41460d9448c20807b3f2589a198ca1dc26481861
angie
  Wed Jul 23 13:23:37 2014 -0700
SNP tracks have an option to include orthologous chimp allele andobserved alleles in the item names.  So far, this option has been
offered only when there is an ortho table for the SNP track, and
alleles have been included only when a chimp allele is found.
However, for comparison with other annotations, it is useful to
see observed alleles even when chimp alleles aren't available.
Now, if there is no ortho table, the option to include just observed
alleles is given.  If enabled, then when there is no ortho table, or
no ortho allele for a particular SNP, observed alleles are added to
the item name.

diff --git src/hg/hgTrackUi/hgTrackUi.c src/hg/hgTrackUi/hgTrackUi.c
index 1f93574..8790a27 100644
--- src/hg/hgTrackUi/hgTrackUi.c
+++ src/hg/hgTrackUi/hgTrackUi.c
@@ -713,31 +713,39 @@
 jsInit();
 struct slName *snp125UnusedClasses = snp125FixClassGlobals(tdb);
 
 if (isNotEmpty(orthoTable) && hTableExists(database, orthoTable))
     {
     printf("<BR><B>Include Chimp state and observed human alleles in name: </B>&nbsp;");
     safef(cartVar, sizeof(cartVar), "%s.extendedNames", tdb->track);
     snp125ExtendedNames = cartUsualBoolean(cart, cartVar,
 			  // Check old cart var name for backwards compatibility w/ old sessions:
 					   cartUsualBoolean(cart, "snp125ExtendedNames", FALSE));
     cgiMakeCheckBox(cartVar, snp125ExtendedNames);
     printf("<BR>(If enabled, chimp allele is displayed first, then '>', then human alleles).");
     printf("<BR><BR>\n");
     }
 else
-    puts("<BR>");
+    {
+    printf("<BR><B>Include observed alleles in name: </B>&nbsp;");
+    safef(cartVar, sizeof(cartVar), "%s.extendedNames", tdb->track);
+    snp125ExtendedNames = cartUsualBoolean(cart, cartVar,
+			  // Check old cart var name for backwards compatibility w/ old sessions:
+					   cartUsualBoolean(cart, "snp125ExtendedNames", FALSE));
+    cgiMakeCheckBox(cartVar, snp125ExtendedNames);
+    puts("<BR><BR>");
+    }
 
 // Make wrapper table for collapsible sections:
 puts("<TABLE border=0 cellspacing=0 cellpadding=0>");
 
 snp125OfferGeneTracksForFunction(tdb);
 
 boolean molTypeHasMito = snp125CheckMolTypeForMito(tdb);
 
 puts("<TR><TD colspan=2><BR></TD></TR>");
 snp125PrintFilterControlSection(tdb, version, molTypeHasMito, snp125UnusedClasses);
 puts("<TR><TD colspan=2><BR></TD></TR>");
 
 snp125PrintColorControlSection(tdb, version, molTypeHasMito);
 // End wrapper table for collapsible sections:
 puts("</TABLE>");