cb9d5c7ec853681999acfa42ce503f1846d546ae
max
  Fri Sep 24 05:03:21 2021 -0700
fixing track vis color on config page, refs #26257

diff --git src/hg/hgTracks/config.c src/hg/hgTracks/config.c
index c81c7ec..b686a4d 100644
--- src/hg/hgTracks/config.c
+++ src/hg/hgTracks/config.c
@@ -1,1012 +1,1014 @@
 /* config - put up track and display configuration page. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory 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"
 
 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.");
 //struct slName* themes = cfgNames();
 if (themes==NULL)
     return;
 
 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 two words
     name = chopPrefix(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",
 };
 
 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",
 };
 
 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);
 }
 
 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");
 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='blueToggleBar'>");
     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 groups'>",
 	    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" : "hiddenText");
+	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);
 
     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" : "normalText",
+                                        (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");
     }
 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");
 
 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>");
     }
 
 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("&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");
 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;&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>");
 }