b73fd861b426ef34c2a56da6a26a311850c276dc
tdreszer
  Mon Jul 16 17:30:32 2012 -0700
Maybe last batch of many checkins as dictated by Jim.  Formatting if and limiting lines to 100 chars.  Changes (mostly) limited to lines last touched by tdreszer (git blame) so as not to ruin history. Some things not mine were 'fixed' so that my changes were in context. None of these changes should affect executables in any way.
diff --git src/hg/hgTracks/searchTracks.c src/hg/hgTracks/searchTracks.c
index cbf580a..4616526 100644
--- src/hg/hgTracks/searchTracks.c
+++ src/hg/hgTracks/searchTracks.c
@@ -1,766 +1,821 @@
 /* Track search code used by hgTracks CGI */
 
 #include "common.h"
 #include "search.h"
 #include "hCommon.h"
 #include "memalloc.h"
 #include "obscure.h"
 #include "dystring.h"
 #include "hash.h"
 #include "cheapcgi.h"
 #include "hPrint.h"
 #include "htmshell.h"
 #include "cart.h"
 #include "hgTracks.h"
 #include "web.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "mdb.h"
 #include "fileUi.h"
 #include "trix.h"
 #include "jsHelper.h"
 #include "imageV2.h"
 
 
 #define TRACK_SEARCH_FORM        "trackSearch"
 #define SEARCH_RESULTS_FORM      "searchResults"
 #define TRACK_SEARCH_CURRENT_TAB "tsCurTab"
 #define TRACK_SEARCH_SIMPLE      "tsSimple"
 #define TRACK_SEARCH_ON_NAME     "tsName"
 #define TRACK_SEARCH_ON_TYPE     "tsType"
 #define TRACK_SEARCH_ON_GROUP    "tsGroup"
 #define TRACK_SEARCH_ON_DESCR    "tsDescr"
 #define TRACK_SEARCH_SORT        "tsSort"
 
 static int gCmpGroup(const void *va, const void *vb)
 /* Compare groups based on label. */
 {
 const struct group *a = *((struct group **)va);
 const struct group *b = *((struct group **)vb);
 return strcmp(a->label, b->label);
 }
 
 // Would like to do a radio button choice ofsorts
 enum sortBy
     {
     sbRelevance=0,
     sbAbc      =1,
     sbHierarchy=2,
     };
 static int gCmpTrackHierarchy(const void *va, const void *vb)
 /* Compare tracks based on longLabel. */
 {
 const struct slRef *aa = *((struct slRef **)va);
 const struct slRef *bb = *((struct slRef **)vb);
 const struct track *a = ((struct track *) aa->val);
 const struct track *b = ((struct track *) bb->val);
      if ( tdbIsFolder(a->tdb) && !tdbIsFolder(b->tdb))
         return -1;
 else if (!tdbIsFolder(a->tdb) &&  tdbIsFolder(b->tdb))
         return 1;
      if ( tdbIsContainer(a->tdb) && !tdbIsContainer(b->tdb))
         return -1;
 else if (!tdbIsContainer(a->tdb) &&  tdbIsContainer(b->tdb))
         return 1;
      if (!tdbIsContainerChild(a->tdb) &&  tdbIsContainerChild(b->tdb))
         return -1;
 else if ( tdbIsContainerChild(a->tdb) && !tdbIsContainerChild(b->tdb))
         return 1;
 return strcasecmp(a->longLabel, b->longLabel);
 }
 
 static int gCmpTrack(const void *va, const void *vb)
 /* Compare tracks based on longLabel. */
 {
 const struct slRef *aa = *((struct slRef **)va);
 const struct slRef *bb = *((struct slRef **)vb);
 const struct track *a = ((struct track *) aa->val);
 const struct track *b = ((struct track *) bb->val);
 return strcasecmp(a->longLabel, b->longLabel);
 }
 
 static void findTracksSort(struct slRef **pTrack, enum sortBy sortBy)
 {
 if (sortBy == sbHierarchy)
     slSort(pTrack, gCmpTrackHierarchy);
 else if (sortBy == sbAbc)
     slSort(pTrack, gCmpTrack);
 else
     slReverse(pTrack);
 }
 
 static int getFormatTypes(char ***pLabels, char ***pTypes)
 {
 char *crudeTypes[] = {
     ANYLABEL,
     "bam",
     "psl",
     "chain",
     "netAlign",
     "maf",
     "bed",
     "bigBed",
     "ctgPos",
     "expRatio",
     "genePred",
     "broadPeak",
     "narrowPeak",
     "rmsk",
     "bedGraph",
     "bigWig",
     "wig",
     "wigMaf"
 };
 // Non-standard:
 // type altGraphX
 // type axt
 // type bed5FloatScore
 // type bed5FloatScoreWithFdr
 // type chromGraph
 // type clonePos
 // type coloredExon
 // type encodeFiveC
 // type factorSource
 // type ld2
 // type logo
 // type maf
 // type sample
 // type wigMafProt 0.0 1.0
 
 char *nicerTypes[] = {
     ANYLABEL,
     "Alignment binary (bam) - binary SAM",
     "Alignment Blast (psl) - Blast output",
     "Alignment Chains (chain) - Pairwise alignment",
     "Alignment Nets (netAlign) - Net alignments",
     "Alignments (maf) - multiple alignment format",
     "bed - browser extensible data",
     "bigBed - self index, often remote bed format",
     "ctgPos - Contigs",
     "expRatio - Expression ratios",
     "Genes (genePred) - Gene prediction and annotation",
     "Peaks Broad (broadPeak) - ENCODE large region peak format",
     "Peaks Narrow (narrowPeak) - ENCODE small region peak format",
     "Repeats (rmsk) - Repeat masking",
     "Signal (bedGraph) - graphically represented bed data",
     "Signal (bigWig) - self index, often remote wiggle format",
     "Signal (wig) - wiggle format",
     "Signal (wigMaf) - multiple alignment wiggle"
 };
 
 int ix = 0, count = sizeof(crudeTypes)/sizeof(char *);
 char **labels;
 char **values;
 AllocArray(labels, count);
 AllocArray(values, count);
 for(ix=0;ix<count;ix++)
     {
     labels[ix] = cloneString(nicerTypes[ix]);
     values[ix] = cloneString(crudeTypes[ix]);
     }
 *pLabels = labels;
 *pTypes = values;
 return count;
 }
 
 static struct slRef *simpleSearchForTracksstruct(char *simpleEntry)
 // Performs the simple search and returns the found tracks.
 {
 struct slRef *tracks = NULL;
 
