b159fa56513cfc78d000a66cc65ff1a85a2e0c27
braney
  Tue Sep 5 17:23:40 2017 -0700
ongoing work on hgCollection

diff --git src/hg/hgCollection/hgCollection.c src/hg/hgCollection/hgCollection.c
index d9ae08b..6732a7a 100644
--- src/hg/hgCollection/hgCollection.c
+++ src/hg/hgCollection/hgCollection.c
@@ -32,30 +32,31 @@
 
 
 // Null terminated list of CGI Variables we don't want to save permanently:
 char *excludeVars[] = {"Submit", "submit", "hgva_startQuery", NULL,};
 
 struct track
 {
 struct track *next;
 struct track *trackList;
 struct trackDb *tdb;
 char *name;
 char *shortLabel;
 char *longLabel;
 char *visibility;
 unsigned long color;
+char *viewFunc;
 };
 
 char *getString(char **input)
 // grab a quoted string out of text blob
 {
 char *ptr = *input;
 
 if (*ptr != '"')
     errAbort("string must start with \"");
 ptr++;
 char *ret = ptr;
 for(; *ptr != '"'; ptr++)
     ;
 *ptr = 0;
 ptr++;
@@ -95,53 +96,61 @@
 
 return NULL;
 }
 
 static boolean trackCanBeAdded(struct trackDb *tdb)
 // are we allowing this track into a custom composite
 {
 return  (tdb->subtracks == NULL) && !startsWith("wigMaf",tdb->type) &&  (startsWith("wig",tdb->type) || startsWith("bigWig",tdb->type)) ;
 }
 
 static void printGroup(char *parent, struct trackDb *tdb, boolean folder, boolean user)
 // output list elements for a group
 {
 char *userString = "";
 char *prefix = "";
+char *viewFunc = "show all";
 
 if (user)
     {
     //prefix = "coll_";
     if (tdb->parent && tdb->subtracks) 
-        userString = "viewType='view'";
+        {
+        viewFunc = trackDbSetting(tdb, "viewFunc");
+        if (viewFunc == NULL)
+            viewFunc = "show all";
+        userString = "viewType='view' class='folder'";
+        }
+    else if (tdb->subtracks)
+        userString = "viewType='track' class='folder'";
     else
         userString = "viewType='track'";
     }
 else
     {
     //prefix = "coll_";
     if (tdb->parent && tdb->subtracks) 
         userString = "class='nodrop' viewType='view'";
     else
         userString = "class='nodrop' viewType='track'";
     }
     
         //userString = "viewType='track data-jstree='{'icon':'images/folderC.png'}''";
     
 #define IMAKECOLOR_32(r,g,b) ( ((unsigned int)b<<0) | ((unsigned int)g << 8) | ((unsigned int)r << 16))
 
-jsInlineF("<li shortLabel='%s' longLabel='%s' color='#%06x' visibility='%s'  name='%s%s' %s>%s",  tdb->shortLabel, tdb->longLabel,IMAKECOLOR_32(tdb->colorR,tdb->colorG,tdb->colorB), hStringFromTv(tdb->visibility), prefix,  trackHubSkipHubName(tdb->track),   userString,  tdb->shortLabel );
+jsInlineF("<li shortLabel='%s' longLabel='%s' color='#%06x' viewFunc='%s' visibility='%s'  name='%s%s' %s>%s",  tdb->shortLabel, tdb->longLabel,IMAKECOLOR_32(tdb->colorR,tdb->colorG,tdb->colorB), viewFunc, hStringFromTv(tdb->visibility), prefix,  trackHubSkipHubName(tdb->track),   userString,  tdb->shortLabel );
 jsInlineF(" (%s)", tdb->longLabel);
 
 
 if (tdb->subtracks)
     {
     struct trackDb *subTdb;
 
     jsInlineF("<ul>");
     for(subTdb = tdb->subtracks; subTdb; subTdb = subTdb->next)
         printGroup(trackHubSkipHubName(tdb->track), subTdb, user && (subTdb->subtracks != NULL), user);
     jsInlineF("</ul>");
     }
 jsInlineF("</li>");
 }
 
@@ -229,83 +238,88 @@
 boolean vis;
 if (cartVis != NULL) 
     vis =  differentString(cartVis, "hide");
 else if (tdbIsSuperTrack(tdb->parent))
     vis = tdb->parent->isShow;
 else
     vis = tdb->parent->visibility != tvHide;
 
 return vis;
 }
 
 
 void addVisibleTracks()
 // add the visible tracks table rows
 {
-printf("<tr name='visible' ><td>All Visible</td><td>All the tracks visible in hgTracks</td></tr>\n");
+jsInlineF("<ul>");
+jsInlineF("<li class='nodrop' name='%s'>%s", "visibile", "Visible Tracks");
+jsInlineF("<ul>");
 struct trackDb *tdb;
 for(tdb = fullTrackList; tdb; tdb = tdb->next)
     {
     if (isParentVisible(tdb) &&  isSubtrackVisible(tdb))
         {
         printGroup("visible", tdb, FALSE, FALSE);
         }
     }
+jsInlineF("</ul>");
+jsInlineF("</li>");
+jsInlineF("</ul>");
 }
 
