8c908f948b09826c6cb4452ee5b282aca41be85e galt Tue Dec 8 21:52:59 2015 -0800 Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it. diff --git src/hg/hgTracks/config.c src/hg/hgTracks/config.c index 87d05ea..0d989cc 100644 --- src/hg/hgTracks/config.c +++ src/hg/hgTracks/config.c @@ -324,36 +324,39 @@ for (track = *pTrackList; track != NULL; track = track->next) { struct trackRef *tr; AllocVar(tr); tr->track = track; slAddHead(&track->group->trackList, tr); } /* Straighten things out, clean up, and go home. */ for (group = *pGroupList;group != NULL; group = group->next) slReverse(&group->trackList); } return count; } -void configPageSetTrackVis(int vis) -/* Do config page after setting track visibility. If vis is -2, then visibility - * is unchanged. If -1 then set visibility to default, otherwise it should - * be tvHide, tvDense, etc. */ + +void configInitTrackList( + int vis, + char **pGroupTarget, + struct track **pTrackList, + struct track **pIdeoTrack, + struct group **pGroupList +) { -struct dyString *title = dyStringNew(0); char *groupTarget = NULL; struct track *trackList = NULL; struct track *ideoTrack = NULL; struct group *groupList = NULL; withPriorityOverride = cartUsualBoolean(cart, configPriorityOverride, FALSE); /* Get track list and group them. */ ctList = customTracksParseCart(database, cart, &browserLines, &ctFileName); trackList = getTrackList(&groupList, vis); if (trackHash == NULL) trackHash = makeGlobalTrackHash(trackList); // Subtrack settings must be removed when composite/view settings are updated parentChildCartCleanup(trackList,cart,oldVars); @@ -362,30 +365,51 @@ /* The ideogram for some reason is considered a track. * We don't really want to process it as one though, so * we see if it's there, and if necessary remove it. */ ideoTrack = chromIdeoTrack(trackList); if (ideoTrack != NULL) removeTrackFromGroup(ideoTrack); /* Fetch group to change on if any from CGI, * and remove var so it doesn't get used again. */ groupTarget = cloneString(cartUsualString(cart, configGroupTarget, "")); cartRemove(cart, configGroupTarget); if (sameString(groupTarget, "none")) freez(&groupTarget); +*pGroupTarget = groupTarget; +*pTrackList = trackList; +*pIdeoTrack = ideoTrack; +*pGroupList = groupList; + +} + +void configPageSetTrackVis(int vis) +/* Do config page after setting track visibility. If vis is -2, then visibility + * is unchanged. If -1 then set visibility to default, otherwise it should + * be tvHide, tvDense, etc. */ +{ +char *groupTarget; +struct track *trackList; +struct track *ideoTrack; +struct group *groupList; + +configInitTrackList(vis, &groupTarget, &trackList, &ideoTrack, &groupList); + +struct dyString *title = dyStringNew(0); + dyStringPrintf(title, "Configure Image"); hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n", hgTracksName(), cartUsualString(cart, "formMethod", "POST")); webStartWrapperDetailedNoArgs(cart, database, "", title->string, FALSE, FALSE, FALSE, FALSE); cartSaveSession(cart); hPrintf("<INPUT TYPE=HIDDEN NAME=\"hgTracksConfigPage\" VALUE=\"\">"); /* do not want all the submit buttons named the same thing, this one is: */ cgiMakeButton("topSubmit", "submit"); // 3 column table hPrintf("<TABLE style=\"border:0px; \">\n"); hPrintf("<TR><TD>image width:"); hPrintf("<TD style=\"text-align: right\">"); @@ -418,31 +442,31 @@ themeDropDown(cart); hTableStart(); if (ideoTrack != NULL) { hPrintf("<TR><TD>"); hCheckBox("ideogram", cartUsualBoolean(cart, "ideogram", TRUE)); hPrintf("</TD><TD>"); hPrintf("Display chromosome ideogram above main graphic"); hPrintf("</TD></TR>\n"); } hPrintf("<TR><TD>"); hCheckBox("guidelines", cartUsualBoolean(cart, "guidelines", TRUE)); hPrintf("</TD><TD>"); -hPrintf("Show light blue vertical guidelines"); +hPrintf("Show light blue vertical guidelines, or light red vertical window separators in multi-region view"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("leftLabels", cartUsualBoolean(cart, "leftLabels", TRUE)); hPrintf("</TD><TD>"); hPrintf("Display labels to the left of items in tracks"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("centerLabels", cartUsualBoolean(cart, "centerLabels", TRUE)); hPrintf("</TD><TD>"); hPrintf("Display description above