 // Prepare for trix search
 if (!isEmpty(simpleEntry))
     {
     int trixWordCount = 0;
     char *tmp = cloneString(simpleEntry);
     char *val = nextWord(&tmp);
     struct slName *el, *trixList = NULL;
     while (val != NULL)
         {
         slNameAddTail(&trixList, val);
         trixWordCount++;
         val = nextWord(&tmp);
         }
     if (trixWordCount > 0)
         {
         // Unfortunately trixSearch can't handle the slName list
         int i;
         char **trixWords = needMem(sizeof(char *) * trixWordCount);
         for(i = 0, el = trixList; el != NULL; i++, el = el->next)
             trixWords[i] = strLower(el->name);
 
         // Now open the trix file
         char trixFile[HDB_MAX_PATH_STRING];
         getSearchTrixFile(database, trixFile, sizeof(trixFile));
         struct trix *trix = trixOpen(trixFile);
 
-        struct trixSearchResult *tsList;
-        for(tsList = trixSearch(trix, trixWordCount, trixWords, TRUE); tsList != NULL; tsList = tsList->next)
+        struct trixSearchResult *tsList = trixSearch(trix, trixWordCount, trixWords, TRUE);
+        for( ; tsList != NULL; tsList = tsList->next)
             {
             struct track *track = (struct track *) hashFindVal(trackHash, tsList->itemId);
-            if (track != NULL)  // It is expected that this is NULL (e.g. when the trix references trackDb tracks which have no tables)
-                {
+            if (track != NULL)  // It is expected that this is NULL
+                {               // (e.g. when trix references trackDb tracks which have no tables)
                 refAdd(&tracks, track);
                 }
             }
         //trixClose(trix);  // don't bother (this is a CGI that is about to end)
         }
     }
 return tracks;
 }
 
 static struct slRef *advancedSearchForTracks(struct sqlConnection *conn,struct group *groupList,
                                              char *nameSearch, char *typeSearch, char *descSearch,
                                              char *groupSearch, struct slPair *mdbPairs)
 // Performs the advanced search and returns the found tracks.
 {
 int tracksFound = 0;
 struct slRef *tracks = NULL;
 int numMetadataNonEmpty = 0;
 struct slPair *pair = mdbPairs;
 for (; pair!= NULL;pair=pair->next)
     {
     if (!isEmpty((char *)(pair->val)))
         numMetadataNonEmpty++;
     }
 
 if(!isEmpty(groupSearch) && sameString(groupSearch,ANYLABEL))
     groupSearch = NULL;
 if(!isEmpty(typeSearch) && sameString(typeSearch,ANYLABEL))
     typeSearch = NULL;
 
 if(isEmpty(nameSearch) && isEmpty(typeSearch) && isEmpty(descSearch)
 && isEmpty(groupSearch) && numMetadataNonEmpty == 0)
     return NULL;
 
 // First do the metaDb searches, which can be done quickly for all tracks with db queries.
 struct hash *matchingTracks = NULL;
 
 if (numMetadataNonEmpty)
     {
     struct mdbObj *mdbObj, *mdbObjs = mdbObjRepeatedSearch(conn,mdbPairs,TRUE,FALSE);
     if (mdbObjs)
         {
         for (mdbObj = mdbObjs; mdbObj != NULL; mdbObj = mdbObj->next)
             {
             if (matchingTracks == NULL)
                 matchingTracks = newHash(0);
             hashAddInt(matchingTracks, mdbObj->obj, 1);
             }
         mdbObjsFree(&mdbObjs);
         }
     if (matchingTracks == NULL)
         return NULL;
     }
 
 // Set the word lists up once
 struct slName *nameList = NULL;
 if (!isEmpty(nameSearch))
     nameList = slNameListOfUniqueWords(cloneString(nameSearch),TRUE); // TRUE means respect quotes
 struct slName *descList = NULL;
 if (!isEmpty(descSearch))
     descList = slNameListOfUniqueWords(cloneString(descSearch),TRUE);
 
 struct group *group;
 for (group = groupList; group != NULL; group = group->next)
     {
     if(isEmpty(groupSearch) || sameString(group->name, groupSearch))
         {
         if (group->trackList == NULL)
             continue;
 
