmp; } chain = NULL; if (chainId != 0) { chain = chainLoadIdRange(database, chainTable, chrom, chromStart, chromEnd, chainId); if (chain != NULL) @@ -15354,47 +15312,45 @@ } return rsId; } void doSnpEntrezGeneLink(struct trackDb *tdb, char *name) /* print link to EntrezGene for this SNP */ { char *table = tdb->table; if (hTableExists(database, "knownGene") && hTableExists(database, "refLink") && hTableExists(database, "mrnaRefseq") && hTableExists(database, table)) { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[512]; - int rowOffset; sqlSafef(query, sizeof(query), "select distinct " " rl.locusLinkID, " " rl.name " "from knownGene kg, " " refLink rl, " " %s snp, " " mrnaRefseq mrs " "where snp.chrom = kg.chrom " " and kg.name = mrs.mrna " " and mrs.refSeq = rl.mrnaAcc " " and kg.txStart < snp.chromStart " " and kg.txEnd > snp.chromEnd " " and snp.name = '%s'", table, name); - rowOffset = hOffsetPastBin(database, seqName, table); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { printf("<BR><A HREF=\"http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?"); printf("geneId=%s\" TARGET=_blank>Entrez Gene for ", row[0]); printf("%s</A><BR>\n", row[1]); } sqlFreeResult(&sr); hFreeConn(&conn); } } void doSnpOld(struct trackDb *tdb, char *itemName) /* Put up info on a SNP. */ { @@ -18418,31 +18374,30 @@ hFreeConn(&conn2); hFreeConn(&conn); } void doJaxPhenotype(struct trackDb *tdb, char *item) /* Show gene prediction position and other info. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row = NULL; boolean hasBin; char query[512]; char aliasTable[256], phenoTable[256]; struct slName *phenoList = NULL, *pheno = NULL; boolean first = TRUE; -int chromStart=0, chromEnd=0; char *selectedPheno = NULL; /* Parse out the selected phenotype passed in from hgTracks. */ if ((selectedPheno = strstr(item, " source=")) != NULL) { *selectedPheno = '\0'; selectedPheno += strlen(" source="); } genericHeader(tdb, item); safef(aliasTable, sizeof(aliasTable), "%sAlias", tdb->table); safef(phenoTable, sizeof(phenoTable), "jaxAllelePheno"); sqlSafefFrag(query, sizeof(query), "name = \"%s\"", item); sr = hRangeQuery(conn, tdb->table, seqName, winStart, winEnd, query, &hasBin); while ((row = sqlNextRow(sr)) != NULL) @@ -18457,32 +18412,30 @@ if (hTableExists(database, aliasTable)) { struct sqlConnection *conn2 = hAllocConn(database); char query2[512]; char buf[512]; char *mgiId; sqlSafef(query2, sizeof(query2), "select alias from %s where name = '%s'", aliasTable, item); mgiId = sqlQuickQuery(conn2, query2, buf, sizeof(buf)); if (mgiId != NULL) printCustomUrl(tdb, mgiId, TRUE); hFreeConn(&conn2); } printPos(bed->chrom, bed->chromStart, bed->chromEnd, bed->strand, FALSE, NULL); - chromStart = bed->chromStart; - chromEnd = bed->chromEnd; bedFree(&bed); } pheno = slNameNew(row[hasBin+12]); slAddHead(&phenoList, pheno); } sqlFreeResult(&sr); printf("<B>Phenotype(s) at this locus: </B> "); first = TRUE; slNameSort(&phenoList); for (pheno = phenoList; pheno != NULL; pheno = pheno->next) { if (first) first = FALSE; else printf(", "); @@ -19468,48 +19421,44 @@ printf("<b>Genbank accession:</b> %s<br>\n", chick->gbkAcc); printf("<b>BLAT alignment:</b> %s<br>\n", chick->blat); printf("<b>Source annotation:</b> %s<br>\n", chick->sourceAnnot); printf("<b>TIGR assigned TC:</b> %s<br>\n", chick->tigrTc); printf("<b>TIGR TC annotation:</b> %s<br>\n", chick->tigrTcAnnot); printf("<b>BLAST determined annotation:</b> %s<br>\n", chick->blastAnnot); printf("<b>Comment:</b> %s<br>\n", chick->comment); } genericBedClick(conn, tdb, item, start, 1); printTrackHtml(tdb); hFreeConn(&conn); } void perlegenDetails(struct trackDb *tdb, char *item) { -char *dupe, *words[16]; -int wordCount; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); char table[64]; boolean hasBin; struct bed *bed; char query[512]; struct sqlResult *sr; char **row; boolean firstTime = TRUE; int numSnpsReq = -1; if(tdb == NULL) errAbort("TrackDb entry null for perlegen, item=%s\n", item); -dupe = cloneString(tdb->type); genericHeader(tdb, item); -wordCount = chopLine(dupe, words); printCustomUrl(tdb, item, FALSE); hFindSplitTable(database, seqName, tdb->table, table, &hasBin); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *name; /* set up for first time */ if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); bed = bedLoadN(row+hasBin, 12); @@ -19542,93 +19491,85 @@ } /* finish off report ... */ printf("<B>Block:</B> %s<BR>\n", name); printf("<B>Number of SNPs in block:</B> %d<BR>\n", bed->blockCount); printf("<B>Number of SNPs to represent block:</B> %d<BR>\n",numSnpsReq); printf("<B>Strand:</B> %s<BR>\n", bed->strand); bedPrintPos(bed, 3, tdb); } printTrackHtml(tdb); hFreeConn(&conn); } void haplotypeDetails(struct trackDb *tdb, char *item) { -char *dupe, *words[16]; -int wordCount; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); char table[64]; boolean hasBin; struct bed *bed; char query[512]; struct sqlResult *sr; char **row; boolean firstTime = TRUE; if(tdb == NULL) errAbort("TrackDb entry null for haplotype, item=%s\n", item); -dupe = cloneString(tdb->type); genericHeader(tdb, item); -wordCount = chopLine(dupe, words); printCustomUrl(tdb, item, TRUE); hFindSplitTable(database, seqName, tdb->table, table, &hasBin); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { /* set up for first time */ if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); bed = bedLoadN(row+hasBin, 12); /* finish off report ... */ printf("<B>Block:</B> %s<BR>\n", bed->name); printf("<B>Number of SNPs in block:</B> %d<BR>\n", bed->blockCount); /* printf("<B>Number of SNPs to represent block:</B> %d<BR>\n",numSnpsReq);*/ printf("<B>Strand:</B> %s<BR>\n", bed->strand); bedPrintPos(bed, 3, tdb); } printTrackHtml(tdb); hFreeConn(&conn); } void mitoDetails(struct trackDb *tdb, char *item) { -char *dupe, *words[16]; -int wordCount; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); char table[64]; boolean hasBin; struct bed *bed; char query[512]; struct sqlResult *sr; char **row; boolean firstTime = TRUE; int numSnpsReq = -1; if(tdb == NULL) errAbort("TrackDb entry null for mitoSnps, item=%s\n", item); -dupe = cloneString(tdb->type); genericHeader(tdb, item); -wordCount = chopLine(dupe, words); printCustomUrl(tdb, item, TRUE); hFindSplitTable(database, seqName, tdb->table, table, &hasBin); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *name; /* set up for first time */ if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); bed = bedLoadN(row+hasBin, 12); @@ -19660,48 +19601,44 @@ break; } /* finish off report ... */ printf("<B>Block:</B> %s<BR>\n", name); printf("<B>Number of SNPs in block:</B> %d<BR>\n", bed->blockCount); printf("<B>Number of SNPs to represent block:</B> %d<BR>\n",numSnpsReq); printf("<B>Strand:</B> %s<BR>\n", bed->strand); bedPrintPos(bed, 3, tdb); } printTrackHtml(tdb); hFreeConn(&conn); } void ancientRDetails(struct trackDb *tdb, char *item) { -char *dupe, *words[16]; -int wordCount; struct sqlConnection *conn = hAllocConn(database); char table[64]; boolean hasBin; struct bed *bed = NULL; char query[512]; struct sqlResult *sr = NULL; char **row; boolean firstTime = TRUE; double ident = -1.0; struct ancientRref *ar = NULL; if(tdb == NULL) errAbort("TrackDb entry null for ancientR, item=%s\n", item); -dupe = cloneString(tdb->type); genericHeader(tdb, item); -wordCount = chopLine(dupe, words); printCustomUrl(tdb, item, TRUE); hFindSplitTable(database, seqName, tdb->table, table, &hasBin); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s'", table, item, seqName ); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *name; /* set up for first time */ if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); bed = bedLoadN(row+hasBin, 12); @@ -20435,31 +20372,30 @@ { int humMusWinSize = 50; int i; char table[64]; boolean hasBin; struct sample *smp; char query[512]; char tempTableName[1024]; struct sqlResult *sr; char **row; char **pslRow; boolean firstTime = TRUE; struct psl *thisPsl; char str[256]; char thisItem[256]; -char *cgiItem; char otherString[256] = ""; struct sqlResult *pslSr; struct sqlConnection *conn2 = hAllocConn(database); int thisStart, thisEnd; int left = cartIntExp( cart, "l" ); int right = cartIntExp( cart, "r" ); char *winOn = cartUsualString( cart, "win", "F" ); hFindSplitTable(database, seqName, tdb->table, table, &hasBin); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s'", table, item, seqName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) @@ -20471,31 +20407,30 @@ hFindSplitTable(database, seqName, pslTableName, table, &hasBin); sqlSafef(query, sizeof query, "select * from %s where tName = '%s' and tEnd >= %d and tStart <= %d" , table, smp->chrom, smp->chromStart+smp->samplePosition[0] , smp->chromStart+smp->samplePosition[smp->sampleCount-1] ); pslSr = sqlGetResult(conn2, query); if(!sameString(winOn,"T")) { while(( pslRow = sqlNextRow(pslSr)) != NULL ) { thisPsl = pslLoad( pslRow+hasBin ); firstAndLastPosition( &thisStart, &thisEnd, thisPsl ); snprintf(thisItem, 256, "%s:%d-%d %s:%d-%d", thisPsl->qName, thisPsl->qStart, thisPsl->qEnd, thisPsl->tName, thisPsl->tStart, thisPsl->tEnd ); - cgiItem = cgiEncode(thisItem); longXenoPsl1Given(tdb, thisItem, otherOrg, "chromInfo", otherDb, thisPsl, pslTableName ); safef(otherString, sizeof otherString, "%d&win=T", thisPsl->tStart ); hgcAnchorSomewhere( tdb->track, cgiEncode(item), otherString, thisPsl->tName ); printf("View individual alignment windows\n</a>"); printf("<br><br>"); } } else { cartSetString( cart, "win", "F" ); printf("<h3>Alignments Windows </h3>\n" "<b>start stop" " L-score</b><br>" ); while(( pslRow = sqlNextRow(pslSr)) != NULL ) @@ -20569,65 +20504,63 @@ smp->chromStart+smp->samplePosition[smp->sampleCount-1] ); printf("Content-Type: text/html\n\n<HTML><BODY><SCRIPT>\n"); printf("location.replace('%s')\n",filename); printf("</SCRIPT> <NOSCRIPT> No JavaScript support. " "Click <b><a href=\"%s\">continue</a></b> for " "the requested GenBank report. </NOSCRIPT>\n", filename); } } void humMusClickHandler(struct trackDb *tdb, char *item, char *targetName, char *targetDb, char *targetTable, boolean printWindowFlag ) /* Put up sample track info. */ { -char *type, *words[16], *dupe = cloneString(tdb->type); +char *words[16], *dupe = cloneString(tdb->type); int num; int wordCount; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); genericHeader(tdb, item); wordCount = chopLine(dupe, words); if (wordCount > 0) { - type = words[0]; num = 0; if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; humMusSampleClick( conn, tdb, item, start, num, targetName, targetDb, targetTable, printWindowFlag ); } printTrackHtml(tdb); freez(&dupe); hFreeConn(&conn); } void footPrinterClickHandler(struct trackDb *tdb, char *item ) /* Put up generic track info. */ { -char *type, *words[16], *dupe = cloneString(tdb->type); +char *words[16], *dupe = cloneString(tdb->type); int num; int wordCount; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); wordCount = chopLine(dupe, words); if (wordCount > 0) { - type = words[0]; num = 0; if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; footPrinterSampleClick(conn, tdb, item, start, num); } printTrackHtml(tdb); freez(&dupe); hFreeConn(&conn); } void hgCustom(char *trackId, char *fileItem) /* Process click on custom track. */ { char *fileName, *itemName; @@ -21255,76 +21188,72 @@ } bedFree(&bed); } else errAbort("query returned no results: \"%s\"", query); sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } void doScaffoldEcores(struct trackDb *tdb, char *item) /* Creates details page and gets the scaffold co-ordinates for unmapped */ /* genomes for display and to use to create the correct outside link URL */ { -char *dupe, *words[16]; -int wordCount; +char *words[16]; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); int num; struct bed *bed = NULL; char query[512]; struct sqlResult *sr; char **row; char *scaffoldName; int scaffoldStart, scaffoldEnd; struct dyString *itemUrl = newDyString(128), *d; char *old = "_"; char *new = ""; char *pat = "fold"; int hasBin = 1; -dupe = cloneString(tdb->type); -wordCount = chopLine(dupe, words); /* get bed size */ num = 0; num = atoi(words[1]); /* get data for this item */ sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chromStart = %d", tdb->table, item, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) bed = bedLoadN(row+hasBin, num); genericHeader(tdb, item); /* convert chromosome co-ordinates to scaffold position and */ /* make into item for URL */ if (hScaffoldPos(database, bed->chrom, bed->chromStart, bed->chromEnd, &scaffoldName, &scaffoldStart, &scaffoldEnd) ) { scaffoldStart += 1; dyStringPrintf(itemUrl, "%s:%d-%d", scaffoldName, scaffoldStart, scaffoldEnd); /* remove underscore in scaffold name and change to "scafN" */ d = dyStringSub(itemUrl->string, old, new); itemUrl = dyStringSub(d->string, pat, new); printCustomUrl(tdb, itemUrl->string, TRUE); } genericBedClick(conn, tdb, item, start, num); printTrackHtml(tdb); dyStringFree(&itemUrl); -freez(&dupe); sqlFreeResult(&sr); hFreeConn(&conn); } char *stripBDGPSuffix(char *name) /* cloneString(name), and if it ends in -R[A-Z], strip that off. */ { char *stripped = cloneString(name); int len = strlen(stripped); if (stripped[len-3] == '-' && stripped[len-2] == 'R' && isalpha(stripped[len-1])) stripped[len-3] = 0; return(stripped); } @@ -22559,61 +22488,59 @@ qSeq = loadGenomePart(db, psl->qName, psl->qStart, psl->qEnd); safef(name, sizeof name, "%s in %s(%d-%d)", item,psl->qName, psl->qStart, psl->qEnd); writeFramesetType(); puts("<HTML>"); printf("<HEAD>\n<TITLE>%s %dk</TITLE>\n</HEAD>\n\n", name, psl->qStart/1000); showSomeAlignment2(psl, qSeq, gftDnaX, psl->qStart, psl->qEnd, name, item, "", psl->qStart, psl->qEnd); } void doPutaFrag(struct trackDb *tdb, char *item) /* display the potential pseudo and coding track */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row, table[256], query[256], *parts[6]; struct putaInfo *info = NULL; -struct psl *psl = NULL; int start = cartInt(cart, "o"), end = cartInt(cart, "t"); char *db = cgiString("db"); char *name = cartString(cart, "i"), *chr = cartString(cart, "c"); char pslTable[256]; -char otherString[256], *tempName = NULL; -int partCount; +char otherString[256]; safef(table, sizeof table, "putaInfo"); safef(pslTable, sizeof pslTable, "potentPsl"); cartWebStart(cart, database, "Putative Coding or Pseudo Fragments"); sqlSafef(query, sizeof query, "SELECT * FROM %s WHERE name = '%s' " "AND chrom = '%s' AND chromStart = %d " "AND chromEnd = %d", table, name, chr, start, end); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if(row != NULL) { info = putaInfoLoad(row+1); } else { errAbort("Can't find information for %s in