12947e6dc054b98b4bb372cf381b40169638aa65
chmalee
  Thu Jan 15 14:44:26 2026 -0800
Make ability to do hgc in popups on by default, still need the cart variable doHgcInPopUp (which also defaults to true) to control whether the popup actually shows up, refs #36953

diff --git src/hg/hgTracks/config.c src/hg/hgTracks/config.c
index 6dfe81e80be..311a0c60c34 100644
--- src/hg/hgTracks/config.c
+++ src/hg/hgTracks/config.c
@@ -1,1112 +1,1112 @@
 /* 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>");
 }
 
 char *freeTypeFontNames[] = {
 "AvantGarde-Book",
 "AvantGarde-Demi",
 "AvantGarde-BookOblique",
 "AvantGarde-DemiOblique",
 "Helvetica",
 "Helvetica-Bold",
 "Helvetica-Oblique",
 "Helvetica-BoldOblique",
 "Helvetica-Narrow",
 "Helvetica-Narrow-Bold",
 "Helvetica-Narrow-Oblique",
 "Helvetica-Narrow-BoldOblique",
 "Times-Roman",
 "Times-Bold",
 "Times-Italic",
 "Times-BoldItalic",
 "Courier",
 "Courier-Bold",
 "Courier-Oblique",
 "Courier-BoldOblique",
 "ZapfChancery-MediumItalic",
 "Atkinson",
 "Atkinson-Bold",
 "Atkinson-Oblique",
 "Atkinson-BoldOblique",
 "Lexend",
 "Lexend-Bold",
 };
 
 char *freeTypeFontFiles[] = {
 "a010013l.pfb",
 "a010015l.pfb",
 "a010033l.pfb",
 "a010035l.pfb",
 "n019003l.pfb",
 "n019004l.pfb",
 "n019023l.pfb",
 "n019024l.pfb",
 "n019043l.pfb",
 "n019044l.pfb",
 "n019063l.pfb",
 "n019064l.pfb",
 "n021003l.pfb",
 "n021004l.pfb",
 "n021023l.pfb",
 "n021024l.pfb",
 "n022003l.pfb",
 "n022004l.pfb",
 "n022023l.pfb",
 "n022024l.pfb",
 "z003034l.pfb",
 "AtkinsonHyperlegible-Regular.ttf",
 "AtkinsonHyperlegible-Bold.ttf",
 "AtkinsonHyperlegible-Italic.ttf",
 "AtkinsonHyperlegible-BoldItalic.ttf",
 "Lexend-Regular.ttf",
 "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). */
 {
 if (!freeTypeOn())
     return;
 
 if (sameString(tl.textFont, "Bitmap"))
     return;
 
 char *fontDir = cfgOptionDefault("freeTypeDir", "../htdocs/urw-fonts");
 char buffer[4096];
 
 int ii;
 for(ii=0; ii < ArraySize(freeTypeFontNames); ii++)
     if (sameString(freeTypeFontNames[ii], tl.textFont))
         break;
 char *fontFile = freeTypeFontFiles[ii];
 char *fontName = freeTypeFontNames[ii];
 safef(buffer, sizeof buffer, "%s/%s", fontDir, fontFile);
 hvGfxSetFontMethod(hvg, FONT_METHOD_FREETYPE, fontName, buffer );
 }
 
 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[sizeof(freeTypeFontNames)];
 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(freeTypeFontNames); ii++)
     {
     char *fontName = cloneString(freeTypeFontNames[ii]);
     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'>&nbsp;&nbsp;",
             idText, indicatorImg, indicator,isOpen?"Collapse":"Expand");
     // TODO XSS filter group->name
     jsOnEventByIdF("click", idText, "return vis.toggleForGroup(this,'%s');", group->name);
 
     hPrintf("<B>&nbsp;%s</B> ", group->label);
     hPrintf("&nbsp;&nbsp;&nbsp;");
     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&c=%s&g=%s&hgTracksConfigPage=configure\">", hgTrackUiName(),
                 cartSessionVarName(), cartSessionId(cart),
                 chromName, RULER_TRACK_NAME);
         hPrintf("%s</A>", RULER_TRACK_LABEL);
 	hPrintf("</TD><TD>");
 	hTvDropDownClass("ruler", rulerMode, FALSE, rulerMode ? "normalText trackVis" : "hiddenText trackVis");
 	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("&nbsp;&nbsp;&nbsp;&nbsp;");
 
         hPrintIcons(tdb);
 
         if (track->hasUi)
             hPrintf("<A TITLE='%s%s...' HREF='%s?%s=%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), track->track);
         hPrintf(" %s", tdb->shortLabel);
         if (track->hasUi)
 	    hPrintf("</A>");
 	hPrintf("</TD><TD NOWRAP>");
         if (tdbIsSuperTrackChild(tdb))
             /* indent members of a supertrack */
             hPrintf("&nbsp;&nbsp;&nbsp;&nbsp;");
 
 	/* 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 */
                 hTvDropDownClassVisOnly(track->track, track->visibility,
                                         rTdbTreeCanPack(track->tdb),
                                         (track->visibility == tvHide) ? "hiddenText trackVis" : "normalText trackVis",
                                         trackDbSetting(track->tdb, "onlyVisibility"));
                 }
 	    }
         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("&nbsp;medium&nbsp;");
     cartMakeRadioButton(cart, "fontType", "fixed", defaultStyle);
     hPrintf("&nbsp;fixed&nbsp;");
     cartMakeRadioButton(cart, "fontType", "bold", defaultStyle);
     hPrintf("&nbsp;bold&nbsp;");
     hPrintf("&nbsp;");
     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", FALSE))
+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");
     }
 
 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("&nbsp;&nbsp;&nbsp;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. &nbsp;&nbsp;");
 // 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 &nbsp; (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 &nbsp; (keyboard shortcut: e then v). &nbsp;&nbsp; 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. &nbsp;&nbsp; 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("&nbsp;&nbsp");
     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("&nbsp;&nbsp");
 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));
 
 
 }