2a4f1d79a36aac4a294c5d332f3b599ebe9be0dc larrym Mon May 14 16:32:21 2012 -0700 fix cruft that was causing an empty "Ensembl" in blue bar for fr2 (pointed out by greg); menuBar => printMenuBar to fix name collision with some new code diff --git src/hg/hgTracks/menu.c src/hg/hgTracks/menu.c index ed3c51a..74d7373 100644 --- src/hg/hgTracks/menu.c +++ src/hg/hgTracks/menu.c @@ -1,457 +1,455 @@ // Code to create hgTracks menu bar #include "common.h" #include "dystring.h" #include "ensFace.h" #include "agpFrag.h" #include "ctgPos.h" #include "hCommon.h" #include "htmshell.h" #include "hash.h" #include "liftOver.h" #include "wikiLink.h" #include "hgTracks.h" /* list of links to display in a menu */ struct hotLink { struct hotLink *next; char *name; char *url; char *id; boolean external; }; static void appendLink(struct hotLink **links, char *url, char *name, char *id, boolean external) { // append to list of links for later printing and/or communication with javascript client struct hotLink *link; AllocVar(link); link->name = cloneString(name); link->url = cloneString(url); link->id = cloneString(id); link->external = external; slAddTail(links, link); } static void printEnsemblAnchor(char *database, char* archive, char *chrName, int start, int end, struct hotLink **links) /* Print anchor to Ensembl display on same window. */ { char *scientificName = hScientificName(database); char *dir = ensOrgNameFromScientificName(scientificName); struct dyString *ensUrl; char *name; int localStart, localEnd; name = chrName; if (sameWord(scientificName, "Takifugu rubripes")) { /* for Fugu, must give scaffold, not chr coordinates */ /* Also, must give "chrom" as "scaffold_N", name below. */ if (differentWord(chromName,"chrM") && !hScaffoldPos(database, chromName, winStart, winEnd, &name, &localStart, &localEnd)) /* position doesn't appear on Ensembl browser. * Ensembl doesn't show scaffolds < 2K */ return; } else if (sameWord(scientificName, "Gasterosteus aculeatus")) { if (differentWord("chrM", chrName)) { char *fixupName = replaceChars(chrName, "chr", "group"); name = fixupName; } } else if (sameWord(scientificName, "Ciona intestinalis")) { if (stringIn("chr0", chrName)) { char *fixupName = replaceChars(chrName, "chr0", "chr"); name = fixupName; } } else if (sameWord(scientificName, "Saccharomyces cerevisiae")) { if (stringIn("2micron", chrName)) { char *fixupName = replaceChars(chrName, "2micron", "2-micron"); name = fixupName; } } if (sameWord(chrName, "chrM")) name = "chrMt"; ensUrl = ensContigViewUrl(database, dir, name, seqBaseCount, start+1, end, archive); appendLink(links, ensUrl->string, "Ensembl", "ensemblLink", TRUE); /* NOTE: you can not freeMem(dir) because sometimes it is a literal * constant */ freeMem(scientificName); dyStringFree(&ensUrl); } static void fr2ScaffoldEnsemblLink(char *archive, struct hotLink **links) /* print out Ensembl link to appropriate scaffold there */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row = NULL; char query[256]; safef(query, sizeof(query), "select * from chrUn_gold where chrom = '%s' and chromStart<%u and chromEnd>%u", chromName, winEnd, winStart); sr = sqlGetResult(conn, query); int itemCount = 0; struct agpFrag *agpItem = NULL; while ((row = sqlNextRow(sr)) != NULL) { agpFragFree(&agpItem); // if there is a second one agpItem = agpFragLoad(row+1); ++itemCount; if (itemCount > 1) break; } sqlFreeResult(&sr); hFreeConn(&conn); if (1 == itemCount) { // verify *entirely* within single contig if ((winEnd <= agpItem->chromEnd) && (winStart >= agpItem->chromStart)) { int agpStart = winStart - agpItem->chromStart; int agpEnd = agpStart + winEnd - winStart; - hPuts("<TD ALIGN=CENTER>"); printEnsemblAnchor(database, archive, agpItem->frag, agpStart, agpEnd, links); - hPrintf("%s</A></TD>", "Ensembl"); } } agpFragFree(&agpItem); // the one we maybe used } -void menuBar() +void printMenuBar() /* Put up the menu bar. */ { boolean gotBlat = hIsBlatIndexedDatabase(database); struct dyString *uiVars = uiStateUrlPart(NULL); char *orgEnc = cgiEncode(organism); boolean psOutput = cgiVarExists("hgt.psOutput"); struct hotLink *link, *links = NULL; hPrintf("<TABLE WIDTH=\"100%%\" BGCOLOR=\"#000000\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"1\"><TR><TD>\n"); hPrintf("<TABLE WIDTH=\"100%%\" BGCOLOR=\"#2636D1\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"0\"><TR>\n"); hPrintf("<TD><TABLE BORDER=\"0\"><TR>\n"); hPrintf("<TD ALIGN=CENTER><A HREF=\"../index.html?org=%s&db=%s&%s=%u\" class=\"topbar\">Home</A> </TD>", orgEnc, database, cartSessionVarName(), cartSessionId(cart)); if (hIsGisaidServer()) { /* disable hgGateway for gisaid for now */ //hPrintf("<TD ALIGN=CENTER> <A HREF=\"../cgi-bin/hgGateway?org=%s&db=%s\" class=\"topbar\">Sequence View Gateway</A> </TD>", orgEnc, database); hPrintf( "<TD ALIGN=CENTER> <A HREF=\"../cgi-bin/gisaidTable?gisaidTable.do.advFilter=filter+%c28now+on%c29&fromProg=hgTracks&%s=%u\" class=\"topbar\">%s</A> </TD>", '%', '%', cartSessionVarName(), cartSessionId(cart), "Select Subjects"); } else if (hIsGsidServer()) { hPrintf("<TD ALIGN=CENTER> <A HREF=\"../cgi-bin/hgGateway?org=%s&db=%s\" class=\"topbar\">Sequence View Gateway</A> </TD>", orgEnc, database); hPrintf( "<TD ALIGN=CENTER> <A HREF=\"../cgi-bin/gsidTable?gsidTable.do.advFilter=filter+%c28now+on%c29&fromProg=hgTracks\" class=\"topbar\">%s</A> </TD>", '%', '%', "Select Subjects"); } else { hPrintf("<TD ALIGN=CENTER> <A HREF=\"../cgi-bin/hgGateway?org=%s&db=%s&%s=%u\" class=\"topbar\">Genomes</A> </TD>", orgEnc, database, cartSessionVarName(), cartSessionId(cart)); } if (psOutput) { hPrintf("<TD ALIGN=CENTER nowrap> <A HREF=\"../cgi-bin/hgTracks?hgTracksConfigPage=notSetorg=%s&db=%s&%s=%u\" class='topbar'>Genome Browser</A> </TD>", orgEnc, database, cartSessionVarName(), cartSessionId(cart)); } if (gotBlat) { hPrintf("<TD ALIGN=CENTER> <A HREF=\"../cgi-bin/hgBlat?%s\" class=\"topbar\">Blat</A> </TD>", uiVars->string); } if (hIsGisaidServer()) { hPrintf("<TD ALIGN=CENTER nowrap> <A HREF=\"../cgi-bin/gisaidTable?db=%s&%s=%u\" class=\"topbar\">%s</A> </TD>", database, cartSessionVarName(), cartSessionId(cart), "Table View"); } else if (hIsGsidServer()) { hPrintf("<TD ALIGN=CENTER nowrap> <A HREF=\"../cgi-bin/gsidTable?db=%s\" class=\"topbar\">%s</A> </TD>", database, "Table View"); } else { /* disable TB for CGB servers */ if (!hIsCgbServer()) { hPrintf("<TD ALIGN=CENTER> <A HREF=\"../cgi-bin/hgTables?db=%s&%s=%u\" " "class=\"topbar\">%s</A> </TD>", database, cartSessionVarName(), cartSessionId(cart), "Tables"); } } if (hgNearOk(database)) { hPrintf("<TD ALIGN=CENTER nowrap> <A HREF=\"../cgi-bin/hgNear?%s\" class=\"topbar\">%s</A> </TD>", uiVars->string, "Gene Sorter"); } if (hgPcrOk(database)) { hPrintf("<TD ALIGN=CENTER> <A HREF=\"../cgi-bin/hgPcr?