         struct trackRef *tr;
         for (tr = group->trackList; tr != NULL; tr = tr->next)
             {
             struct track *track = tr->track;
             char *trackType = cloneFirstWord(track->tdb->type); // will be spilled
             if ((matchingTracks == NULL || hashLookup(matchingTracks, track->track) != NULL)
-            && (isEmpty(typeSearch) || (sameWord(typeSearch, trackType) && !tdbIsComposite(track->tdb)))
+            && (  isEmpty(typeSearch)
+               || (sameWord(typeSearch, trackType) && !tdbIsComposite(track->tdb)))
             && (isEmpty(nameSearch) || searchNameMatches(track->tdb, nameList))
             && (isEmpty(descSearch) || searchDescriptionMatches(track->tdb, descList)))
                 {
                 if (track != NULL)
                     {
                     tracksFound++;
                     refAdd(&tracks, track);
                     }
                 else
                     warn("found group track is NULL.");
                 }
             if (track->subtracks != NULL)
                 {
                 struct track *subTrack;
                 for (subTrack = track->subtracks; subTrack != NULL; subTrack = subTrack->next)
                     {
                     trackType = cloneFirstWord(subTrack->tdb->type); // will be spilled
-                    if ((matchingTracks == NULL || hashLookup(matchingTracks, subTrack->track) != NULL)
+                    if (  (matchingTracks == NULL
+                       || hashLookup(matchingTracks, subTrack->track) != NULL)
                     && (isEmpty(typeSearch) || sameWord(typeSearch, trackType))
                     && (isEmpty(nameSearch) || searchNameMatches(subTrack->tdb, nameList))
                     && (isEmpty(descSearch) // subtracks inherit description
                         || searchDescriptionMatches(subTrack->tdb, descList)
                         || (tdbIsCompositeChild(subTrack->tdb) && subTrack->parent
                             && searchDescriptionMatches(subTrack->parent->tdb, descList))))
                         {
                         if (track != NULL)
                             {
                             tracksFound++;
                             refAdd(&tracks, subTrack);
                             }
                         else
                             warn("found subtrack is NULL.");
                         }
                     }
                 }
             }
         }
     }
 
 return tracks;
 }
 
 #define MAX_FOUND_TRACKS 100
 static void findTracksPageLinks(int tracksFound, int startFrom)
 {
 if (tracksFound <= MAX_FOUND_TRACKS)
     return;
 
 // Opener
 int willStartAt = 0;
 int curPage  = (startFrom/MAX_FOUND_TRACKS) + 1;
 int endAt = startFrom+MAX_FOUND_TRACKS;
 if (endAt > tracksFound)
     endAt = tracksFound;
-hPrintf("<span><em style='font-size:.9em;'>Listing %d - %d of %d tracks</em>&nbsp;&nbsp;&nbsp;",startFrom+1,endAt,tracksFound);
+hPrintf("<span><em style='font-size:.9em;'>Listing %d - %d of %d tracks</em>&nbsp;&nbsp;&nbsp;",
+        startFrom+1,endAt,tracksFound);
 
 // << and <
 if (startFrom >= MAX_FOUND_TRACKS)
     {
-    hPrintf("<a href='../cgi-bin/hgTracks?%s=Search&%s=0' title='First page of found tracks' onclick='return findTracks.page(\"%s\",0);'>&#171;</a>&nbsp;",
+    hPrintf("<a href='../cgi-bin/hgTracks?%s=Search&%s=0' title='First page of found tracks' "
+            "onclick='return findTracks.page(\"%s\",0);'>&#171;</a>&nbsp;",
             TRACK_SEARCH,TRACK_SEARCH_PAGER,TRACK_SEARCH_PAGER);
     willStartAt = startFrom - MAX_FOUND_TRACKS;
-    hPrintf("&nbsp;<a href='../cgi-bin/hgTracks?%s=Search&%s=%d' title='Previous page of found tracks' onclick='return findTracks.page(\"%s\",%d);'>&#139;</a>&nbsp;",
+    hPrintf("&nbsp;<a href='../cgi-bin/hgTracks?%s=Search&%s=%d' title='Previous page of found "
+            "tracks' onclick='return findTracks.page(\"%s\",%d);'>&#139;</a>&nbsp;",
             TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt,TRACK_SEARCH_PAGER,willStartAt);
     }
 
 // page number links
 int lastPage = (tracksFound/MAX_FOUND_TRACKS);
 if ((tracksFound % MAX_FOUND_TRACKS) > 0)
     lastPage++;
 
 int thisPage = curPage - 3; // Window of 3 pages above and below
 if (thisPage < 1)
     thisPage = 1;
 for (;thisPage <= lastPage && thisPage <= curPage + 3; thisPage++)
     {
     if (thisPage != curPage)
         {
         willStartAt = ((thisPage - 1) * MAX_FOUND_TRACKS);
         endAt = willStartAt+ MAX_FOUND_TRACKS;
         if (endAt > tracksFound)
             endAt = tracksFound;
-        hPrintf("&nbsp;<a href='../cgi-bin/hgTracks?%s=Search&%s=%d' title='Page %d (%d - %d) tracks' onclick='return findTracks.page(\"%s\",%d);'>%d</a>&nbsp;",
-                TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt,thisPage,willStartAt+1,endAt,TRACK_SEARCH_PAGER,willStartAt,thisPage);
+        hPrintf("&nbsp;<a href='../cgi-bin/hgTracks?%s=Search&%s=%d' title='Page %d (%d - %d) "
+                "tracks' onclick='return findTracks.page(\"%s\",%d);'>%d</a>&nbsp;",
+                TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt,thisPage,willStartAt+1,endAt,
+                TRACK_SEARCH_PAGER,willStartAt,thisPage);
         }
     else
         hPrintf("&nbsp;<em style='color:%s;'>%d</em>&nbsp;",COLOR_DARKGREY,thisPage);
     }
 