each track"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); @@ -463,36 +487,37 @@ hPrintf("Next/previous exon navigation"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("exonNumbers", cartUsualBoolean(cart, "exonNumbers", TRUE)); hPrintf("</TD><TD>"); hPrintf("Show exon numbers"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("enableHighlightingDialog", cartUsualBoolean(cart, "enableHighlightingDialog", TRUE)); hPrintf("</TD><TD>"); hPrintf("Enable highlight with drag-and-select " "(if unchecked, drag-and-select always zooms to selection)"); hPrintf("</TD></TR>\n"); - hTableEnd(); + + cgiDown(0.9); -char *freeze = hFreezeFromDb(database); char buf[256]; +char *freeze = hFreezeFromDb(database); if (freeze == NULL) safef(buf, sizeof buf, "Configure Tracks on %s %s: %s", organization, browserName, trackHubSkipHubName(organism)); else if (stringIn(database, freeze)) safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s", organization, browserName, trackHubSkipHubName(organism), freeze); else safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s (%s)", organization, browserName, trackHubSkipHubName(organism), freeze, trackHubSkipHubName(database)); webNewSection("%s",buf); hPrintf("Tracks: "); if (isSearchTracksSupported(database,cart)) { cgiMakeButtonWithMsg(TRACK_SEARCH, TRACK_SEARCH_BUTTON,TRACK_SEARCH_HINT); hPrintf(" "); @@ -512,15 +537,216 @@ "more selectively below.</div>"); trackConfig(trackList, groupList, groupTarget, vis); dyStringFree(&title); freez(&groupTarget); webEndSectionTables(); hPrintf("</FORM>"); } void configPage() /* Put up configuration page. */ { configPageSetTrackVis(-2); } +// TODO GALT there is duplication still between config and configMultiRegionPageSetTrackVis +// that could maybe be addressed by pulling the code that initializes the tracklist, +// and the code that draws the multi-region options, into 2 functions to be called by each. + +void configMultiRegionPage() +/* Do multi-region config page after setting track visibility. If vis is -2, then visibility + * is unchanged. If -1 then set visibility to default, otherwise it should + * be tvHide, tvDense, etc. */ +{ +char *groupTarget; +struct track *trackList; +struct track *ideoTrack; +struct group *groupList; +int vis = -2; + +configInitTrackList(vis, &groupTarget, &trackList, &ideoTrack, &groupList); + +hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n", hgTracksName(), + cartUsualString(cart, "formMethod", "POST")); + +webStartWrapperDetailedNoArgs(cart, database, "", "", FALSE, FALSE, FALSE, FALSE); + +cartSaveSession(cart); + + +hPrintf("<BR>\n"); + +hTableStart(); + +virtModeType = cartUsualString(cart, "virtModeType", virtModeType); + +hPrintf("<TR><TD>"); +cgiMakeRadioButton("virtModeType", "default", sameWord("default", virtModeType)); +hPrintf("</TD><TD>"); +hPrintf("Show single-chromsome view (default)"); +hPrintf("</TD></TR>\n"); + +struct sqlConnection *conn = NULL; +if (!trackHubDatabase(database)) // no db conn for assembly hubs + conn = hAllocConn(database); + +// Do we have a gene table for exonMostly? +findBestEMGeneTable(trackList); +if (emGeneTable) + { + hPrintf("<TR><TD>"); + cgiMakeRadioButton("virtModeType", "exonMostly", sameWord("exonMostly", virtModeType)); + hPrintf("</TD><TD>"); + hPrintf("Show exons or "); + cgiMakeRadioButton("virtModeType", "geneMostly", sameWord("geneMostly", virtModeType)); + hPrintf("genes using %s. Use padding of: ", emGeneTrack->shortLabel); + hIntVar("emPadding", cartUsualInt(cart, "emPadding", emPadding), 3); + hPrintf(" bases."); + hPrintf("</TD></TR>\n"); + } + +/* obsolete +if (conn && sqlTableExists(conn,"knownCanonical")) + { + hPrintf("<TR><TD>"); + cgiMakeRadioButton("virtModeType", "kcGenes", sameWord("kcGenes", virtModeType)); + hPrintf("</TD><TD>"); + hPrintf("Show gene regions genome-wide."); + hPrintf("</TD></TR>\n"); + } +*/ + +hPrintf("<TR><TD>"); +cgiMakeRadioButton("virtModeType", "customUrl", sameWord("customUrl", virtModeType)); +hPrintf("</TD><TD>"); +hPrintf("Custom regions from BED URL: "); +hTextVar("multiRegionsBedUrl", cartUsualString(cart, "multiRegionsBedUrl", multiRegionsBedUrl), 60); +hPrintf("</TD></TR>\n"); + + +/* The AllChroms option will be released