void webEnd() /* output the footer of the HTML page */ { if(!webInTextMode) { webEndSectionTables(); #ifndef GBROWSE googleAnalytics(); #endif /* GBROWSE */ puts( "</BODY></HTML>"); webPopErrHandlers(); } }
void doSearchTracks(struct group *groupList) { if (!advancedJavascriptFeaturesEnabled(cart)) { warn("Requires advanced javascript features."); return; } struct group *group; char *groups[128]; char *labels[128]; int numGroups = 1; groups[0] = ANYLABEL; labels[0] = ANYLABEL; char *currentTab = cartUsualString(cart, TRACK_SEARCH_CURRENT_TAB, "simpleTab"); char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME); #ifdef TRACK_SEARCH_ON_TYPE char *typeSearch = cartOptionalString(cart, TRACK_SEARCH_ON_TYPE); #else///ifndef TRACK_SEARCH_ON_TYPE char *typeSearch = NULL; #endif///def TRACK_SEARCH_ON_TYPE char *descSearch; char *groupSearch = cartOptionalString(cart, TRACK_SEARCH_ON_GROUP); boolean doSearch = sameString(cartOptionalString(cart, TRACK_SEARCH), "Search") || cartUsualInt(cart, TRACK_SEARCH_PAGER, -1) >= 0; struct sqlConnection *conn = hAllocConn(database); boolean metaDbExists = sqlTableExists(conn, "metaDb"); int numMetadataSelects, tracksFound = 0; int numMetadataNonEmpty = 0; char **mdbVar = NULL; char **mdbVal = NULL; #ifdef ONE_FUNC struct hash *parents = newHash(4); #endif///def ONE_FUNC boolean simpleSearch; struct trix *trix; char trixFile[HDB_MAX_PATH_STRING]; char **descWords = NULL; int descWordCount = 0; boolean searchTermsExist = FALSE; int cols; char buf[512]; if(sameString(currentTab, "simpleTab")) { descSearch = cartOptionalString(cart, TRACK_SEARCH_SIMPLE); simpleSearch = TRUE; freez(&nameSearch); #ifdef TRACK_SEARCH_ON_TYPE freez(&typeSearch); #endif///def TRACK_SEARCH_ON_TYPE freez(&groupSearch); } else { descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR); simpleSearch = FALSE; } if(descSearch) stripChar(descSearch, '"'); trackList = getTrackList(&groupList, -2); // global makeGlobalTrackHash(trackList); // NOTE: This is necessary when container cfg by '*' results in vis changes // This will handle composite/view override when subtrack specific vis exists, AND superTrack reshaping. parentChildCartCleanup(trackList,cart,oldVars); // Subtrack settings must be removed when composite/view settings are updated getSearchTrixFile(database, trixFile, sizeof(trixFile)); trix = trixOpen(trixFile); slSort(&groupList, gCmpGroup); for (group = groupList; group != NULL; group = group->next) { groupTrackListAddSuper(cart, group); if (group->trackList != NULL) { groups[numGroups] = cloneString(group->name); labels[numGroups] = cloneString(group->label); numGroups++; if (numGroups >= ArraySize(groups)) internalErr(); } } safef(buf, sizeof(buf),"Search for Tracks in the %s %s Assembly", organism, hFreezeFromDb(database)); webStartWrapperDetailedNoArgs(cart, database, "", buf, FALSE, FALSE, FALSE, FALSE); hPrintf("<div style='max-width:1080px;'>"); hPrintf("<form action='%s' name='%s' id='%s' method='get'>\n\n", hgTracksName(),TRACK_SEARCH_FORM,TRACK_SEARCH_FORM); cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo safef(buf, sizeof(buf), "%lu", clock1()); cgiMakeHiddenVar("hgt_", buf); // timestamps page to avoid browser cache hPrintf("<input type='hidden' name='db' value='%s'>\n", database); hPrintf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n", TRACK_SEARCH_CURRENT_TAB, currentTab); hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_DEL_ROW); hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_ADD_ROW); hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_PAGER); hPrintf("<div id='tabs' style='display:none; %s'>\n" "<ul>\n" "<li><a href='#simpleTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Search</B></a></li>\n" "<li><a href='#advancedTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Advanced</B></a></li>\n" "</ul>\n" "<div