 // > and >>
 if ((startFrom + MAX_FOUND_TRACKS) < tracksFound)
     {
     willStartAt = startFrom + MAX_FOUND_TRACKS;
-    hPrintf("&nbsp;<a href='../cgi-bin/hgTracks?%s=Search&%s=%d' title='Next page of found tracks' onclick='return findTracks.page(\"%s\",%d);'>&#155;</a>&nbsp;",
+    hPrintf("&nbsp;<a href='../cgi-bin/hgTracks?%s=Search&%s=%d' title='Next page of found tracks' "
+            "onclick='return findTracks.page(\"%s\",%d);'>&#155;</a>&nbsp;",
             TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt,TRACK_SEARCH_PAGER,willStartAt);
     willStartAt =  tracksFound - (tracksFound % MAX_FOUND_TRACKS);
     if (willStartAt == tracksFound)
         willStartAt -= MAX_FOUND_TRACKS;
-    hPrintf("&nbsp;<a href='../cgi-bin/hgTracks?%s=Search&%s=%d' title='Last page of found tracks' onclick='return findTracks.page(\"%s\",%d);'>&#187;</a></span>\n",
+    hPrintf("&nbsp;<a href='../cgi-bin/hgTracks?%s=Search&%s=%d' title='Last page of found tracks' "
+            "onclick='return findTracks.page(\"%s\",%d);'>&#187;</a></span>\n",
             TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt,TRACK_SEARCH_PAGER,willStartAt);
     }
 }
 
-static void displayFoundTracks(struct cart *cart, struct slRef *tracks, int tracksFound,enum sortBy sortBy)
+static void displayFoundTracks(struct cart *cart, struct slRef *tracks, int tracksFound,
+                               enum sortBy sortBy)
 // Routine for displaying found tracks
 {
-hPrintf("<div id='found' style='display:none;'>\n"); // This div allows the clear button to empty it
+hPrintf("<div id='found' style='display:none;'>\n"); // This div is emptied with 'clear' button
 if(tracksFound < 1)
     {
     hPrintf("<p>No tracks found</p>\n");
     }
 else
     {
-    hPrintf("<form action='%s' name='%s' id='%s' method='post'>\n\n", hgTracksName(),SEARCH_RESULTS_FORM,SEARCH_RESULTS_FORM);
+    hPrintf("<form action='%s' name='%s' id='%s' method='post'>\n\n",
+            hgTracksName(),SEARCH_RESULTS_FORM,SEARCH_RESULTS_FORM);
     cartSaveSession(cart);  // Creates hidden var of hgsid to avoid bad voodoo
 
     int startFrom = 0;
     hPrintf("<table id='foundTracks'>\n");
 
     // Opening view in browser button and foundTracks count
     #define ENOUGH_FOUND_TRACKS 10
     if(tracksFound >= ENOUGH_FOUND_TRACKS)
         {
         hPrintf("<tr><td nowrap colspan=3>\n");
-        hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='return to browser' class='viewBtn' style='font-size:.8em;'>");
+        hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='return to browser' class='viewBtn' "
+                "style='font-size:.8em;'>");
         hPrintf("&nbsp;&nbsp;&nbsp;&nbsp;<span class='selCbCount'></span>\n");
 
         startFrom = cartUsualInt(cart,TRACK_SEARCH_PAGER,0);
         if (startFrom > 0 && startFrom < tracksFound)
             {
             int countUp = 0;
             for(countUp=0; countUp < startFrom;countUp++)
                 {
                 if (slPopHead(&tracks) == NULL) // memory waste
                     break;
                 }
             }
         hPrintf("</td><td align='right' valign='bottom'>\n");
         findTracksPageLinks(tracksFound,startFrom);
         hPrintf("</td></tr>\n");
         }
 
     // Begin foundTracks table
     //hPrintf("<table id='foundTracks'><tr><td colspan='2'>\n");
     hPrintf("<tr><td colspan='2'>\n");
     hPrintf("</td><td align='right'>\n");
     hPrintf("</td></tr><tr bgcolor='#%s'><td>",HG_COL_HEADER);
 #ifdef BUTTONS_BY_CSS
-    #define BUTTON_PM  "<span class='pmButton' onclick='findTracks.checkAllWithWait(%s)' title='%s all found tracks'>%c</span>"
+    #define BUTTON_PM  "<span class='pmButton' onclick='findTracks.checkAllWithWait(%s)' " \
+                       "title='%s all found tracks'>%c</span>"
     hPrintf(BUTTON_PM,"true",   "Select",'+');
     hPrintf(BUTTON_PM,"false","Unselect",'-');
 #else///ifndef BUTTONS_BY_CSS
-    #define PM_BUTTON "<IMG height=18 width=18 onclick=\"return findTracks.checkAllWithWait(%s);\" id='btn_%s' src='../images/%s' title='%s all found tracks'>"
+    #define PM_BUTTON \
+            "<IMG height=18 width=18 onclick=\"return findTracks.checkAllWithWait(%s);\" " \
+            "id='btn_%s' src='../images/%s' title='%s all found tracks'>"
     hPrintf(PM_BUTTON,"true",  "plus_all",   "add_sm.gif",  "Select");
     hPrintf(PM_BUTTON,"false","minus_all","remove_sm.gif","Unselect");
 #endif///ndef BUTTONS_BY_CSS
     hPrintf("</td><td><b>Visibility</b></td><td colspan=2>&nbsp;&nbsp;<b>Track Name</b>\n");
 
     // Sort options?
     if(tracksFound >= ENOUGH_FOUND_TRACKS)
         {
         hPrintf("<span style='float:right;'>Sort:");
-        cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "0", (sortBy == sbRelevance),"onclick=\"findTracks.sortNow(this);\"");
+        cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "0", (sortBy == sbRelevance),
+                                  "onclick=\"findTracks.sortNow(this);\"");
         hPrintf("by Relevance");
-        cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "1", (sortBy == sbAbc),      "onclick=\"findTracks.sortNow(this);\"");
+        cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "1", (sortBy == sbAbc),
+                                  "onclick=\"findTracks.sortNow(this);\"");
         hPrintf("Alphabetically");
-        cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "2",(sortBy == sbHierarchy), "onclick=\"findTracks.sortNow(this);\"");
+        cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "2",(sortBy == sbHierarchy),
+                                  "onclick=\"findTracks.sortNow(this);\"");
         hPrintf("by Hierarchy&nbsp;&nbsp;</span>\n");
         }
     hPrintf("</td></tr>\n");
 
