bd85159b36db7ff8c02b32eb18d96ed6066feb8f braney Wed Aug 5 13:59:46 2026 -0700 hgTracks: measure text with the same font engine that will draw it, refs #38027 Pack mode works out how many rows a track needs by measuring its item labels, and mgFontStringWidth answers from whichever text engine is loaded at the time. FreeType was only loaded when an image was created, so the measuring could happen on the bitmap engine while the drawing happened on FreeType -- and which one you got depended on whether the ideogram image had been built first. Load the engine in initTl(), alongside the rest of the font setup, before anything measures a string. maybeNewFonts() and the new initFontEngine() share chosenFreeTypeFont(), and mgLoadFontEngine() loads an engine without attaching it to an image. ftInitialize() now keeps the face it already has when asked for the same font file, so the glyph cache hanging off that face survives the extra call. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/hgTracks/config.c src/hg/hgTracks/config.c index 28257e86458..2dacb531f32 100644 --- src/hg/hgTracks/config.c +++ src/hg/hgTracks/config.c @@ -1,1165 +1,1187 @@ /* config - put up track and display configuration page. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "dystring.h" #include "cheapcgi.h" #include "htmshell.h" #include "hdb.h" #include "hCommon.h" #include "cart.h" #include "web.h" #include "customTrack.h" #include "hgTracks.h" #include "hgConfig.h" #include "jsHelper.h" #include "imageV2.h" #include "search.h" #include "hubConnect.h" #include "fileUi.h" #include "trackHub.h" #include "versionInfo.h" static void themeDropDown(struct cart* cart) /* Create drop down for UI themes. * specfied in hg.conf like this * browser.theme.modern=background.png,HGStyle * */ { struct slName* themes = cfgNamesWithPrefix("browser.theme."); if (themes==NULL) return; slNameSort(&themes); hPrintf("<TR><TD>website style:"); hPrintf("<TD style=\"text-align: right\">"); // create labels for drop down box by removing prefix from hg.conf keys char *labels[50]; struct slName* el; int i = 0; el = themes; for (el = themes; el != NULL && i<50; el = el->next) { char* name = el->name; name = chopPrefix(name); // chop off first three words name = chopPrefix(name); name = chopPrefix(name); replaceChar(name, '_', ' '); labels[i] = name; i++; } char* currentTheme = cartOptionalString(cart, "theme"); hDropList("theme", labels, i, currentTheme); slFreeList(themes); hPrintf("</TD>"); } /* HOW TO ADD A NEW FONT * * The browser draws track text with either the old bitmap engine or, when * freeType is on (hg.conf "freeType=on", the default in a FreeType build), the * FreeType engine. The fonts the FreeType engine offers are the freeTypeFonts[] * table below. To add one: * * 1. Put the font file where the engine can find it. At run time the file is * looked up under freeTypeDir, which defaults to "../htdocs/urw-fonts". * That path is relative to the CGI's working directory, so it resolves to * the *shared* htdocs/urw-fonts even from a per-user sandbox -- you do not * need a urw-fonts directory under your own htdocs-USER. (You can point * somewhere else with "freeTypeDir" in hg.conf.) Both Type-1 (.pfb) and * TrueType (.ttf) files work. * * 2. Add a row to freeTypeFonts[] giving the name and the file. The name is * what shows up in the configure-page Font dropdown. The configure page * splits the name on the first '-' into a face and a style: the part before * the '-' is the face shown in the Font menu, the part after is an entry in * the Style menu. So a plain weight is just the face name ("Lexend") and a * variant is "Face-Style" ("Lexend-Bold"). Group a face's variants on * consecutive rows so the Style menu lists them together. * * Gotchas: * * - Avoid variable fonts (e.g. InterVariable.ttf). FreeType is opened on face * index 0 with no named instance selected, so a variable font renders only * its default master -- usually not the weight you expected, which looks like * "the option appeared but a different font was drawn". Use a static, * single-weight file instead (e.g. Inter-Regular.ttf). * * - The name in the dropdown must match the name in this table exactly, * including the face/style split above. A selected name that matches no row * falls back to the bitmap engine (see maybeNewFonts). */ struct freeTypeFont /* A font offered to the FreeType text engine. The name and its file live on * one row so the two can never drift out of sync (this used to be two parallel * arrays indexed by position, which silently rendered the wrong font when they * disagreed). */ { char *name; /* Label shown in the configure-page dropdown. A normal-weight * font is just the face ("Lexend"); a variant is "Face-Style" * ("Lexend-Bold"). The dropdown splits this on the first '-'. */ char *file; /* Font file (.pfb Type-1 or .ttf TrueType) found under * freeTypeDir (hg.conf freeTypeDir, default ../htdocs/urw-fonts). */ }; struct freeTypeFont freeTypeFonts[] = { {"AvantGarde-Book", "a010013l.pfb"}, {"AvantGarde-Demi", "a010015l.pfb"}, {"AvantGarde-BookOblique", "a010033l.pfb"}, {"AvantGarde-DemiOblique", "a010035l.pfb"}, {"Helvetica", "n019003l.pfb"}, {"Helvetica-Bold", "n019004l.pfb"}, {"Helvetica-Oblique", "n019023l.pfb"}, {"Helvetica-BoldOblique", "n019024l.pfb"}, {"Helvetica-Narrow", "n019043l.pfb"}, {"Helvetica-Narrow-Bold", "n019044l.pfb"}, {"Helvetica-Narrow-Oblique", "n019063l.pfb"}, {"Helvetica-Narrow-BoldOblique", "n019064l.pfb"}, {"Times-Roman", "n021003l.pfb"}, {"Times-Bold", "n021004l.pfb"}, {"Times-Italic", "n021023l.pfb"}, {"Times-BoldItalic", "n021024l.pfb"}, {"Courier", "n022003l.pfb"}, {"Courier-Bold", "n022004l.pfb"}, {"Courier-Oblique", "n022023l.pfb"}, {"Courier-BoldOblique", "n022024l.pfb"}, {"ZapfChancery-MediumItalic", "z003034l.pfb"}, {"Atkinson", "AtkinsonHyperlegible-Regular.ttf"}, {"Atkinson-Bold", "AtkinsonHyperlegible-Bold.ttf"}, {"Atkinson-Oblique", "AtkinsonHyperlegible-Italic.ttf"}, {"Atkinson-BoldOblique", "AtkinsonHyperlegible-BoldItalic.ttf"}, {"Lexend", "Lexend-Regular.ttf"}, {"Lexend-Bold", "Lexend-Bold.ttf"}, }; char *emptyStyles[] = { "Normal" }; static boolean freeTypeOn() { #ifdef USE_FREETYPE char *defaultState = "on"; #else // USE_FREETYPE char *defaultState = "off"; #endif // USE_FREETYPE return sameString(cfgOptionDefault("freeType", defaultState), "on"); } -void maybeNewFonts(struct hvGfx *hvg) -/* Check to see if we want to use the alternate font engine (FreeType2). */ +static char *chosenFreeTypeFont(char **retFontName) +/* Return the file holding the FreeType font the user has picked, and its name in + * retFontName. NULL means stay on the bitmap engine. */ { if (!freeTypeOn()) - return; + return NULL; if (sameString(tl.textFont, "Bitmap")) - return; - -char *fontDir = cfgOptionDefault("freeTypeDir", "../htdocs/urw-fonts"); -char buffer[4096]; + return NULL; int ii; for(ii=0; ii < ArraySize(freeTypeFonts); ii++) if (sameString(freeTypeFonts[ii].name, tl.textFont)) break; if (ii == ArraySize(freeTypeFonts)) - return; // not a font we know about; leave the bitmap engine in place -char *fontFile = freeTypeFonts[ii].file; -char *fontName = freeTypeFonts[ii].name; -safef(buffer, sizeof buffer, "%s/%s", fontDir, fontFile); -hvGfxSetFontMethod(hvg, FONT_METHOD_FREETYPE, fontName, buffer ); + return NULL; // not a font we know about; leave the bitmap engine in place + +static char buffer[PATH_LEN]; +char *fontDir = cfgOptionDefault("freeTypeDir", "../htdocs/urw-fonts"); +safef(buffer, sizeof