in future +if (emGeneTable && sqlTableExists(conn, emGeneTable)) + { + hPrintf("<TR><TD>"); + cgiMakeRadioButton("virtModeType", "singleTrans", sameWord("singleTrans", virtModeType)); + hPrintf("</TD><TD>"); + hPrintf("Show only one transcript using an ID from %s : ", emGeneTrack->shortLabel); + char *trans = cartUsualString(cart, "singleTransId", singleTransId); + char sql[1024]; + sqlSafef(sql, sizeof sql, "select name from %s where name='%s'", emGeneTable, trans); + char *result = sqlQuickString(conn, sql); + if (!result) + { + sqlSafef(sql, sizeof sql, "select name from %s limit 1", emGeneTable); + trans = sqlQuickString(conn, sql); + } + hTextVar("singleTransId", trans, 20); + hPrintf("</TD></TR>\n"); + } +*/ + +if (conn && sqlTableExists(conn, "altLocations")) + { + hPrintf("<TR><TD>"); + cgiMakeRadioButton("virtModeType", "singleAltHaplo", sameWord("singleAltHaplo", virtModeType)); + hPrintf("</TD><TD>"); + hPrintf("Show one alternate haplotype, placed on its chromosome, using ID: "); + char *haplo = cartUsualString(cart, "singleAltHaploId", singleAltHaploId); + char sql[1024]; + sqlSafef(sql, sizeof sql, "select name from altLocations where name='%s'", haplo); + char *result = sqlQuickString(conn, sql); + if (!result) + { + sqlSafef(sql, sizeof sql, "select name from altLocations limit 1"); + haplo = sqlQuickString(conn, sql); + } + hTextVar("singleAltHaploId", haplo, 20); + hPrintf("</TD></TR>\n"); + } + +/* disable demo for now +if (sameString(database,"hg19") || sameString(database, "hg38")) + { + hPrintf("<TR><TD>"); + cgiMakeRadioButton("virtModeType", "demo1", sameWord("demo1", virtModeType)); + hPrintf("</TD><TD>"); + hPrintf("demo1 two windows on two chroms (default pos on chr21, and same loc on chr22)"); + hPrintf("</TD></TR>\n"); + } +*/ + + +/* Disabled for now +hPrintf("<TR><TD>"); +cgiMakeRadioButton("virtModeType", "demo2", sameWord("demo2", virtModeType)); +hPrintf("</TD><TD>"); +hPrintf("demo2 multiple "); +hIntVar("demo2NumWindows", cartUsualInt(cart, "demo2NumWindows", demo2NumWindows), 3); +hPrintf(" windows on one chrom chr21 def posn, window size "); +hIntVar("demo2WindowSize", cartUsualInt(cart, "demo2WindowSize", demo2WindowSize), 3); +hPrintf(" and step size "); +hIntVar("demo2StepSize", cartUsualInt(cart, "demo2StepSize", demo2StepSize), 3); +hPrintf(" exon-like"); +hPrintf("</TD></TR>\n"); +*/ + +/* The AllChroms option will be released in future +if (conn) // requires chromInfo from database. + { // TODO allow it to use assembly hubs via trackHubAllChromInfo() ? + hPrintf("<TR><TD>"); + cgiMakeRadioButton("virtModeType", "allChroms", sameWord("allChroms", virtModeType)); + hPrintf("</TD><TD>"); + hPrintf("<br>Show all chromosomes.<br><span style='color:red'>Warning:</span> Turn off all tracks except bigBed, bigWig, and very sparse tracks.<br>Press Hide All to hide all tracks."); + hPrintf("</TD></TR>\n"); + } +*/ + + +/* Disabled for now +hPrintf("<TR><TD>"); +cgiMakeRadioButton("virtModeType", "demo4", sameWord("demo4", virtModeType)); +hPrintf("</TD><TD>"); +hPrintf("demo4 multiple (311) windows showing exons from TITIN gene uc031rqd.1."); +hPrintf("</TD></TR>\n"); +*/ + +/* Disabled for now +hPrintf("<TR><TD>"); +cgiMakeRadioButton("virtModeType", "demo5", sameWord("demo5", virtModeType)); +hPrintf("</TD><TD>"); +hPrintf("demo5 alt locus on hg38. Shows alt chrom surrounded by regions of same size from reference genome."); +hPrintf("</TD></TR>\n"); +*/ + +/* Disabled for now +hPrintf("<TR><TD>"); +cgiMakeRadioButton("virtModeType", "demo6", sameWord("demo6", virtModeType)); +hPrintf("</TD><TD>"); +hPrintf("demo6 shows zoomed in exon-exon junction from SOD1 gene, between exon1 and exon2."); +hPrintf("</TD></TR>\n"); +*/ + + +hTableEnd(); + +hPrintf("<BR>\n"); +hPrintf("<TABLE style=\"border:0px; \">\n"); +hPrintf("<TR><TD>"); +hCheckBox("emAltHighlight", cartUsualBoolean(cart, "emAltHighlight", FALSE)); +hPrintf("</TD><TD>"); +hPrintf("Highlight alternating regions in multi-region view"); +hPrintf("</TD></TR>\n"); +hPrintf("</TABLE>\n"); + +hPrintf("<BR>\n"); +cgiMakeButton("topSubmit", "submit"); + +hFreeConn(&conn); + +cgiDown(0.9); + +freez(&groupTarget); +webEndSectionTables(); +hPrintf("</FORM>"); +} +