     // Set up json for js functionality
     struct jsonElement *jsonTdbVars = newJsonObject(newHash(8));
 
     int trackCount=0;
     boolean containerTrackCount = 0;
     struct slRef *ptr;
     while((ptr = slPopHead(&tracks)))
         {
         if(++trackCount > MAX_FOUND_TRACKS)
             break;
 
         struct track *track = (struct track *) ptr->val;
-        jsonTdbSettingsBuild(jsonTdbVars, track, FALSE); // FALSE: No configuration from track search
+        jsonTdbSettingsBuild(jsonTdbVars, track, FALSE); // FALSE: No config from track search
 
         if (tdbIsFolder(track->tdb)) // supertrack
             hPrintf("<tr class='bgLevel4' valign='top' class='found'>\n");
         else if (tdbIsContainer(track->tdb))
             hPrintf("<tr class='bgLevel3' valign='top' class='found'>\n");
         else
             hPrintf("<tr class='bgLevel2' valign='top' class='found'>\n");
 
         hPrintf("<td align='center'>\n");
 
         // Determine visibility and checked state
         track->visibility = tdbVisLimitedByAncestors(cart, track->tdb, TRUE, TRUE);
         boolean checked = ( track->visibility != tvHide );
         if(tdbIsContainerChild(track->tdb))
             {
-            checked = fourStateVisible(subtrackFourStateChecked(track->tdb,cart)); // Don't need all 4 states here.  Visible=checked&&enabled
-            checked = (checked && ( track->visibility != tvHide )); // Checked is only if subtrack level vis is also set!
+            // Don't need all 4 states here.  Visible=checked&&enabled
+            checked = fourStateVisible(subtrackFourStateChecked(track->tdb,cart));
+            // Checked is only if subtrack level vis is also set!
+            checked = (checked && ( track->visibility != tvHide ));
             }
 
         // Setup the check box
         #define CB_HIDDEN_VAR "<INPUT TYPE=HIDDEN disabled=true NAME='%s_sel' VALUE='%s'>"
-        if (tdbIsContainerChild(track->tdb) || tdbIsFolderContent(track->tdb))  // subtracks and folder children get "_sel" var.  ("_sel" var is temporary on folder children)
+        // subtracks and folder children get "_sel" var. ("_sel" var is temp on folder children)
+        if (tdbIsContainerChild(track->tdb) || tdbIsFolderContent(track->tdb))
             hPrintf(CB_HIDDEN_VAR,track->track,checked?"1":CART_VAR_EMPTY);
-        #define CB_SEEN "<INPUT TYPE=CHECKBOX id='%s_sel_id' VALUE='on' class='selCb' onclick='findTracks.clickedOne(this,true);'%s>"
+        #define CB_SEEN "<INPUT TYPE=CHECKBOX id='%s_sel_id' VALUE='on' class='selCb' " \
+                        "onclick='findTracks.clickedOne(this,true);'%s>"
         hPrintf(CB_SEEN,track->track,(checked?" CHECKED":""));
         hPrintf("</td><td>\n");
 
         // Setup the visibility drop down
         #define VIS_HIDDEN_VAR "<INPUT TYPE=HIDDEN disabled=true NAME='%s' VALUE='%s'>"
         hPrintf(VIS_HIDDEN_VAR,track->track,CART_VAR_EMPTY); // All tracks get vis hidden var
         char extra[512];
         if (tdbIsFolder(track->tdb))
             {
-            safef(extra,sizeof(extra),"id='%s_id' onchange='findTracks.changeVis(this)'",track->track);
-            hideShowDropDownWithClassAndExtra(track->track, (track->visibility != tvHide), "normalText visDD",extra);
+            safef(extra,sizeof(extra),"id='%s_id' onchange='findTracks.changeVis(this)'",
+                  track->track);
+            hideShowDropDownWithClassAndExtra(track->track, (track->visibility != tvHide),
+                                              "normalText visDD",extra);
             }
         else
             {
-            safef(extra,sizeof(extra),"id='%s_id' onchange='findTracks.changeVis(this)'",track->track);
-            hTvDropDownClassWithJavascript(NULL, track->visibility,track->canPack,"normalText seenVis",extra);
+            safef(extra,sizeof(extra),"id='%s_id' onchange='findTracks.changeVis(this)'",
+                  track->track);
+            hTvDropDownClassWithJavascript(NULL, track->visibility,track->canPack,
+                                           "normalText seenVis",extra);
             }
 
         // If this is a container track, allow configuring...
         if (tdbIsContainer(track->tdb) || tdbIsFolder(track->tdb))
             {
             containerTrackCount++; // Using onclick ensures return to search tracks on submit
-            hPrintf("&nbsp;<IMG SRC='../images/folderWrench.png' style='cursor:pointer;' title='Configure this track container...' onclick='findTracks.configSet(\"%s\");'>&nbsp;", track->track);
+            hPrintf("&nbsp;<IMG SRC='../images/folderWrench.png' style='cursor:pointer;' "
+                    "title='Configure this track container...' "
+                    "onclick='findTracks.configSet(\"%s\");'>&nbsp;", track->track);
             }
 //#define SHOW_PARENT_FOLDER
 #ifdef SHOW_PARENT_FOLDER
         else if (tdbIsContainerChild(track->tdb) || tdbIsFolderContent(track->tdb))
             {
-            struct trackDb *parentTdb = tdbIsContainerChild(track->tdb) ? tdbGetContainer(track->tdb) : tdbGetImmediateFolder(track->tdb);
+            struct trackDb *parentTdb =
+                            tdbIsContainerChild(track->tdb) ? tdbGetContainer(track->tdb)
+                                                            : tdbGetImmediateFolder(track->tdb);
             if (parentTdb != NULL) // Using href will not return to search tracks on submit
-                hPrintf("&nbsp;<A HREF='../cgi-bin/hgTrackUi?g=%s'><IMG SRC='../images/folderC.png' title='Navigate to parent container...'></A>&nbsp;", parentTdb->track);
+                hPrintf("&nbsp;<A HREF='../cgi-bin/hgTrackUi?g=%s'><IMG SRC='../images/folderC.png'"
+                        " title='Navigate to parent container...'></A>&nbsp;", parentTdb->track);
             }
 #endif///def SHOW_PARENT_FOLDER
         hPrintf("</td>\n");
 