 void doTable()
 // output the tree table
 {
 char *hubName = hubNameFromUrl(getHubName(database));
 struct grp *curGroup;
 for(curGroup = fullGroupList; curGroup;  curGroup = curGroup->next)
     {
     if ((hubName != NULL) && sameString(curGroup->name, hubName))
         break;
     }
 if (curGroup != NULL)
     {
     // print out all the tracks in this group
     struct trackDb *tdb;
     jsInlineF("$('#currentCollection').append(\"");
     for(tdb = fullTrackList; tdb;  tdb = tdb->next)
         {
         if (sameString(tdb->grp, hubName))
             {
             jsInlineF("<div id='%s' shortLabel='%s'>", trackHubSkipHubName(tdb->track), tdb->shortLabel);
             jsInlineF("<ul>");
             printGroup("collections", tdb, TRUE, TRUE);
-            jsInlineF("<ul>");
+            jsInlineF("</ul>");
             jsInlineF("</div>");
             }
         }
     jsInlineF("\");\n");
     
     // print out all the tracks in this group
     jsInlineF("$('#collectionList').append(\"");
     for(tdb = fullTrackList; tdb;  tdb = tdb->next)
         {
         if (sameString(tdb->grp, hubName))
             {
             jsInlineF("<li class='nodrop' id='%s'  name='%s'>%s</li>", trackHubSkipHubName(tdb->track),trackHubSkipHubName(tdb->track), tdb->shortLabel);
             //printGroup("collections", tdb, TRUE, TRUE);
             }
         }
     jsInlineF("\");\n");
     }
-//addVisibleTracks();
 jsInlineF("$('#tracks').append(\"");
+addVisibleTracks();
 for(curGroup = fullGroupList; curGroup;  curGroup = curGroup->next)
     {
     if ((hubName != NULL) && sameString(curGroup->name, hubName))
         continue;
     jsInlineF("<ul>");
     jsInlineF("<li class='nodrop' name='%s'>%s", curGroup->name, curGroup->label );
     struct trackDb *tdb;
     jsInlineF("<ul>");
     for(tdb = fullTrackList; tdb;  tdb = tdb->next)
         {
         if ( sameString(tdb->grp, curGroup->name))
             {
             printGroup(curGroup->name, tdb, FALSE, FALSE);
             }
         }
@@ -337,31 +351,31 @@
 printf(
 "            <i id='%s' title='Jump to top of page' \n"
 "               class='gbIconArrow fa fa-lg fa-arrow-circle-up'></i>\n",
 DATA_INFO_JUMP_ARROW_ID
 );
 onclickJumpToTop(DATA_INFO_JUMP_ARROW_ID);
 puts(
 "       </div>\n"
 "    </div>\n"
 );
 puts(
 "    <div class='row gbTrackDescriptionPanel'>\n"
 "       <div class='gbTrackDescription'>\n");
 puts("<div class='dataInfo'>");
 puts("</div>");
-webIncludeHelpFileSubst("hgCompositeHelp", NULL, FALSE);
+webIncludeHelpFileSubst("hgCollectionHelp", NULL, FALSE);
 
 puts("<div class='dataInfo'>");
 puts("</div>");
 
 puts(
 "     </div>\n"
 "   </div>\n");
 }
 
 void doMainPage()
 /* Print out initial HTML of control page. */
 {
 webStartGbNoBanner(cart, database, "Collections");
 webIncludeResourceFile("gb.css");
 webIncludeResourceFile("spectrum.min.css");
@@ -465,80 +479,83 @@
 
 }
 
 int snakePalette2[] =
 {
 0x1f77b4, 0xaec7e8, 0xff7f0e, 0xffbb78, 0x2ca02c, 0x98df8a, 0xd62728, 0xff9896, 0x9467bd, 0xc5b0d5, 0x8c564b, 0xc49c94, 0xe377c2, 0xf7b6d2, 0x7f7f7f, 0xc7c7c7, 0xbcbd22, 0xdbdb8d, 0x17becf, 0x9edae5
 };
 
 static char *skipColl(char *str)
 {
 if (startsWith("coll_", str))
     return &str[5];
 return str;
 }
 
-static void outView(FILE *f, struct sqlConnection *conn, char *db, struct track *view, char *parent, struct hash *nameHash, struct hash *collectionNameHash)
+static int outView(FILE *f, struct sqlConnection *conn, char *db, struct track *view, char *parent, struct hash *nameHash, struct hash *collectionNameHash, int priority)
 // output a view to a trackhub
 {
 fprintf(f,"\ttrack %s\n\
 \tshortLabel %s\n\
 \tlongLabel %s\n\
 \tview %s \n\
+\tcontainer mathWig\n\
+\tautoScale on  \n\
 \tparent %s \n\
 \tcolor %ld,%ld,%ld \n\
-\tvisibility %s\n", view->name, view->shortLabel, view->longLabel, view->name, parent, 0xff& (view->color >> 16),0xff& (view->color >> 8),0xff& (view->color), view->visibility);
+\tviewFunc %s \n\
+\tvisibility %s\n", view->name, view->shortLabel, view->longLabel, view->name, parent, 0xff& (view->color >> 16),0xff& (view->color >> 8),0xff& (view->color), view->viewFunc, view->visibility);
 //fprintf(f,"\tequation +\n");
 fprintf(f, "\n");
 
