41e92aca41621f3fe3c5caf951261db487875dc8 larrym Fri May 4 15:59:07 2012 -0700 refactor menu bar code into a new file to get ready for new menu bar design (#5245) diff --git src/hg/hgTracks/menu.c src/hg/hgTracks/menu.c new file mode 100644 index 0000000..ed3c51a --- /dev/null +++ src/hg/hgTracks/menu.c @@ -0,0 +1,457 @@ +// 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() +/* 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"); +}