26a76b91d8d8dc555c7bb64d8bbe33b485f98c0d
angie
  Sun Sep 14 09:11:47 2014 -0700
Removing dead code for "useTarg" (#ifndef'd out with BRANEY_SAYS_USETARG_IS_OBSOLETE).
diff --git src/hg/hgTracks/wigMafTrack.c src/hg/hgTracks/wigMafTrack.c
index 9885473..f925c39 100644
--- src/hg/hgTracks/wigMafTrack.c
+++ src/hg/hgTracks/wigMafTrack.c
@@ -155,72 +155,47 @@
 struct wigMafItem *newSpeciesItems(struct track *track, int height)
 /* Make up item list for all species configured in track settings */
 {
 struct dyString *order = dyStringNew(256);
 char option[MAX_SP_SIZE];
 char *species[MAX_SP_SIZE];
 char *groups[20];
 char *defaultOff[MAX_SP_SIZE];
 char sGroup[24];
 struct wigMafItem *mi = NULL, *miList = NULL;
 int group;
 int i;
 int speciesCt = 0, groupCt = 1;
 int speciesOffCt = 0;
 struct hash *speciesOffHash = newHash(0);
-#define BRANEY_SAYS_USETARG_IS_OBSOLETE
-#ifndef BRANEY_SAYS_USETARG_IS_OBSOLETE
-char *speciesTarget = trackDbSetting(track->tdb, SPECIES_TARGET_VAR);
-char *speciesTree = trackDbSetting(track->tdb, SPECIES_TREE_VAR);
-bool useTarg;	/* use phyloTree to find shortest path */
-struct phyloTree *tree = NULL;
-#endif///ndef BRANEY_SAYS_USETARG_IS_OBSOLETE
 char *speciesUseFile = trackDbSetting(track->tdb, SPECIES_USE_FILE);
 char *msaTable = NULL;
 
 /* either speciesOrder or speciesGroup is specified in trackDb */
 char *speciesOrder = trackDbSetting(track->tdb, SPECIES_ORDER_VAR);
 char *speciesGroup = trackDbSetting(track->tdb, SPECIES_GROUP_VAR);
 char *speciesOff = trackDbSetting(track->tdb, SPECIES_DEFAULT_OFF_VAR);
 
 bool lowerFirstChar = TRUE;
 char *firstCase;
 
 firstCase = trackDbSetting(track->tdb, ITEM_FIRST_CHAR_CASE);
 if (firstCase != NULL)
     {
     if (sameWord(firstCase, "noChange")) lowerFirstChar = FALSE;
     }
 
-#ifndef BRANEY_SAYS_USETARG_IS_OBSOLETE
-char buffer[128];
-// According to Tim, this makes no sense as ".vis"
-safef(buffer, sizeof(buffer), "%s.vis",track->track);
-if (!cartVarExists(cart, buffer) && (speciesTarget != NULL))
-    useTarg = TRUE;
-else
-    {
-    char *val;
-
-    val = cartUsualString(cart, buffer, "useCheck");
-    useTarg = sameString("useTarg",val);
-    }
-
-if (useTarg && (tree = phyloParseString(speciesTree)) == NULL)
-    useTarg = FALSE;
-#endif///ndef BRANEY_SAYS_USETARG_IS_OBSOLETE
-
 if (speciesOrder == NULL && speciesGroup == NULL && speciesUseFile == NULL)
     return getSpeciesFromMaf(track, height);
 
 if (speciesGroup)
     groupCt = chopLine(cloneString(speciesGroup), groups);
 
 if (speciesUseFile)
     {
     if ((speciesGroup != NULL) || (speciesOrder != NULL))
 	errAbort("Can't specify speciesUseFile and speciesGroup or speciesOrder");
     if (hIsGsidServer())
 	{
 	msaTable = trackDbSetting(track->tdb, "msaTable");
     	if (msaTable != NULL)
 	    {
@@ -248,83 +223,44 @@
 
 char *prefix = track->track; // use when setting things to the cart
 if (tdbIsContainerChild(track->tdb))
     prefix = tdbGetContainer(track->tdb)->track;
 
 /* Make up items for other organisms by scanning through group & species
    track settings */
 for (group = 0; group < groupCt; group++)
     {
     if (groupCt != 1 || !speciesOrder)
         {
         safef(sGroup, sizeof sGroup, "%s%s",
                                 SPECIES_GROUP_PREFIX, groups[group]);
         speciesOrder = trackDbRequiredSetting(track->tdb, sGroup);
         }
-#ifndef BRANEY_SAYS_USETARG_IS_OBSOLETE
-    if (useTarg)
-	{
-        warn("BRANEY_SAYS useTarg should never be TRUE!");
-	char *ptr, *path;
-	struct hash *orgHash = newHash(0);
-	int numNodes, ii;
-	char *nodeNames[512];
-	char *species = NULL;
-	char *lowerString;
-
-	path = phyloNodeNames(tree);
-	numNodes = chopLine(path, nodeNames);
-	for(ii=0; ii < numNodes; ii++)
-	    {
-	    if ((ptr = hOrganism(nodeNames[ii])) != NULL)
-		{
-		ptr[0] = tolower(ptr[0]);
-		hashAdd(orgHash, ptr, nodeNames[ii]);
-		}
-	    else
-		{
-		hashAdd(orgHash, nodeNames[ii], nodeNames[ii]);
-		}
-	    }
-
-	lowerString = cartUsualString(cart, SPECIES_HTML_TARGET,speciesTarget);
-	lowerString[0] = tolower(lowerString[0]);
-	species = hashFindVal(orgHash, lowerString);
-	if ((ptr = phyloFindPath(tree, database, species)) != NULL)
-	    speciesOrder = ptr;
-	}
-#endif///ndef BRANEY_SAYS_USETARG_IS_OBSOLETE
-
     speciesCt = chopLine(cloneString(speciesOrder), species);
     for (i = 0; i < speciesCt; i++)
         {
-#ifndef BRANEY_SAYS_USETARG_IS_OBSOLETE
-	if (!useTarg)
-#endif///ndef BRANEY_SAYS_USETARG_IS_OBSOLETE
-	    {
         /* skip this species if UI checkbox was unchecked */
         if (!cartVarExistsAnyLevel(cart, track->tdb,FALSE,species[i]))
             {
             if (hashLookup(speciesOffHash, species[i]))
                 {
                 safef(option, sizeof(option), "%s.%s", prefix, species[i]);
                 cartSetBoolean(cart, option, FALSE);
                 }
             }
         if (!cartUsualBooleanClosestToHome(cart, track->tdb, FALSE, species[i],TRUE))
             continue;
-	    }
         mi = newMafItem(species[i], group, lowerFirstChar);
         slAddHead(&miList, mi);
         }
     }
 
 slReverse(&miList);
 for (mi = miList; mi != NULL; mi = mi->next)
     {
     mi->height = height;
     dyStringPrintf(order, "%s ",mi->db);
     }
 safef(option, sizeof(option), "%s.speciesOrder", prefix);
 cartSetString(cart, option, order->string);
 slReverse(&miList);