id='simpleTab' style='max-width:inherit;'>\n",cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;"); hPrintf("<table style='width:100%%; font-size:.9em;'><tr><td colspan='2'>"); hPrintf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' style='max-width:1000px; width:100%%;' onkeyup='findTracksSearchButtonsEnable(true);'>\n", TRACK_SEARCH_SIMPLE,descSearch == NULL ? "" : descSearch); if (simpleSearch && descSearch) searchTermsExist = TRUE; hPrintf("</td></tr><td style='max-height:4px;'></td></tr></table>"); //hPrintf("</td></tr></table>"); hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", TRACK_SEARCH); hPrintf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracksClear();'>\n"); hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n"); hPrintf("</div>\n"); // Advanced tab hPrintf("<div id='advancedTab' style='width:inherit;'>\n" "<table cellSpacing=0 style='width:inherit; font-size:.9em;'>\n"); cols = 8; // Track Name contains hPrintf("<tr><td colspan=3></td>"); hPrintf("<td nowrap><b style='max-width:100px;'>Track Name:</b></td>"); hPrintf("<td align='right'>contains</td>\n"); hPrintf("<td colspan='%d'>", cols - 4); hPrintf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' onkeyup='findTracksSearchButtonsEnable(true);' style='min-width:326px; font-size:.9em;'>", TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch); hPrintf("</td></tr>\n"); // Description contains hPrintf("<tr><td colspan=2></td><td align='right'>and </td>"); hPrintf("<td><b style='max-width:100px;'>Description:</b></td>"); hPrintf("<td align='right'>contains</td>\n"); hPrintf("<td colspan='%d'>", cols - 4); hPrintf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' onkeyup='findTracksSearchButtonsEnable(true);' style='max-width:536px; width:536px; font-size:.9em;'>", TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch); hPrintf("</td></tr>\n"); if (!simpleSearch && descSearch) searchTermsExist = TRUE; hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n"); hPrintf("<td><b style='max-width:100px;'>Group:</b></td>"); hPrintf("<td align='right'>is</td>\n"); hPrintf("<td colspan='%d'>", cols - 4); cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch, "class='groupSearch' style='min-width:40%; font-size:.9em;'"); hPrintf("</td></tr>\n"); if (!simpleSearch && groupSearch) searchTermsExist = TRUE; #ifdef TRACK_SEARCH_ON_TYPE // Track Type is (drop down) hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n"); hPrintf("<td nowrap><b style='max-width:100px;'>Data Format:</b></td>"); hPrintf("<td align='right'>is</td>\n"); hPrintf("<td colspan='%d'>", cols - 4); char **formatTypes = NULL; char **formatLabels = NULL; int formatCount = getFormatTypes(&formatLabels, &formatTypes); cgiMakeDropListFull(TRACK_SEARCH_ON_TYPE, formatLabels, formatTypes, formatCount, typeSearch, "class='typeSearch' style='min-width:40%; font-size:.9em;'"); hPrintf("</td></tr>\n"); if (!simpleSearch && typeSearch) searchTermsExist = TRUE; #endif///def TRACK_SEARCH_ON_TYPE // Metadata selects require careful accounting if(metaDbExists) numMetadataSelects = printMdbSelects(conn, cart, simpleSearch, &mdbVar, &mdbVal, &numMetadataNonEmpty, cols); else numMetadataSelects = 0; hPrintf("</table>\n"); hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", TRACK_SEARCH); hPrintf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracksClear();'>\n"); hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n"); //hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a>\n"); hPrintf("</div>\n</div>\n"); hPrintf("</form>\n"); hPrintf("</div>"); // Restricts to max-width:1000px; if(descSearch != NULL && !strlen(descSearch)) descSearch = NULL; if(groupSearch != NULL && sameString(groupSearch, ANYLABEL)) groupSearch = NULL; if(typeSearch != NULL && sameString(typeSearch, ANYLABEL)) typeSearch = NULL; if(!isEmpty(descSearch)) { char *tmp = cloneString(descSearch); char *val = nextWord(&tmp); struct slName *el, *descList = NULL; int i; while (val != NULL) { slNameAddTail(&descList, val); descWordCount++; val = nextWord(&tmp); } descWords = needMem(sizeof(char *) * descWordCount); for(i = 0, el = descList; el != NULL; i++, el = el->next) descWords[i] = strLower(el->name); } if (doSearch && simpleSearch && descWordCount <= 0) doSearch = FALSE; if(doSearch) { // Now search struct slRef *tracks = NULL; if(simpleSearch) tracks = simpleSearchForTracksstruct(trix,descWords,descWordCount); else tracks = advancedSearchForTracks(conn,groupList,descWords,descWordCount,nameSearch,typeSearch,descSearch,groupSearch,numMetadataNonEmpty,numMetadataSelects,mdbVar,mdbVal); // Sort and Print results enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance); tracksFound = slCount(tracks); if(tracksFound > 1) findTracksSort(&tracks,simpleSearch,sortBy); displayFoundTracks(cart,tracks,tracksFound,sortBy); } hFreeConn(&conn); webNewSection("About Track Search"); if(metaDbExists) hPrintf("<p>Search for terms in track names, descriptions, groups, and ENCODE " "metadata. If multiple terms are entered, only tracks with all terms " "will be part of the results."); else hPrintf("<p>Search for terms in track descriptions, groups, and names. " "If multiple terms are entered, only tracks with all terms " "will be part of the results."); hPrintf("<BR><a target='_blank' href='../goldenPath/help/trackSearch.html'>more help</a></p>\n"); webEndSectionTables(); }
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("Exit multi-region mode"); 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 using %s. Use padding of: ", emGeneTrack->shortLabel); hIntVar("emPadding", cartUsualInt(cart, "emPadding", emPadding), 3); hPrintf(" bases."); hPrintf("</TD></TR>\n"); } if (emGeneTable) { hPrintf("<TR><TD>"); cgiMakeRadioButton("virtModeType", "geneMostly", sameWord("geneMostly", virtModeType)); hPrintf("</TD><TD>"); hPrintf("Show genes using %s. Use padding of: ", emGeneTrack->shortLabel); hIntVar("gmPadding", cartUsualInt(cart, "gmPadding", gmPadding), 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("Enter Custom regions as BED, or a URL to them:<br>"); multiRegionsBedUrl = cartUsualString(cart, "multiRegionsBedUrl", multiRegionsBedUrl); struct dyString *dyMultiRegionsBedInput = dyStringNew(256); if (strstr(multiRegionsBedUrl,"://")) { dyStringAppend(dyMultiRegionsBedInput, multiRegionsBedUrl); } else { if (fileExists(multiRegionsBedUrl)) { struct lineFile *lf = lineFileMayOpen(multiRegionsBedUrl, TRUE); char *line; int lineSize; while (lineFileNext(lf, &line, &lineSize)) { dyStringPrintf(dyMultiRegionsBedInput, "%s\n", line); } lineFileClose(&lf); } } hPrintf("<TEXTAREA NAME='multiRegionsBedInput' ID='multiRegionsBedInput' rows='4' cols='58' style='white-space: pre;'>%s</TEXTAREA>", dyMultiRegionsBedInput->string); 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) { boolean altLocExists = sqlTableExists(conn, "altLocations"); boolean fixLocExists = sqlTableExists(conn, "fixLocations"); if (altLocExists || fixLocExists) { hPrintf("<TR><TD>"); cgiMakeRadioButton("virtModeType", "singleAltHaplo", sameWord("singleAltHaplo", virtModeType)); hPrintf("</TD><TD>"); hPrintf("Show one alternate haplotype"); if (fixLocExists) hPrintf(" or fix patch"); hPrintf(", placed on its chromosome, using ID: "); char *haplo = cartUsualString(cart, "singleAltHaploId", singleAltHaploId); char *foundHaplo = NULL; char sql[1024]; if (altLocExists) { sqlSafef(sql, sizeof sql, "select name from altLocations where name rlike '^%s(:[0-9-]+)?'", haplo); foundHaplo = sqlQuickString(conn, sql); } if (!foundHaplo && fixLocExists) { sqlSafef(sql, sizeof sql, "select name from fixLocations where name rlike '^%s(:[0-9-]+)?'", haplo); foundHaplo = sqlQuickString(conn, sql); } if (!foundHaplo) { if (altLocExists) sqlSafef(sql, sizeof sql, "select name from altLocations limit 1"); else sqlSafef(sql, sizeof sql, "select name from fixLocations limit 1"); haplo = sqlQuickString(conn, sql); chopSuffixAt(haplo, ':'); } hTextVar("singleAltHaploId", haplo, 60); 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"); hPrintf("<TABLE style=\"border:0px;width:650px \">\n"); hPrintf("<TR><TD>"); cgiMakeButton("topSubmit", "submit"); hPrintf("</TD><TD align=right>"); hPrintf("<A HREF=\"../goldenPath/help/multiRegionHelp.html\" target=_blank>Help</A>\n"); hPrintf("</TD></TR>\n"); hPrintf("</TABLE>\n"); hFreeConn(&conn); cgiDown(0.9); freez(&groupTarget); webEndSectionTables(); hPrintf("</FORM>"); }
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\">"); hIntVar("pix", tl.picWidth, 4); hPrintf("<TD>pixels</TR>"); hPrintf("<TR><TD>label area width:"); hPrintf("<TD style=\"text-align: right\">"); hIntVar("hgt.labelWidth", leftLabelWidthChars, 2); hPrintf("<TD>characters<TD></TR>"); hPrintf("<TR><TD>text size:"); hPrintf("<TD style=\"text-align: right\">"); textSizeDropDown(); hPrintf("</TD>"); if (trackLayoutInclFontExtras()) { hPrintf("<TD>"); char *defaultStyle = cartUsualString(cart, "fontType", "medium"); cartMakeRadioButton(cart, "fontType", "medium", defaultStyle); hPrintf(" medium "); cartMakeRadioButton(cart, "fontType", "fixed", defaultStyle); hPrintf(" fixed "); cartMakeRadioButton(cart, "fontType", "bold", defaultStyle); hPrintf(" bold "); hPrintf(" "); hPrintf("</TD>"); } hPrintf("</TR>"); 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, 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>"); hCheckBox("trackControlsOnMain", cartUsualBoolean(cart, "trackControlsOnMain", TRUE)); hPrintf("</TD><TD>"); hPrintf("Show track controls under main graphic"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("nextItemArrows", cartUsualBoolean(cart, "nextItemArrows", FALSE)); hPrintf("</TD><TD>"); hPrintf("Next/previous item navigation"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("nextExonArrows", cartUsualBoolean(cart, "nextExonArrows", TRUE)); hPrintf("</TD><TD>"); 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 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(" "); } cgiMakeButtonWithMsg(configHideAll, "hide all","Hide all tracks in this genome assembly"); hPrintf(" "); cgiMakeButtonWithMsg(configShowAll, "show all","Show all tracks in this genome assembly"); hPrintf(" "); cgiMakeButtonWithMsg(configDefaultAll, "default","Display only default tracks"); hPrintf(" Groups: "); hButtonWithOnClick("hgt.collapseGroups", "collapse all", "Collapse all track groups", "return vis.expandAllGroups(false)"); hPrintf(" "); hButtonWithOnClick("hgt.expandGroups", "expand all", "Expand all track groups", "return vis.expandAllGroups(true)"); hPrintf("<div style='margin-top:.2em; margin-bottom:.9em;'>Control track and group visibility " "more selectively below.</div>"); trackConfig(trackList, groupList, groupTarget, vis); dyStringFree(&title); freez(&groupTarget); webEndSectionTables(); hPrintf("</FORM>"); }
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. */ { 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); /* 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); 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\">"); hIntVar("pix", tl.picWidth, 4); hPrintf("<TD>pixels</TR>"); hPrintf("<TR><TD>label area width:"); hPrintf("<TD style=\"text-align: right\">"); hIntVar("hgt.labelWidth", leftLabelWidthChars, 2); hPrintf("<TD>characters<TD></TR>"); hPrintf("<TR><TD>text size:"); hPrintf("<TD style=\"text-align: right\">"); textSizeDropDown(); hPrintf("<TD>"); if (trackLayoutInclFontExtras()) { char *defaultStyle = cartUsualString(cart, "fontType", "medium"); cartMakeRadioButton(cart, "fontType", "medium", defaultStyle); hPrintf(" medium "); cartMakeRadioButton(cart, "fontType", "fixed", defaultStyle); hPrintf(" fixed "); cartMakeRadioButton(cart, "fontType", "bold", defaultStyle); hPrintf(" bold "); hPrintf(" "); } hPrintf("<TR><BR>"); 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("</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>"); hCheckBox("trackControlsOnMain", cartUsualBoolean(cart, "trackControlsOnMain", TRUE)); hPrintf("</TD><TD>"); hPrintf("Show track controls under main graphic"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("nextItemArrows", cartUsualBoolean(cart, "nextItemArrows", FALSE)); hPrintf("</TD><TD>"); hPrintf("Next/previous item navigation"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("nextExonArrows", cartUsualBoolean(cart, "nextExonArrows", TRUE)); hPrintf("</TD><TD>"); hPrintf("Next/previous exon navigation"); hPrintf("</TD></TR>\n"); #ifdef PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("<TR><TD>"); char *javascript="onClick=\"document.mainForm.hgTracksConfigPage.value='configure';document.mainForm.submit();\""; hCheckBoxJS(configPriorityOverride, cartUsualBoolean(cart, configPriorityOverride , FALSE), javascript); hPrintf("</TD><TD>"); hPrintf("Enable track re-ordering"); hPrintf("</TD></TR>\n"); #endif///def PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("<TR><TD>"); hCheckBox("enableAdvancedJavascript", advancedJavascriptFeaturesEnabled(cart)); hPrintf("</TD><TD>"); hPrintf("Enable advanced javascript features"); hPrintf("</TD></TR>\n"); hTableEnd(); char *freeze = hFreezeFromDb(database); char buf[128]; if (stringIn(database, freeze)) safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s", organization, browserName, organism, freeze); else safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s (%s)", organization, browserName, organism, freeze, database); webNewSection(buf); hPrintf("Tracks: "); if(isSearchTracksSupported(database,cart)) { cgiMakeButtonWithMsg(TRACK_SEARCH, TRACK_SEARCH_BUTTON,TRACK_SEARCH_HINT); hPrintf(" "); } cgiMakeButtonWithMsg(configHideAll, "hide all","Hide all tracks in this genome assembly"); hPrintf(" "); cgiMakeButtonWithMsg(configShowAll, "show all","Show all tracks in this genome assembly"); hPrintf(" "); cgiMakeButtonWithMsg(configDefaultAll, "default","Display only default tracks"); hPrintf(" Groups: "); hButtonWithOnClick("hgt.collapseGroups", "collapse all", "Collapse all track groups", "return setAllTrackGroupVisibility(false)"); hPrintf(" "); hButtonWithOnClick("hgt.expandGroups", "expand all", "Expand all track groups", "return setAllTrackGroupVisibility(true)"); hPrintf("<P STYLE=\"margin-top:5;\">Control track and group visibility more selectively below.<P>"); trackConfig(trackList, groupList, groupTarget, vis); dyStringFree(&title); freez(&groupTarget); webEndSectionTables(); hPrintf("</FORM>"); }
void doSearchTracks(struct group *groupList) { webIncludeResourceFile("ui.dropdownchecklist.css"); jsIncludeFile("ui.dropdownchecklist.js",NULL); // This line is needed to get the multi-selects initialized jsIncludeFile("ddcl.js",NULL); struct group *group; char *groups[128]; char *labels[128]; int numGroups = 1; groups[0] = ANYLABEL; labels[0] = ANYLABEL; char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME); char *typeSearch = cartUsualString( cart, TRACK_SEARCH_ON_TYPE,ANYLABEL); char *simpleEntry = cartOptionalString(cart, TRACK_SEARCH_SIMPLE); char *descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR); char *groupSearch = cartUsualString( cart, TRACK_SEARCH_ON_GROUP,ANYLABEL); boolean doSearch = sameString(cartOptionalString(cart, TRACK_SEARCH), "Search") || cartUsualInt(cart, TRACK_SEARCH_PAGER, -1) >= 0; struct sqlConnection *conn = hAllocConn(database); boolean metaDbExists = sqlTableExists(conn, "metaDb"); int tracksFound = 0; boolean searchTermsExist = FALSE; int cols; char buf[512]; char *currentTab = cartUsualString(cart, TRACK_SEARCH_CURRENT_TAB, "simpleTab"); enum searchTab selectedTab = (sameString(currentTab, "advancedTab") ? advancedTab : simpleTab); // NOTE: could support quotes in simple tab by detecting quotes and choosing // to use doesNameMatch() || doesDescriptionMatch() if (selectedTab == simpleTab && !isEmpty(simpleEntry)) stripChar(simpleEntry, '"'); trackList = getTrackList(&groupList, -2); // global makeGlobalTrackHash(trackList); // NOTE: This is necessary when container cfg by '*' results in vis changes // This will handle composite/view override when subtrack specific vis exists, // AND superTrack reshaping. // Subtrack settings must be removed when composite/view settings are updated parentChildCartCleanup(trackList,cart,oldVars); slSort(&groupList, gCmpGroup); for (group = groupList; group != NULL; group = group->next) { groupTrackListAddSuper(cart, group); if (group->trackList != NULL) { groups[numGroups] = cloneString(group->name); labels[numGroups] = cloneString(group->label); numGroups++; if (numGroups >= ArraySize(groups)) internalErr(); } } safef(buf, sizeof(buf),"Search for Tracks in the %s %s Assembly", organism, hFreezeFromDb(database)); webStartWrapperDetailedNoArgs(cart, database, "", buf, FALSE, FALSE, FALSE, FALSE); hPrintf("<div style='max-width:1080px;'>"); hPrintf("<form action='%s' name='%s' id='%s' method='get'>\n\n", hgTracksName(),TRACK_SEARCH_FORM,TRACK_SEARCH_FORM); cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo safef(buf, sizeof(buf), "%lu", clock1()); cgiMakeHiddenVar("hgt_", buf); // timestamps page to avoid browser cache hPrintf("<input type='hidden' name='db' value='%s'>\n", database); hPrintf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n", TRACK_SEARCH_CURRENT_TAB, currentTab); hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_DEL_ROW); hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_ADD_ROW); hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_PAGER); hPrintf("<div id='tabs' style='display:none; %s'>\n<ul>\n<li><a href='#simpleTab'>" "<B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Search</B>" "</a></li>\n<li><a href='#advancedTab'>" "<B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Advanced</B>" "</a></li>\n</ul>\n<div id='simpleTab' style='max-width:inherit;'>\n", cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;"); hPrintf("<table id='simpleTable' style='width:100%%; font-size:.9em;'><tr><td colspan='2'>"); hPrintf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' " "style='max-width:1000px; width:100%%;' onkeyup='findTracks.searchButtonsEnable(true);'>\n", TRACK_SEARCH_SIMPLE,simpleEntry == NULL ? "" : simpleEntry); if (selectedTab==simpleTab && simpleEntry) searchTermsExist = TRUE; hPrintf("</td></tr><td style='max-height:4px;'></td></tr></table>"); //hPrintf("</td></tr></table>"); hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' " "style='font-size:.8em;'>\n", TRACK_SEARCH); hPrintf("<input type='button' name='clear' value='clear' class='clear' " "style='font-size:.8em;' onclick='findTracks.clear();'>\n"); hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' " "style='font-size:.8em;'>\n"); hPrintf("</div>\n"); // Advanced tab hPrintf("<div id='advancedTab' style='width:inherit;'>\n" "<table id='advancedTable' cellSpacing=0 style='width:inherit; font-size:.9em;'>\n"); cols = 8; // Track Name contains hPrintf("<tr><td colspan=3></td>"); hPrintf("<td nowrap><b style='max-width:100px;'>Track Name:</b></td>"); hPrintf("<td align='right'>contains</td>\n"); hPrintf("<td colspan='%d'>", cols - 4); hPrintf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' " "onkeyup='findTracks.searchButtonsEnable(true);' style='min-width:326px; font-size:.9em;'>", TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch); hPrintf("</td></tr>\n"); // Description contains hPrintf("<tr><td colspan=2></td><td