buffer, "%s/%s", fontDir, freeTypeFonts[ii].file); +*retFontName = freeTypeFonts[ii].name; +return buffer; +} + +void initFontEngine() +/* Load the text engine the user has picked, before anything measures a string. + * Pack mode reserves room for an item by measuring its label, and + * mgFontStringWidth answers from whichever engine is loaded at the time. Doing + * this up front keeps the packing from depending on whether some earlier image + * on the page -- the ideogram -- happened to load FreeType first. */ +{ +char *fontName = NULL; +char *fontFile = chosenFreeTypeFont(&fontName); +if (fontFile != NULL) + mgLoadFontEngine(FONT_METHOD_FREETYPE, fontFile); +} + +void maybeNewFonts(struct hvGfx *hvg) +/* Check to see if we want to use the alternate font engine (FreeType2). */ +{ +char *fontName = NULL; +char *fontFile = chosenFreeTypeFont(&fontName); +if (fontFile != NULL) + hvGfxSetFontMethod(hvg, FONT_METHOD_FREETYPE, fontName, fontFile); } static void textFontDropDown() /* Create drop down for font size. */ { /* get current values for font and style */ char *currentFontName = cloneString(tl.textFont); char *currentStyle = strchr(currentFontName, '-'); if (currentStyle) *currentStyle++ = 0; else currentStyle = "Normal"; char *faceNames[ArraySize(freeTypeFonts) + 1]; // +1 for the "Bitmap" entry below int ii; int numFonts = 0; struct dyString *dy = dyStringNew(1024); dyStringPrintf(dy, " fontStyles = [];\n"); int numStyle = 0; char *lastName = NULL; faceNames[numFonts++] = "Bitmap"; dyStringPrintf(dy, " fontStyles['Bitmap'] = ['Normal'];"); for (ii=0; ii < ArraySize(freeTypeFonts); ii++) { char *fontName = cloneString(freeTypeFonts[ii].name); char *style = strchr(fontName, '-'); if (style) *style++ = 0; if ((lastName == NULL) || differentString(lastName, fontName)) { faceNames[numFonts] = fontName; if (lastName != NULL) dyStringPrintf(dy, " ];\n"); dyStringPrintf(dy, " fontStyles['%s'] = [", fontName); numStyle = 0; numFonts++; } if (style == NULL) style = cloneString("Normal"); if (numStyle) dyStringPrintf(dy, ","); dyStringPrintf(dy, "'%s'", style); numStyle++; lastName = fontName; } dyStringPrintf(dy, " ];\n"); dyStringPrintf(dy, "$(\"[name='%s']\").change(function()\n", textFontVar); dyStringPrintf(dy, "{\n"); dyStringPrintf(dy, " $(\"[name='textStyle']\").empty();"); dyStringPrintf(dy, " val= $(this).find(':selected').val(); \n"); dyStringPrintf(dy, " if (fontStyles[val].length == 1) {\n"); dyStringPrintf(dy, " $(\"[id='textStyleDrop']\").hide();$(\"[id='textStyleName']\").hide();\n"); dyStringPrintf(dy, " $(\"[name='textStyle']\").val('Normal');\n"); dyStringPrintf(dy, " } else {\n"); dyStringPrintf(dy, " $(\"[id='textStyleDrop']\").show();$(\"[id='textStyleName']\").show();\n"); dyStringPrintf(dy, " }\n"); dyStringPrintf(dy, " for(ii=0; ii < fontStyles[val].length; ii++) { $(\"[name='textStyle']\").append( new Option(fontStyles[val][ii],fontStyles[val][ii],))};\n"); dyStringPrintf(dy, "});\n"); dyStringPrintf(dy, "$(\"[name='textFont']\").change();\n"); dyStringPrintf(dy, "$(\"[name='textStyle']\").val('%s');\n", currentStyle); jsInline(dy->string); hDropList(textFontVar, faceNames, numFonts, currentFontName); jsInline("$('[name=\"textFont\"]')[0].style.width='15em';\n"); // hDropList has no 'style' nor 'id' argument <-> no opt args in C } static void textStyleDropDown() /* Create drop down for font size. */ { hDropList(textStyleVar, emptyStyles, ArraySize(emptyStyles), emptyStyles[0]); } static void textSizeDropDown() /* Create drop down for font size. */ { static char *sizes[] = {"6", "8", "10", "12", "14", "18", "24", "34"}; hDropList(textSizeVar, sizes, ArraySize(sizes), tl.textSize); } static void trackConfig(struct track *trackList, struct group *groupList, char *groupTarget, int changeVis) /* Put up track