3cd12608e8522ce11807b6dcad6396b97ef55687
tdreszer
  Wed Jan 22 16:27:56 2014 -0800
Cleaned up the hgTracks configure group tables at Donna's request.  All groups are combined into a single table divided by empty data rows. Redmine #12546
diff --git src/hg/hgTracks/config.c src/hg/hgTracks/config.c
index 6127a30..2937214 100644
--- src/hg/hgTracks/config.c
+++ src/hg/hgTracks/config.c
@@ -1,527 +1,524 @@
 /* config - put up track and display configuration page. */
 
 #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>");
 }
 
 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("<TABLE BORDER='1' CELLSPACING='0' style='background-color:#%s; width:54em;'>\n",
-            HG_COL_INSIDE);
     hPrintf("<TR NOWRAP class='blueToggleBar'>");
     hPrintf("<TH NOWRAP align='left' colspan=3>");
-    hPrintf("<table style='width:100%%;'><tr><td style='text-align:left;'>");
+    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));
 //#define BUTTONS_BY_CSS_NOT_HERE
 #ifdef BUTTONS_BY_CSS_NOT_HERE
     hPrintf("<span class='pmButton toggleButton' onclick=\"vis.toggleForGroup(this,'%s')\" "
             "id='%s_button' title='%s this group'>%s</span>&nbsp;&nbsp;",
             group->name, group->name, isOpen?"Collapse":"Expand", indicator);
 #else///ifndef BUTTONS_BY_CSS_NOT_HERE
     hPrintf("<IMG class='toggleButton' onclick=\"return vis.toggleForGroup(this,'%s');\" "
             "id='%s_button' src='%s' alt='%s' title='%s this group'>&nbsp;&nbsp;",
             group->name, group->name, indicatorImg, indicator,isOpen?"Collapse":"Expand");
 #endif///ndef BUTTONS_BY_CSS_NOT_HERE
     hPrintf("<B>&nbsp;%s</B> ", group->label);
     hPrintf("&nbsp;&nbsp;&nbsp;");
     hPrintf("</td><td style='text-align:right;'>\n");
     hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" "
             "onClick=\"document.mainForm.%s.value='%s'; %s\" "
             "title='Hide all tracks in this groups'>",
 	    configHideAll, "hide all", configGroupTarget, group->name,
 	    jsSetVerticalPosition("mainForm"));
     hPrintf(" ");
     hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" "
             "onClick=\"document.mainForm.%s.value='%s'; %s\" "
             "title='Show all tracks in this groups'>",
 	    configShowAll, "show all", configGroupTarget, group->name,
 	    jsSetVerticalPosition("mainForm"));
     hPrintf(" ");
     hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" "
             "onClick=\"document.mainForm.%s.value='%s'; %s\" "
             "title='Show default tracks in this group'>",
 	    configDefaultAll, "default", configGroupTarget, group->name,
 	    jsSetVerticalPosition("mainForm"));
     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>\n");
-    hPrintf("</TR>\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=%u&c=%s&g=%s&hgTracksConfigPage=configure\">", hgTrackUiName(),
                 cartSessionVarName(), cartSessionId(cart),
                 chromName, RULER_TRACK_NAME);
         hPrintf("%s</A>", RULER_TRACK_LABEL);
-	hPrintf("</TD>");
-	hPrintf("<TD>");
+	hPrintf("</TD><TD>");
 	hTvDropDownClass("ruler", rulerMode, FALSE, rulerMode ? "normalText" : "hiddenText");
-	hPrintf("</TD>");
-	hPrintf("<TD>");
+	hPrintf("</TD><TD>");
 	hPrintf("Chromosome position in bases.  (Clicks here zoom in 3x)");
-	hPrintf("</TD>");
-	hPrintf("</TR>\n");
+	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("<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;");
 