         // shortLabel has description popup and longLabel has "..." metadata
-        hPrintf("<td><a target='_top' onclick=\"popUp.hgTrackUi('%s',true); return false;\" href='%s' title='Display track details'>%s</a></td>\n", track->track, trackUrl(track->track, NULL), track->shortLabel);
+        hPrintf("<td><a target='_top' onclick=\"popUp.hgTrackUi('%s',true); return false;\" "
+                "href='%s' title='Display track details'>%s</a></td>\n",
+                track->track, trackUrl(track->track, NULL), track->shortLabel);
         hPrintf("<td>%s", track->longLabel);
         compositeMetadataToggle(database, track->tdb, NULL, TRUE, FALSE);
         hPrintf("</td></tr>\n");
         }
     //hPrintf("</table>\n");
 
     // Closing view in browser button and foundTracks count
     hPrintf("<tr><td nowrap colspan=3>");
-    hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='Return to Browser' class='viewBtn' style='font-size:.8em;'>");
+    hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='Return to Browser' class='viewBtn' "
+            "style='font-size:.8em;'>");
     hPrintf("&nbsp;&nbsp;&nbsp;&nbsp;<span class='selCbCount'></span>");
     if(tracksFound >= ENOUGH_FOUND_TRACKS)
         {
         hPrintf("</td><td align='right' valign='top'>\n");
         findTracksPageLinks(tracksFound,startFrom);
         hPrintf("</td></tr>\n");
         }
     hPrintf("</table>\n");
 
     if(containerTrackCount > 0)
-        hPrintf("<BR><IMG SRC='../images/folderWrench.png'>&nbsp;Tracks so marked are containers which group related data tracks.  Containers may need additional configuration (by clicking on the <IMG SRC='../images/folderWrench.png'> icon) before they can be viewed in the browser.<BR>\n");
-        //hPrintf("* Tracks so marked are containers which group related data tracks.  These may not be visible unless further configuration is done.  Click on the * to configure these.<BR><BR>\n");
+        hPrintf("<BR><IMG SRC='../images/folderWrench.png'>&nbsp;Tracks so marked are containers "
+                "which group related data tracks.  Containers may need additional configuration "
+                "(by clicking on the <IMG SRC='../images/folderWrench.png'> icon) before they can "
+                "be viewed in the browser.<BR>\n");
+        //hPrintf("* Tracks so marked are containers which group related data tracks.  These may "
+        //        "not be visible unless further configuration is done.  Click on the * to "
+        //        "configure these.<BR><BR>\n");
     hPrintf("\n</form>\n");
 
     // be done with json
     jsonTdbSettingsUse(jsonTdbVars);
     }
 hPrintf("</div>"); // This div allows the clear button to empty it
 }
 
 void doSearchTracks(struct group *groupList)
 {
 webIncludeResourceFile("ui.dropdownchecklist.css");
 jsIncludeFile("ui.dropdownchecklist.js",NULL);
 // This line is needed to get the multi-selects initialized
 jsIncludeFile("ddcl.js",NULL);
 
 struct group *group;
 char *groups[128];
 char *labels[128];
 int numGroups = 1;
 groups[0] = ANYLABEL;
 labels[0] = ANYLABEL;
 char *nameSearch  = cartOptionalString(cart, TRACK_SEARCH_ON_NAME);
 char *typeSearch  = cartUsualString(   cart, TRACK_SEARCH_ON_TYPE,ANYLABEL);
 char *simpleEntry = cartOptionalString(cart, TRACK_SEARCH_SIMPLE);
 char *descSearch  = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR);
 char *groupSearch = cartUsualString(  cart, TRACK_SEARCH_ON_GROUP,ANYLABEL);
-boolean doSearch = sameString(cartOptionalString(cart, TRACK_SEARCH), "Search") || cartUsualInt(cart, TRACK_SEARCH_PAGER, -1) >= 0;
+boolean doSearch = sameString(cartOptionalString(cart, TRACK_SEARCH), "Search")
+                   || cartUsualInt(cart, TRACK_SEARCH_PAGER, -1) >= 0;
 struct sqlConnection *conn = hAllocConn(database);
 boolean metaDbExists = sqlTableExists(conn, "metaDb");
 int tracksFound = 0;
 boolean searchTermsExist = FALSE;
 int cols;
 char buf[512];
 
 char *currentTab = cartUsualString(cart, TRACK_SEARCH_CURRENT_TAB, "simpleTab");
 enum searchTab selectedTab = (sameString(currentTab, "advancedTab") ? advancedTab : simpleTab);
 
-if(selectedTab == simpleTab && !isEmpty(simpleEntry)) // NOTE: could support quotes in simple tab by detecting quotes and choosing to use doesNameMatch() || doesDescriptionMatch()
+// NOTE: could support quotes in simple tab by detecting quotes and choosing
+//       to use doesNameMatch() || doesDescriptionMatch()
+if (selectedTab == simpleTab && !isEmpty(simpleEntry))
     stripChar(simpleEntry, '"');
 trackList = getTrackList(&groupList, -2); // global
 makeGlobalTrackHash(trackList);
 