configurations. If groupTarget is * NULL then set visibility for tracks in all groups. Otherwise, * just set it for the given group. If vis is -2, then visibility is * unchanged. If -1 then set visibility to default, otherwise it should * be tvHide, tvDense, etc. */ { struct group *group; boolean showedRuler = FALSE; setRulerMode(); changeTrackVis(groupList, groupTarget, changeVis); /* Set up ruler mode according to changeVis. */ #ifdef BOB_DOESNT_LIKE if (changeVis != -2) { if (groupTarget == NULL || (groupList != NULL && sameString(groupTarget, groupList->name))) { if (changeVis == -1) rulerMode = tvFull; else rulerMode = changeVis; } } #endif /* BOB_DOESNT_LIKE */ jsInit(); cgiMakeHiddenVar(configGroupTarget, "none"); // Now all groups are in a single table, divided by an empty borderless row hPrintf("<TABLE BORDER='0' CELLSPACING='0' class='groupLists'>\n"); struct hash *superHash = hashNew(8); for (group = groupList; group != NULL; group = group->next) { struct trackRef *tr; if (group->trackList == NULL) continue; /* check if group section should be displayed */ char *otherState; char *indicator; char *indicatorImg; boolean isOpen = !isCollapsedGroup(group); collapseGroupGoodies(isOpen, FALSE, &indicatorImg, &indicator, &otherState); hPrintf("<TR NOWRAP class='nativeToggleBar'>"); hPrintf("<TH NOWRAP align='left' colspan=3>"); hPrintf("<table style='width:100%%;'><tr class='noData'><td style='text-align:left;'>"); hPrintf("\n<A NAME='%sGroup'></A>",group->name); hPrintf("<input type=hidden name='%s' id='%s' value=%d>", collapseGroupVar(group->name),collapseGroupVar(group->name), (isOpen?0:1)); char idText[256]; safef(idText, sizeof idText, "%s_button", group->name); hPrintf("<IMG class='toggleButton' " "id='%s' src='%s' alt='%s' title='%s this group'> ", idText, indicatorImg, indicator,isOpen?"Collapse":"Expand"); // TODO XSS filter group->name jsOnEventByIdF("click", idText, "return vis.toggleForGroup(this,'%s');", group->name); hPrintf("<B> %s</B> ", group->label); hPrintf(" "); hPrintf("</td><td style='text-align:right;'>\n"); safef(idText, sizeof idText, "%s_hideAllBut", group->name); hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" id='%s' VALUE=\"%s\" " "title='Hide all tracks in this group'>", configHideAll, idText, "Hide all"); // TODO XSS filter configGroupTarget char jsText[256]; // used several times safef(jsText, sizeof jsText, "document.mainForm.%s.value='%s'; %s", configGroupTarget, group->name, jsSetVerticalPosition("mainForm")); jsOnEventById("click", idText, jsText); hPrintf(" "); safef(idText, sizeof idText, "%s_showAllBut", group->name); hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" id='%s' VALUE=\"%s\" " "title='Show all tracks in this groups'>", configShowAll, idText, "Show all"); jsOnEventById("click", idText, jsText); hPrintf(" "); safef(idText, sizeof idText, "%s_defaultBut", group->name); hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" id='%s' VALUE=\"%s\" " "title='Show default tracks in this group'>", configDefaultAll, idText, "Default"); jsOnEventById("click", idText, jsText); hPrintf(" "); /* do not want all the submit buttons named the same. It is * confusing to the javascript submit() function. */ char submitName[256]; safef(submitName, sizeof(submitName), "%sSubmit", group->name); cgiMakeButtonWithMsg(submitName, "Submit","Submit your selections and view them in the browser"); hPrintf("</td></tr></table>\n"); hPrintf("</TH></TR>\n"); /* First non-CT, non-hub group gets ruler. */ if (!showedRuler && !isHubTrack(group->name) && differentString(group->name, "user")) { showedRuler = TRUE; hPrintf("<TR %sid='%s-0'>",(isOpen ? "" : "style='display: none'"), group->name); hPrintf("<TD>"); hPrintf("<A HREF=\"%s?