045e182a27b1059a13c90c5a1ed9fdc8a31b18f2
braney
  Thu Jul 19 14:45:08 2018 -0700
more changes to enable using Ensembl id as primary id in knownGene.

diff --git src/hg/hgTrackUi/hgTrackUi.c src/hg/hgTrackUi/hgTrackUi.c
index 6d76af2..25138b6 100644
--- src/hg/hgTrackUi/hgTrackUi.c
+++ src/hg/hgTrackUi/hgTrackUi.c
@@ -1738,37 +1738,46 @@
 }
 
 void knownGeneShowWhatUi(struct trackDb *tdb)
 /* Put up line of controls that describe what parts to show. */
 {
 char varName[64];
 printf("<B>Show:</B> ");
 safef(varName, sizeof(varName), "%s.show.noncoding", tdb->track);
 boolean option = cartUsualBoolean(cart, varName, TRUE);
 cgiMakeCheckBox(varName, option);
 printf(" %s&nbsp;&nbsp;&nbsp;", "non-coding genes");
 safef(varName, sizeof(varName), "%s.show.spliceVariants", tdb->track);
 option = cartUsualBoolean(cart, varName, TRUE);
 cgiMakeCheckBox(varName, option);
 printf(" %s&nbsp;&nbsp;&nbsp;", "splice variants");
-char *isGencode = trackDbSetting(tdb, "isGencode");
-if (isGencode != NULL)
+boolean isGencode = trackDbSettingOn(tdb, "isGencode");
+boolean isGencode2 = trackDbSettingOn(tdb, "isGencode2");
+if (isGencode || isGencode2)
     {
     safef(varName, sizeof(varName), "%s.show.comprehensive", tdb->track);
     option = cartUsualBoolean(cart, varName, FALSE);
     cgiMakeCheckBox(varName, option);
     printf(" %s&nbsp;&nbsp;&nbsp;", "show comprehensive set");
+
+    if (isGencode2)
+        {
+        safef(varName, sizeof(varName), "%s.show.pseudo", tdb->track);
+        option = cartUsualBoolean(cart, varName, FALSE);
+        cgiMakeCheckBox(varName, option);
+        printf(" %s&nbsp;&nbsp;&nbsp;", "show pseudogenes");
+        }
     }
 printf("<BR>\n");
 }
 
 void knownGeneUI(struct trackDb *tdb)
 /* Put up refGene-specific controls */
 {
 /* This is incompatible with adding Protein ID to lf->extra */
 knownGeneIdConfig(tdb);
 knownGeneShowWhatUi(tdb);
 baseColorDrawOptDropDown(cart, tdb);
 wigOption(cart, "knownGene", "UCSC Genes", tdb);
 }
 
 void omimLocationUI(struct trackDb *tdb)