 // NOTE: This is necessary when container cfg by '*' results in vis changes
-// This will handle composite/view override when subtrack specific vis exists, AND superTrack reshaping.
-parentChildCartCleanup(trackList,cart,oldVars); // Subtrack settings must be removed when composite/view settings are updated
+// This will handle composite/view override when subtrack specific vis exists,
+// AND superTrack reshaping.
+
+// Subtrack settings must be removed when composite/view settings are updated
+parentChildCartCleanup(trackList,cart,oldVars);
 
 slSort(&groupList, gCmpGroup);
 for (group = groupList; group != NULL; group = group->next)
     {
     groupTrackListAddSuper(cart, group);
     if (group->trackList != NULL)
         {
         groups[numGroups] = cloneString(group->name);
         labels[numGroups] = cloneString(group->label);
         numGroups++;
         if (numGroups >= ArraySize(groups))
             internalErr();
         }
     }
 
-safef(buf, sizeof(buf),"Search for Tracks in the %s %s Assembly", organism, hFreezeFromDb(database));
+safef(buf, sizeof(buf),"Search for Tracks in the %s %s Assembly",
+      organism, hFreezeFromDb(database));
 webStartWrapperDetailedNoArgs(cart, database, "", buf, FALSE, FALSE, FALSE, FALSE);
 
 hPrintf("<div style='max-width:1080px;'>");
-hPrintf("<form action='%s' name='%s' id='%s' method='get'>\n\n", hgTracksName(),TRACK_SEARCH_FORM,TRACK_SEARCH_FORM);
+hPrintf("<form action='%s' name='%s' id='%s' method='get'>\n\n",
+        hgTracksName(),TRACK_SEARCH_FORM,TRACK_SEARCH_FORM);
 cartSaveSession(cart);  // Creates hidden var of hgsid to avoid bad voodoo
 safef(buf, sizeof(buf), "%lu", clock1());
 cgiMakeHiddenVar("hgt_", buf);  // timestamps page to avoid browser cache
 
 
 hPrintf("<input type='hidden' name='db' value='%s'>\n", database);
-hPrintf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n", TRACK_SEARCH_CURRENT_TAB, currentTab);
+hPrintf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n",
+        TRACK_SEARCH_CURRENT_TAB, currentTab);
 hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_DEL_ROW);
 hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_ADD_ROW);
 hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_PAGER);
 
-hPrintf("<div id='tabs' style='display:none; %s'>\n"
-        "<ul>\n"
-        "<li><a href='#simpleTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Search</B></a></li>\n"
-        "<li><a href='#advancedTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Advanced</B></a></li>\n"
-        "</ul>\n"
-        "<div id='simpleTab' style='max-width:inherit;'>\n",cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;");
+hPrintf("<div id='tabs' style='display:none; %s'>\n<ul>\n<li><a href='#simpleTab'>"
+        "<B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Search</B>"
+        "</a></li>\n<li><a href='#advancedTab'>"
+        "<B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Advanced</B>"
+        "</a></li>\n</ul>\n<div id='simpleTab' style='max-width:inherit;'>\n",
+        cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;");
 
 hPrintf("<table id='simpleTable' style='width:100%%; font-size:.9em;'><tr><td colspan='2'>");
-hPrintf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' style='max-width:1000px; width:100%%;' onkeyup='findTracks.searchButtonsEnable(true);'>\n",
+hPrintf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' "
+        "style='max-width:1000px; width:100%%;' onkeyup='findTracks.searchButtonsEnable(true);'>\n",
         TRACK_SEARCH_SIMPLE,simpleEntry == NULL ? "" : simpleEntry);
 if (selectedTab==simpleTab && simpleEntry)
     searchTermsExist = TRUE;
 
 hPrintf("</td></tr><td style='max-height:4px;'></td></tr></table>");
 //hPrintf("</td></tr></table>");
-hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", TRACK_SEARCH);
-hPrintf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracks.clear();'>\n");
-hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n");
+hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' "
+        "style='font-size:.8em;'>\n", TRACK_SEARCH);
+hPrintf("<input type='button' name='clear' value='clear' class='clear' "
+        "style='font-size:.8em;' onclick='findTracks.clear();'>\n");
+hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' "
+        "style='font-size:.8em;'>\n");
 hPrintf("</div>\n");
 
 // Advanced tab
 hPrintf("<div id='advancedTab' style='width:inherit;'>\n"
         "<table id='advancedTable' cellSpacing=0 style='width:inherit; font-size:.9em;'>\n");
 cols = 8;
 
 // Track Name contains
 hPrintf("<tr><td colspan=3></td>");
 hPrintf("<td nowrap><b style='max-width:100px;'>Track&nbsp;Name:</b></td>");
 hPrintf("<td align='right'>contains</td>\n");
 hPrintf("<td colspan='%d'>", cols - 4);
-hPrintf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' onkeyup='findTracks.searchButtonsEnable(true);' style='min-width:326px; font-size:.9em;'>",
+hPrintf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' "
+        "onkeyup='findTracks.searchButtonsEnable(true);' style='min-width:326px; font-size:.9em;'>",
         TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch);
 hPrintf("</td></tr>\n");
 