%s=%s&db=%s&c=%s&g=%s&hgTracksConfigPage=configure\">", hgTrackUiName(), cartSessionVarName(), cartSessionId(cart), database, chromName, RULER_TRACK_NAME); hPrintf("%s</A>", RULER_TRACK_LABEL); hPrintf("</TD><TD>"); hTvDropDownClassVisOnlyWithLabel("ruler", rulerMode, FALSE, rulerMode ? "normalText trackVis" : "hiddenText trackVis", NULL, RULER_TRACK_LABEL); hPrintf("</TD><TD>"); hPrintf("Chromosome position in bases. (Clicks here zoom in 3x)"); hPrintf("</TD></TR>\n"); } /* Scan track list to determine which supertracks have visible member * tracks, and to insert a track in the list for the supertrack. * Sort tracks and supertracks together by priority */ makeGlobalTrackHash(trackList); groupTrackListAddSuper(cart, group, superHash, trackHash); if (!withPriorityOverride) { /* sort hierarchically by priority, considering supertracks */ struct trackRef *refList = NULL, *ref; for (tr = group->trackList; tr != NULL; tr = tr->next) { struct track *track = tr->track; if (tdbIsSuperTrackChild(track->tdb)) /* ignore supertrack member tracks till supertrack is found */ continue; AllocVar(ref); ref->track = track; slAddTail(&refList, ref); if (tdbIsSuper(track->tdb)) { struct slRef *child = track->tdb->children; for (; child != NULL; child=child->next) { struct trackDb *childTdb = child->val; struct track *childTrack = hashFindVal(trackHash, childTdb->track); // Try adding downloadsOnly track if (childTrack == NULL && tdbIsDownloadsOnly(childTdb)) { AllocVar(childTrack); // Fake a track! childTrack->tdb = childTdb; childTrack->hasUi = FALSE; } if (childTrack != NULL) { AllocVar(ref); ref->track = childTrack; slAddTail(&refList, ref); } } } } group->trackList = refList; } /* Loop through this group and display */ int rowCount=1; for (tr = group->trackList; tr != NULL; tr = tr->next) { struct track *track = tr->track; struct trackDb *tdb = track->tdb; hPrintf("<TR %sid='%s-%d'>",(isOpen ? "" : "style='display: none;'"), group->name, rowCount++); hPrintf("<TD NOWRAP>"); if (tdbIsSuperTrackChild(tdb)) /* indent members of a supertrack */ hPrintf(" "); hPrintIcons(tdb); if (track->hasUi) hPrintf("<A TITLE='%s%s...' HREF='%s?%s=%s&db=%s&g=%s&hgTracksConfigPage=configure'>", tdb->parent ? "Part of super track: " : "Configure ", tdb->parent ? tdb->parent->shortLabel : tdb->shortLabel, hTrackUiForTrack(tdb->track), cartSessionVarName(), cartSessionId(cart), database, track->track); hPrintf(" %s", tdb->shortLabel); if (track->hasUi) hPrintf("</A>"); hPrintf("</TD><TD NOWRAP>"); if (tdbIsSuperTrackChild(tdb)) /* indent members of a supertrack */ hPrintf(" "); /* If track is not on this chrom print an informational message for the user. */ if (tdbIsDownloadsOnly(tdb)) // No vis display for downloadsOnly hPrintf("<A TITLE='Downloadable files...' HREF='%s?%s=%s&g=%s'>Downloads</A>", hgFileUiName(),cartSessionVarName(), cartSessionId(cart), tdb->track); else if (hTrackOnChrom(track->tdb, chromName)) { if (tdbIsSuper(track->tdb)) { /* supertrack dropdown is hide/show */ superTrackDropDown(cart, track->tdb, 1); } else { /* check for option of limiting visibility to one mode */ hTvDropDownClassVisOnlyWithLabel(track->track, track->visibility, rTdbTreeCanPack(track->tdb), (track->visibility == tvHide) ? "hiddenText trackVis" : "normalText trackVis", trackDbSetting(track->tdb, "onlyVisibility"), tdb->shortLabel); } } else hPrintf("[No data-%s]", chromName); hPrintf("</TD><TD NOWRAP>"); hPrintf("%s", tdb->longLabel); hPrintf("</TD></TR>\n"); } hPrintf("<tr class='noData'><td colspan=3>"); cgiDown(0.9); hPrintf("</td></tr>\n"); } hashFree(&superHash); hPrintf("</TABLE>\n"); jsInline("$(document).ready( cfgPageAddListeners )"); } static int addDownloadOnlyTracks(char *db,struct group **pGroupList,struct track **pTrackList) // Download only tracks are not normaly