 //int useColor = 0;
 struct track *track = view->trackList;
-int priority = 1;
 for(; track; track = track->next)
     {
     struct trackDb *tdb = hashMustFindVal(nameHash, skipColl(track->name));
 
     outTdb(conn, db, f, skipColl(track->name),tdb, view->name, track->visibility, track->color, track,  nameHash, collectionNameHash, 2, priority++);
     //useColor++;
     }
 
+return priority;
 }
 
 void updateHub(char *db, struct track *collectionList, struct hash *nameHash)
 // save our state to the track hub
 {
 char *hubName = getHubName(db);
 
 chmod(hubName, 0666);
 FILE *f = mustOpen(hubName, "w");
 struct hash *collectionNameHash = newHash(6);
 
 outHubHeader(f, db, hubName);
 //int useColor = 0;
 struct track *collection;
 struct sqlConnection *conn = hAllocConn(db);
 for(collection = collectionList; collection; collection = collection->next)
     {
     outComposite(f, collection);
     struct trackDb *tdb;
     struct track *track;
     int priority = 1;
     for (track = collection->trackList; track; track = track->next)
         {
         if (track->trackList != NULL)
             {
-            outView(f, conn, db, track, collection->name,  nameHash, collectionNameHash);
+            priority = outView(f, conn, db, track, collection->name,  nameHash, collectionNameHash, priority);
             }
         else
             {
             tdb = hashMustFindVal(nameHash, track->name);
 
             outTdb(conn, db, f, track->name,tdb, collection->name, track->visibility, track->color, track,  nameHash, collectionNameHash, 1, priority++);
             /*
             useColor++;
             if (useColor == (sizeof snakePalette2 / sizeof(int)))
                 useColor = 0;
                 */
             }
         }
     }
 fclose(f);
@@ -593,30 +610,33 @@
     if (attEle)
         {
         struct hash *attrHash = jsonObjectVal(attEle, "name");
         struct jsonElement *strEle = (struct jsonElement *)hashMustFindVal(attrHash, "name");
         track->name = jsonStringEscape(strEle->val.jeString);
         hashAdd(trackHash, parentId, track);
 
         strEle = (struct jsonElement *)hashMustFindVal(attrHash, "shortlabel");
         track->shortLabel = jsonStringEscape(strEle->val.jeString);
         strEle = (struct jsonElement *)hashMustFindVal(attrHash, "longlabel");
         track->longLabel = jsonStringEscape(strEle->val.jeString);
         strEle = (struct jsonElement *)hashMustFindVal(attrHash, "visibility");
         track->visibility = jsonStringEscape(strEle->val.jeString);
         strEle = (struct jsonElement *)hashMustFindVal(attrHash, "color");
         track->color = hexStringToLong(jsonStringEscape(strEle->val.jeString));
+        strEle = (struct jsonElement *)hashFindVal(attrHash, "viewfunc");
+        if (strEle)
+            track->viewFunc = jsonStringEscape(strEle->val.jeString);
         }
     }
 }
 
 static struct track *parseJsonElements( struct jsonElement *collectionElements)
 // parse the JSON returned from the ap
 {
 struct track *collectionList = NULL;
 struct hash *trackHash = hashNew(5);
 struct jsonParseData jpd = {&collectionList, trackHash};
 jsonElementRecurse(collectionElements, NULL, FALSE, jsonObjStart, NULL, &jpd);
 
 slReverse(&collectionList);
 return collectionList;
 }
@@ -624,31 +644,31 @@
 void doAjax(char *db, char *jsonText, struct hash *nameHash)
 // Save our state
 {
 cgiDecodeFull(jsonText, jsonText, strlen(jsonText));
 struct jsonElement *collectionElements = jsonParse(jsonText);
 struct track *collectionList = parseJsonElements(collectionElements);
 
 updateHub(db, collectionList, nameHash);
 }
 
 static void buildNameHash(struct hash *nameHash, struct trackDb *list)
 {
 if (list == NULL)
     return;
 
-struct trackDb *tdb;
+struct trackDb *tdb = list;
 for(tdb = list; tdb;  tdb = tdb->next)
     {
     hashAdd(nameHash, trackHubSkipHubName(tdb->track), tdb);
     buildNameHash(nameHash, tdb->subtracks);
     }
 }
 
 static struct trackDb *traverseTree(struct trackDb *oldList, struct hash *groupHash)
 // add acceptable tracks to our tree
 {
 struct trackDb *newList = NULL, *tdb, *tdbNext;
 
 for(tdb = oldList;  tdb ; tdb = tdbNext)
     {
     tdbNext = tdb->next;