 // Description contains
 hPrintf("<tr><td colspan=2></td><td align='right'>and&nbsp;</td>");
 hPrintf("<td><b style='max-width:100px;'>Description:</b></td>");
 hPrintf("<td align='right'>contains</td>\n");
 hPrintf("<td colspan='%d'>", cols - 4);
-hPrintf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' onkeyup='findTracks.searchButtonsEnable(true);' style='max-width:536px; width:536px; font-size:.9em;'>",
+hPrintf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' "
+        "onkeyup='findTracks.searchButtonsEnable(true);' "
+        "style='max-width:536px; width:536px; font-size:.9em;'>",
         TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch);
 hPrintf("</td></tr>\n");
 if (selectedTab==advancedTab && !isEmpty(descSearch))
     searchTermsExist = TRUE;
 
 hPrintf("<tr><td colspan=2></td><td align='right'>and&nbsp;</td>\n");
 hPrintf("<td><b style='max-width:100px;'>Group:</b></td>");
 hPrintf("<td align='right'>is</td>\n");
 hPrintf("<td colspan='%d'>", cols - 4);
-cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch, "class='groupSearch' style='min-width:40%; font-size:.9em;'");
+cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch,
+                    "class='groupSearch' style='min-width:40%; font-size:.9em;'");
 hPrintf("</td></tr>\n");
 if (selectedTab==advancedTab && !isEmpty(groupSearch) && !sameString(groupSearch,ANYLABEL))
     searchTermsExist = TRUE;
 
 // Track Type is (drop down)
 hPrintf("<tr><td colspan=2></td><td align='right'>and&nbsp;</td>\n");
 hPrintf("<td nowrap><b style='max-width:100px;'>Data Format:</b></td>");
 hPrintf("<td align='right'>is</td>\n");
 hPrintf("<td colspan='%d'>", cols - 4);
 char **formatTypes = NULL;
 char **formatLabels = NULL;
 int formatCount = getFormatTypes(&formatLabels, &formatTypes);
-cgiMakeDropListFull(TRACK_SEARCH_ON_TYPE, formatLabels, formatTypes, formatCount, typeSearch, "class='typeSearch' style='min-width:40%; font-size:.9em;'");
+cgiMakeDropListFull(TRACK_SEARCH_ON_TYPE, formatLabels, formatTypes, formatCount, typeSearch,
+                    "class='typeSearch' style='min-width:40%; font-size:.9em;'");
 hPrintf("</td></tr>\n");
 if (selectedTab==advancedTab && !isEmpty(typeSearch) && !sameString(typeSearch,ANYLABEL))
     searchTermsExist = TRUE;
 
 // mdb selects
 struct slPair *mdbSelects = NULL;
 if(metaDbExists)
     {
     struct slPair *mdbVars = mdbVarsSearchable(conn,TRUE,FALSE); // Tables but not file only objects
     mdbSelects = mdbSelectPairs(cart, mdbVars);
     char *output = mdbSelectsHtmlRows(conn,mdbSelects,mdbVars,cols,FALSE);  // not a fileSearch
     if (output)
         {
         puts(output);
         freeMem(output);
         }
     slPairFreeList(&mdbVars);
     }
 
 hPrintf("</table>\n");
-hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", TRACK_SEARCH);
-hPrintf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracks.clear();'>\n");
-hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n");
+hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' "
+        "style='font-size:.8em;'>\n", TRACK_SEARCH);
+hPrintf("<input type='button' name='clear' value='clear' class='clear' "
+        "style='font-size:.8em;' onclick='findTracks.clear();'>\n");
+hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' "
+        "style='font-size:.8em;'>\n");
 //hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a>\n");
 hPrintf("</div>\n");
 
 hPrintf("</div>\n");
 
 hPrintf("</form>\n");
 hPrintf("</div>"); // Restricts to max-width:1000px;
 cgiDown(0.8);
 
 if (measureTiming)
     measureTime("Rendered tabs");
 
 if(doSearch)
     {
     // Now search
     struct slRef *tracks = NULL;
     if(selectedTab==simpleTab && !isEmpty(simpleEntry))
         tracks = simpleSearchForTracksstruct(simpleEntry);
     else if(selectedTab==advancedTab)
-        tracks = advancedSearchForTracks(conn,groupList,nameSearch,typeSearch,descSearch,groupSearch,mdbSelects);
+        tracks = advancedSearchForTracks(conn,groupList,nameSearch,typeSearch,descSearch,
+                                         groupSearch,mdbSelects);
 
     if (measureTiming)
         measureTime("Searched for tracks");
 
     // Sort and Print results
     if(selectedTab!=filesTab)
         {
         enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance);
         tracksFound = slCount(tracks);
         if(tracksFound > 1)
             findTracksSort(&tracks,sortBy);
 
         displayFoundTracks(cart,tracks,tracksFound,sortBy);
 
         if (measureTiming)
             measureTime("Displayed found tracks");
         }
     slPairFreeList(&mdbSelects);
     }
 hFreeConn(&conn);
 
 webNewSection("About Track Search");
 if(metaDbExists)
     hPrintf("<p>Search for terms in track names, descriptions, groups, and ENCODE "
             "metadata.  If multiple terms are entered, only tracks with all terms "
             "will be part of the results.");
 else
     hPrintf("<p>Search for terms in track descriptions, groups, and names. "
             "If multiple terms are entered, only tracks with all terms "
             "will be part of the results.");
 
 hPrintf("<BR><a target='_blank' href='../goldenPath/help/trackSearch.html'>more help</a></p>\n");
-// NOTE: Could use ajax and dynamically popup the html file in a box:
-//hPrintf("<BR><a href='#' onclick=\"retrieveHtml('../goldenPath/help/trackSearch.html'); return false;\">more help</a></p>\n");
-// NOTE: OR by declaring a div and passing it to retrieveHtml, the html file could be embedded in the div.
-// However, this is not desired here because of the titles.
-//hPrintf("<BR><a href='#' onclick=\"retrieveHtml('../goldenPath/help/trackSearch.html',$('#moreHelp'),true); return false;\">more help</a></p>\n");
-//hPrintf("<div id='moreHelp'></div>\n");
 webEndSectionTables();
 }