incorporated into the grou and track lists { int count = 0; struct track *track = NULL; struct group *group = NULL; struct trackDb *tdbList = hTrackDb(db); struct trackDb *tdb = tdbList; for (;tdb != NULL; tdb = tdb->next) { if (!tdbIsDownloadsOnly(tdb) || tdbIsFolderContent(tdb) || tdbIsCompositeChild(tdb)) continue; // Must find group if (tdb->grp == NULL) continue; for (group = *pGroupList;group != NULL; group = group->next) { if (sameWord(group->name,tdb->grp)) break; } if (group == NULL) continue; // Make the track track = trackFromTrackDb(tdb); track->group = group; track->groupName = cloneString(group->name); slAddHead(pTrackList,track); count++; } if (count > 0) { // Going to have to make all new group->trackLists slSort(pGroupList, gCmpPriority); for (group = *pGroupList;group != NULL; group = group->next) slFreeList(&group->trackList); // Sort the tracks anew and add each on into it's group. slSort(pTrackList, tgCmpPriority); 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 configInitTrackList( int vis, char **pGroupTarget, struct track **pTrackList, struct track **pIdeoTrack, struct group **pGroupList ) { 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); addDownloadOnlyTracks(database,&groupList,&trackList); /* 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 - Genome Browser V%s", CGI_VERSION); 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(leftLabelWidthVar, tl.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>"); if (freeTypeOn()) { hPrintf("<TR><TD>Font:"); hPrintf("<TD style=\"text-align: right\">"); textFontDropDown(); hPrintf("</TD></TR>"); hPrintf("<TR><TD id='textStyleName'>Style:"); hPrintf("<TD style=\"text-align: right\" id='textStyleDrop' >"); textStyleDropDown(); hPrintf("</TR>"); hPrintf("</TR>"); } if (cfgOptionBooleanDefault("showMouseovers", FALSE)) { /* I predict most people will want the browser text size as the tooltip text size * but just in case, users can change the value and it will remain independent * of the font size by saving to localStorage. */ hPrintf("<tr><td>Tooltip text size:</td>"); hPrintf("<td style=\"text-align: right\">"); static char *sizes[] = {"6", "8", "10", "12", "14", "18", "24", "34"}; int i; hPrintf("<select name='tooltipTextSize'>"); for (i = 0; i < ArraySize(sizes); i++) { hPrintf("<option "); if (sameString(tl.textSize,sizes[i])) {hPrintf("selected");} hPrintf(">%s</option>", sizes[i]); } hPrintf("</select>"); hPrintf("</td>"); hPrintf("</tr>"); jsInlineF("" "function updateSelectedTooltipSize(newSize) {\n" " let options = document.getElementsByName('tooltipTextSize')[0];\n" " let i = 0;\n" " for (i; i < options.length; i++) {\n" " if (options[i].value === newSize) {\n" " options[i].selected = true;\n" " localStorage.setItem('tooltipTextSize', options[i].value);\n" " } else {\n" " options[i].selected = false;\n" " }\n" " }\n" "}\n" "\n" "// set the tooltip text size based on localStorage values\n" "let currTooltipSize = localStorage.getItem('tooltipTextSize');\n" "let browserTextSize = document.getElementsByName('textSize')[0];\n" "if (currTooltipSize === null) {\n" " localStorage.setItem('tooltipTextSize', browserTextSize.value);\n" "} else {\n" " updateSelectedTooltipSize(currTooltipSize);\n" "}" "document.getElementsByName('tooltipTextSize')[0].addEventListener('change', function(e) {\n" " updateSelectedTooltipSize(document.getElementsByName('tooltipTextSize')[0].selectedOptions[0].value);\n" "});\n" ); } hPrintf("<TR><TD>Maximum track load time: "); printInfoIcon("Maximum time in seconds the Genome Browser will wait for any individual track to " "load. This limit can be hit by slower network connections, or densely populated tracks, especially in large regions."); hPrintf("<TD style=\"text-align: right\">"); hIntVar("parallelFetch.timeout", getParaLoadTimeout(), 3); hPrintf("<TD>seconds<TD></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("showDinkButtons", cartUsualBoolean(cart, "showDinkButtons", FALSE)); hPrintf("</TD><TD>"); hPrintf("Show move left/right limit buttons under image"); 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"); // check if we can do hgc pages in a pop up before putting up the user control if (cfgOptionBooleanDefault("canDoHgcInPopUp", TRUE)) { // put a checkbox, on by default, to control whether item clicks stay on hgTracks or // go to hgTracks hPrintf("<tr><td>"); hCheckBox("doHgcInPopUp", cartUsualBoolean(cart, "doHgcInPopUp", TRUE)); hPrintf("<td>Enable pop-up when clicking items</td></tr>\n"); } // My Variants navigation preference reset - stored in localStorage if (cfgOptionBooleanDefault("doMyVariants", FALSE)) { hPrintf("<TR><TD>"); hPrintf("<input type='checkbox' id='resetMyVariantsNav' name='resetMyVariantsNav'>"); hPrintf("</TD><TD>"); hPrintf("Reset 'My Annotations' navigation preference (currently: <span id='myVariantsNavPrefDisplay'>not set</span>)"); hPrintf("</TD></TR>\n"); // Display current preference and clear localStorage on form submit if checkbox is checked jsInlineF( "document.addEventListener('DOMContentLoaded', function() {" " var prefSpan = document.getElementById('myVariantsNavPrefDisplay');" " if (prefSpan) {" " var pref = localStorage.getItem('myVariants_navPref');" " prefSpan.textContent = pref ? pref : 'not set';" " }" " var form = document.forms['TrackForm'] || document.forms['TrackHeaderForm'];" " if (form) {" " form.addEventListener('submit', function() {" " var cb = document.getElementById('resetMyVariantsNav');" " if (cb && cb.checked) {" " localStorage.removeItem('myVariants_navPref');" " }" " });" " }" "});" ); } 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 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("<a href=\"../goldenPath/help/multiRegionHelp.html\" target='_blank' class='blueLink'>" "<b>Multi-region display</b></a>" " 'slices' the genome to allow viewing discontinuous regions" " together in the browser window. "); // mode-specific message filled in by JS when dialog opened hPrintf("<span id='multiRegionConfigStatusMsg'></span>"); hPrintf("<p></p>"); hTableStart(); virtModeType = cartUsualString(cart, "virtModeType", virtModeType); hPrintf("<TR><TD>"); cgiMakeRadioButton("virtModeType", "default", sameWord("default", virtModeType)); hPrintf("</TD>"); hPrintf("<TD id='virtModeTypeDefaultLabel'>"); hPrintf("Exit multi-region mode (keyboard shortcut: d then v)"); 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 (keyboard shortcut: e then v). 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); // option to set viewing window to show all regions. This id also known to JS. if (cfgOptionBooleanDefault(MULTI_REGION_CFG_BUTTON_TOP, FALSE)) { boolean isChecked = cartUsualBoolean(cart, MULTI_REGION_BED_WIN_FULL, FALSE); hPrintf("  "); cgiMakeCheckBoxUtil(MULTI_REGION_BED_WIN_FULL, isChecked, "If unchecked, when regions are changed here the view is zoomed in and does not display all regions", MULTI_REGION_BED_WIN_FULL); hPrintf("Show all"); 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("  "); cgiMakeCancelButton("Cancel"); hPrintf("</TD></TR>\n"); hPrintf("</TABLE>\n"); hFreeConn(&conn); cgiDown(0.9); freez(&groupTarget); webEndSectionTables(); hPrintf("</FORM>"); // The previous version of the hgTracks js object will get over-written by this page, // so add all the variables needed htere. So any new hgTracks.somefield references // added to hgTracks.js may need to be put here. if (differentString(virtModeType, "default")) jsonObjectAdd(jsonForClient, "virtModeType", newJsonString(virtModeType)); }