         // Print an icon before the title when one is defined
         hPrintPennantIcon(tdb);
 
         if (track->hasUi)
             hPrintf("<A TITLE='%s%s...' HREF='%s?%s=%u&g=%s&hgTracksConfigPage=configure'>",
                     tdb->parent ? "Part of super track: " : "Configure ",
                     tdb->parent ? tdb->parent->shortLabel : tdb->shortLabel,
                     hgTrackUiName(),cartSessionVarName(), cartSessionId(cart), track->track);
         hPrintf(" %s", tdb->shortLabel);
         if (tdbIsSuper(tdb))
             hPrintf("...");
         if (track->hasUi)
 	    hPrintf("</A>");
-	hPrintf("</TD>");
-        hPrintf("<TD NOWRAP>");
+	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=%u&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",
                                         trackDbSetting(track->tdb, "onlyVisibility"));
                 }
 	    }
         else
 	    hPrintf("[No data-%s]", chromName);
-	hPrintf("</TD>");
-	hPrintf("<TD NOWRAP>");
+	hPrintf("</TD><TD NOWRAP>");
         hPrintf("%s", tdb->longLabel);
-	hPrintf("</TD>");
-	hPrintf("</TR>\n");
+	hPrintf("</TD></TR>\n");
 	}
-    hPrintf("</TABLE>\n");
+    hPrintf("<tr class='noData'><td colspan=3>");
     cgiDown(0.9);
+    hPrintf("</td></tr>\n");
     }
+hPrintf("</TABLE>\n");
 }
 
 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 configPageSetTrackVis(int vis)
 /* Do config page after setting track visibility. If vis is -2, then visibility
  * is unchanged.  If -1 then set visibility to default, otherwise it should
  * be tvHide, tvDense, etc. */
 {
 struct dyString *title = dyStringNew(0);
 char *groupTarget = NULL;
 struct track *trackList =  NULL;
 struct track *ideoTrack = NULL;
 struct group *groupList = NULL;
 
 withPriorityOverride = cartUsualBoolean(cart, configPriorityOverride, FALSE);
 
 /* Get track list and group them. */
 ctList = customTracksParseCart(database, cart, &browserLines, &ctFileName);
 trackList = getTrackList(&groupList, vis);
 
 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);
 
 dyStringPrintf(title, "Configure Image");
 
 hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n", hgTracksName(),
 	cartUsualString(cart, "formMethod", "POST"));
 webStartWrapperDetailedNoArgs(cart, database, "", title->string, FALSE, FALSE, FALSE, FALSE);
 cartSaveSession(cart);
 
 hPrintf("<INPUT TYPE=HIDDEN NAME=\"hgTracksConfigPage\" VALUE=\"\">");
 /* do not want all the submit buttons named the same thing, this one is: */
 cgiMakeButton("topSubmit", "submit");
 
 // 3 column table
 hPrintf("<TABLE style=\"border:0px; \">\n");
 hPrintf("<TR><TD>image width:");
 hPrintf("<TD style=\"text-align: right\">");
 hIntVar("pix", tl.picWidth, 4);
 hPrintf("<TD>pixels</TR>");
 
 hPrintf("<TR><TD>label area width:");
 hPrintf("<TD style=\"text-align: right\">");
 hIntVar("hgt.labelWidth", leftLabelWidthChars, 2);
 hPrintf("<TD>characters<TD></TR>");
 
 hPrintf("<TR><TD>text size:");
 hPrintf("<TD style=\"text-align: right\">");
 textSizeDropDown();
 hPrintf("</TD>");
 if (trackLayoutInclFontExtras())
     {
     hPrintf("<TD>");
     char *defaultStyle = cartUsualString(cart, "fontType", "medium");
     cartMakeRadioButton(cart, "fontType", "medium", defaultStyle);
     hPrintf("&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>");
 
 themeDropDown(cart);
 
 hTableStart();
 if (ideoTrack != NULL)
     {
     hPrintf("<TR><TD>");
     hCheckBox("ideogram", cartUsualBoolean(cart, "ideogram", TRUE));
     hPrintf("</TD><TD>");
     hPrintf("Display chromosome ideogram above main graphic");
     hPrintf("</TD></TR>\n");
     }
 hPrintf("<TR><TD>");
 hCheckBox("guidelines", cartUsualBoolean(cart, "guidelines", TRUE));
 hPrintf("</TD><TD>");
 hPrintf("Show light blue vertical guidelines");
 hPrintf("</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("enableHighlightingDialog", cartUsualBoolean(cart, "enableHighlightingDialog", TRUE));
 hPrintf("</TD><TD>");
 hPrintf("Enable highlight with drag-and-select "
         "(if unchecked, drag-and-select always zooms to selection)");
 hPrintf("</TD></TR>\n");
 
 hTableEnd();
 cgiDown(0.9);
 
 char *freeze = hFreezeFromDb(database);
 char buf[128];
 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(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);
 }