%s\" class=\"topbar\">PCR</A> </TD>", uiVars->string); } if (!psOutput) { hPrintf("<TD ALIGN=CENTER> <A HREF=\"%s&o=%d&g=getDna&i=mixed&c=%s&l=%d&r=%d&db=%s&%s\" class=\"topbar\" id='dnaLink'>" "%s</A> </TD>", hgcNameAndSettings(), winStart, chromName, winStart, winEnd, database, uiVars->string, "DNA"); } if (!psOutput) { /* disable Convert function for CGB servers for the time being */ if (!hIsCgbServer()) if (liftOverChainForDb(database) != NULL) { hPrintf("<TD ALIGN=CENTER> <A HREF=\"../cgi-bin/hgConvert?%s&db=%s", uiVars->string, database); hPrintf("\" class=\"topbar\">Convert</A> </TD>"); } } if (!psOutput) { hPrintf("<TD ALIGN=CENTER> <A HREF=\"../cgi-bin/hgTracks?%s=%u&hgt.psOutput=on\" id='pdfLink' class=\"topbar\">%s</A> </TD>",cartSessionVarName(), cartSessionId(cart), "PS/PDF"); } if (!psOutput) { if (wikiLinkEnabled()) { printf("<TD ALIGN=CENTER> <A HREF=\"../cgi-bin/hgSession?%s=%u" "&hgS_doMainPage=1\" class=\"topbar\">Session</A> </TD>", cartSessionVarName(), cartSessionId(cart)); } } char ensVersionString[256]; char ensDateReference[256]; ensGeneTrackVersion(database, ensVersionString, ensDateReference, sizeof(ensVersionString)); if (!psOutput) { if (differentWord(database,"susScr2")) { /* Print Ensembl anchor for latest assembly of organisms we have * supported by Ensembl == if versionString from trackVersion exists */ if (sameWord(database,"hg19")) { printEnsemblAnchor(database, NULL, chromName, winStart, winEnd, &links); } else if (sameWord(database,"hg18")) { printEnsemblAnchor(database, "ncbi36", chromName, winStart, winEnd, &links); } else if (sameWord(database,"oryCun2") || sameWord(database,"anoCar2") || sameWord(database,"calJac3")) { printEnsemblAnchor(database, NULL, chromName, winStart, winEnd, &links); } else if (ensVersionString[0]) { char *archive = NULL; if (ensDateReference[0] && differentWord("current", ensDateReference)) archive = cloneString(ensDateReference); /* Can we perhaps map from a UCSC random chrom to an Ensembl contig ? */ if (isUnknownChrom(database, chromName)) { // which table to check char *ctgPos = "ctgPos"; if (sameWord(database,"fr2")) fr2ScaffoldEnsemblLink(archive, &links); else if (hTableExists(database, UCSC_TO_ENSEMBL)) printEnsemblAnchor(database, archive, chromName, winStart, winEnd, &links); else if (hTableExists(database, ctgPos)) /* see if we are entirely within a single contig */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row = NULL; char query[256]; safef(query, sizeof(query), "select * from %s where chrom = '%s' and chromStart<%u and chromEnd>%u", ctgPos, chromName, winEnd, winStart); sr = sqlGetResult(conn, query); int itemCount = 0; struct ctgPos *ctgItem = NULL; while ((row = sqlNextRow(sr)) != NULL) { ctgPosFree(&ctgItem); // if there is a second one ctgItem = ctgPosLoad(row); ++itemCount; if (itemCount > 1) break; } sqlFreeResult(&sr); hFreeConn(&conn); if (1 == itemCount) { // verify *entirely* within single contig if ((winEnd <= ctgItem->chromEnd) && (winStart >= ctgItem->chromStart)) { int ctgStart = winStart - ctgItem->chromStart; int ctgEnd = ctgStart + winEnd - winStart; printEnsemblAnchor(database, archive, ctgItem->contig, ctgStart, ctgEnd, &links); } } ctgPosFree(&ctgItem); // the one we maybe used } } else { printEnsemblAnchor(database, archive, chromName, winStart, winEnd, &links); } } } } if (!psOutput) { char buf[2056]; /* Print NCBI MapView anchor */ if (sameString(database, "hg18")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&build=previous&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } if (sameString(database, "hg19")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } if (sameString(database, "mm8")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } if (sameString(database, "danRer2")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=7955&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } if (sameString(database, "galGal3")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9031&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } if (sameString(database, "canFam2")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9615&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } if (sameString(database, "rheMac2")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9544&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } if (sameString(database, "panTro2")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9598&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } if (sameString(database, "anoGam1")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=7165&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } if (sameString(database, "bosTau6")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9913&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } if (startsWith("oryLat", database)) { safef(buf, sizeof(buf), "http://medaka.utgenome.org/browser_ens_jump.php?revision=version1.0&chr=chromosome%s&start=%d&end=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "UTGB", "medakaLink", TRUE); } if (sameString(database, "cb3")) { safef(buf, sizeof(buf), "http://www.wormbase.org/db/seq/gbrowse/briggsae?name=%s:%d-%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE); } if (sameString(database, "cb4")) { safef(buf, sizeof(buf), "http://www.wormbase.org/db/gb2/gbrowse/c_briggsae?name=%s:%d-%d", chromName, winStart+1, winEnd); appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE); } if (sameString(database, "ce10")) { safef(buf, sizeof(buf), "http://www.wormbase.org/db/gb2/gbrowse/c_elegans?name=%s:%d-%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE); } if (sameString(database, "ce4")) { safef(buf, sizeof(buf), "http://ws170.wormbase.org/db/seq/gbrowse/wormbase?name=%s:%d-%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE); } if (sameString(database, "ce2")) { safef(buf, sizeof(buf), "http://ws120.wormbase.org/db/seq/gbrowse/wormbase?name=%s:%d-%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE); } } for(link = links; link != NULL; link = link->next) hPrintf("<TD ALIGN=CENTER> <A HREF=\"%s\" TARGET=\"_blank\" class=\"topbar\" id=\"%s\">%s</A> </TD>\n", link->url, link->id, link->name); if (hIsGisaidServer()) { //hPrintf("<TD ALIGN=CENTER> <A HREF=\"/goldenPath/help/gisaidTutorial.html#SequenceView\" TARGET=_blank class=\"topbar\">%s</A> </TD>\n", "Help"); hPrintf("<TD ALIGN=CENTER> <A HREF=\"../cgi-bin/hgNotYet\" TARGET=_blank class=\"topbar\">%s</A> </TD>\n", "Help"); } else if (hIsGsidServer()) { hPrintf("<TD ALIGN=CENTER> <A HREF=\"/goldenPath/help/gsidTutorial.html#SequenceView\" TARGET=_blank class=\"topbar\">%s</A> </TD>\n", "Help"); } else { hPrintf("<TD ALIGN=CENTER> <A HREF=\"../goldenPath/help/hgTracksHelp.html\" TARGET=_blank class=\"topbar\">%s</A> </TD>\n", "Help"); } hPuts("<TD colspan=20> </TD></TR></TABLE></TD>"); hPuts("</TR></TABLE>"); hPuts("</TD></TR></TABLE>\n"); }