data base\n", name); } sqlFreeResult(&sr); -tempName = cloneString(name); -partCount = chopByChar(tempName, '|',parts, 4); +char *tempName = cloneString(name); +chopByChar(tempName, '|',parts, 4); printf("<B>%s</B> is homologous to the known gene: <A HREF=\"", name); printEntrezNucleotideUrl(stdout, parts[0]); printf("\" TARGET=_blank>%s</A><BR>\n", parts[0]); printf("<B>%s </B>is aligned here with score : %d<BR><BR>\n", parts[0], info->score); /* print the info about the stamper gene */ printf("<B> %s</B><BR>\n", parts[0]); printf("<B>Genomic location of the mapped part of %s</B>: <A HREF=\"" "%s?db=%s&position=%s:%d-%d\" TARGET=_blank>%s(%s):%d-%d </A> <BR>\n", parts[0], hgTracksName(), db, info->oChrom, info->oChromStart, info->oChromEnd, info->oChrom, parts[2],info->oChromStart+1, info->oChromEnd); printf("<B>Mapped %s Exons</B>: %d of %d. <BR> <B>Mapped %s CDS exons</B>: %d of %d <BR>\n", parts[0], info->qExons[0], info->qExons[1], parts[0], info->qExons[2], info->qExons[3]); printf("<b>Aligned %s bases</B>:%d of %d with %f identity. <BR> <B>Aligned %s CDS bases</B>: %d of %d with %f identity.<BR><BR>\n", parts[0],info->qBases[0], info->qBases[1], info->id[0], parts[0], info->qBases[2], info->qBases[3], info->id[1]); @@ -22645,31 +22572,30 @@ /* show genome sequence */ hgcAnchorSomewhere("htcGeneInGenome", cgiEncode(info->name), tdb->track, seqName); printf("View DNA for this putative fragment</A><BR>\n"); /* show the detail alignment */ sqlSafef(query, sizeof query, "SELECT * FROM %s WHERE " "tName = '%s' AND tStart = %d " "AND tEnd = %d AND strand = '%c%c'", pslTable, info->chrom, info->chromStart, info->chromEnd, parts[2][0], info->strand[0]); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if(row != NULL) { - psl = pslLoad(row+1); safef(otherString, sizeof otherString, "&db=%s&pslTable=%s&chrom=%s&cStart=%d&cEnd=%d&strand=%s&qStrand=%s", database, pslTable, info->chrom,info->chromStart, info->chromEnd, info->strand, parts[2]); hgcAnchorSomewhere("potentPsl", cgiEncode(parts[0]), otherString, info->chrom); printf("<BR>View details of parts of alignment </A>.</BR>\n"); } sqlFreeResult(&sr); putaInfoFree(&info); hFreeConn(&conn); } void doInterPro(struct trackDb *tdb, char *itemName) { char condStr[255]; char *desc; struct sqlConnection *conn; @@ -24104,31 +24030,31 @@ printTrackHtml(tdb); hFreeConn(&conn); } void doUCSFDemo(struct trackDb *tdb, char *item) { genericHeader(tdb, item); printf("<B>Name:</B> %s<BR>\n", item); /* this prints the detail page for the clinical information for Cancer Demo datasets */ char *table = tdb->table; char *cliniTable=NULL, *key=NULL; char query[256]; struct sqlConnection *conn = hAllocConn(database); -struct sqlResult *sr, *startSr; +struct sqlResult *sr; char **row; if (sameString(table, "CGHBreastCancerUCSF") || sameString(table, "expBreastCancerUCSF")) { cliniTable = "phenBreastTumors"; key = "id"; /* er, pr */ printf("<BR>"); printf("<TABLE BORDER=1>\n"); printf("<TR><TH>ER</TH> <TH>PR</TH></TR>\n"); sqlSafef(query, sizeof(query), "select er, pr from %s where %s = '%s' ", cliniTable, key, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { @@ -24289,32 +24215,30 @@ { cliniTable = "tspLungClinical"; key = "tumorID"; } else return; htmlHorizontalLine(); sqlSafef(query, sizeof(query), "select * from %s where %s = '%s' ", cliniTable, key,item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { - startSr = sr; - int numFields = sqlCountColumns(sr); int i; char *fieldName=NULL, *value=NULL; for (i=0; i< numFields; i++) { fieldName = sqlFieldName(sr); value = row[i]; printf("%s: <B>%s</B><BR>\n", fieldName, value); } } sqlFreeResult(&sr); //printTrackHtml(tdb); //hFreeConn }