align='right'>and </td>"); hPrintf("<td><b style='max-width:100px;'>Description:</b></td>"); hPrintf("<td align='right'>contains</td>\n"); hPrintf("<td colspan='%d'>", cols - 4); hPrintf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' " "onkeyup='findTracks.searchButtonsEnable(true);' " "style='max-width:536px; width:536px; font-size:.9em;'>", TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch); hPrintf("</td></tr>\n"); if (selectedTab==advancedTab && !isEmpty(descSearch)) searchTermsExist = TRUE; hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n"); hPrintf("<td><b style='max-width:100px;'>Group:</b></td>"); hPrintf("<td align='right'>is</td>\n"); hPrintf("<td colspan='%d'>", cols - 4); cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch, "class='groupSearch' style='min-width:40%; font-size:.9em;'"); hPrintf("</td></tr>\n"); if (selectedTab==advancedTab && !isEmpty(groupSearch) && !sameString(groupSearch,ANYLABEL)) searchTermsExist = TRUE; // Track Type is (drop down) hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n"); hPrintf("<td nowrap><b style='max-width:100px;'>Data Format:</b></td>"); hPrintf("<td align='right'>is</td>\n"); hPrintf("<td colspan='%d'>", cols - 4); char **formatTypes = NULL; char **formatLabels = NULL; int formatCount = getFormatTypes(&formatLabels, &formatTypes); cgiMakeDropListFull(TRACK_SEARCH_ON_TYPE, formatLabels, formatTypes, formatCount, typeSearch, "class='typeSearch' style='min-width:40%; font-size:.9em;'"); hPrintf("</td></tr>\n"); if (selectedTab==advancedTab && !isEmpty(typeSearch) && !sameString(typeSearch,ANYLABEL)) searchTermsExist = TRUE; // mdb selects struct slPair *mdbSelects = NULL; if (metaDbExists) { struct slPair *mdbVars = mdbVarsSearchable(conn,TRUE,FALSE); // Tables but not file only objects mdbSelects = mdbSelectPairs(cart, mdbVars); char *output = mdbSelectsHtmlRows(conn,mdbSelects,mdbVars,cols,FALSE); // not a fileSearch if (output) { puts(output); freeMem(output); } slPairFreeList(&mdbVars); } hPrintf("</table>\n"); hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' " "style='font-size:.8em;'>\n", TRACK_SEARCH); hPrintf("<input type='button' name='clear' value='clear' class='clear' " "style='font-size:.8em;' onclick='findTracks.clear();'>\n"); hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' " "style='font-size:.8em;'>\n"); //hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a>\n"); hPrintf("</div>\n"); hPrintf("</div>\n"); hPrintf("</form>\n"); hPrintf("</div>"); // Restricts to max-width:1000px; cgiDown(0.8); if (measureTiming) measureTime("Rendered tabs"); if (doSearch) { // Now search struct slRef *tracks = NULL; if (selectedTab==simpleTab && !isEmpty(simpleEntry)) tracks = simpleSearchForTracksstruct(simpleEntry); else if (selectedTab==advancedTab) tracks = advancedSearchForTracks(conn,groupList,nameSearch,typeSearch,descSearch, groupSearch,mdbSelects); if (measureTiming) measureTime("Searched for tracks"); // Sort and Print results if (selectedTab!=filesTab) { enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance); tracksFound = slCount(tracks); if (tracksFound > 1) findTracksSort(&tracks,sortBy); displayFoundTracks(cart,tracks,tracksFound,sortBy); if (measureTiming) measureTime("Displayed found tracks"); } slPairFreeList(&mdbSelects); } hFreeConn(&conn); webNewSection("About Track Search"); if (metaDbExists) hPrintf("<p>Search for terms in track names, descriptions, groups, and ENCODE " "metadata. If multiple terms are entered, only tracks with all terms " "will be part of the results."); else hPrintf("<p>Search for terms in track descriptions, groups, and names. " "If multiple terms are entered, only tracks with all terms " "will be part of the results."); hPrintf("<BR><a target='_blank' href='../goldenPath/help/trackSearch.html'>more help</a></p>\n"); webEndSectionTables(); }