08e4ee4ee040fe5296616615c6f4ddb73987e2b9
braney
  Thu May 23 16:18:42 2013 -0700
add some blue bars for duplications in HAL snakes
diff --git src/hg/hgTracks/hgTracks.h src/hg/hgTracks/hgTracks.h
index bb86dbc..783f9e4 100644
--- src/hg/hgTracks/hgTracks.h
+++ src/hg/hgTracks/hgTracks.h
@@ -312,30 +312,34 @@
     int tallStart, tallEnd;		/* Start/end of fat display. */
     int grayIx;				/* Average of components. */
     int filterColor;			/* Filter color (-1 for none) */
     float score;                        /* score for this feature */
     char *name;				/* Accession of query seq. Usually also the label. */
     int orientation;                    /* Orientation. */
     struct simpleFeature *components;   /* List of component simple features. */
     struct simpleFeature *codons;       /* If zoomed to CDS or codon level.*/
     void *extra;			/* Extra info that varies with type. */
     void *original;			/* The structure that was converted
 					   into this (when needed later).  */
     struct itemAttr *itemAttr;          /* itemAttr object for this lf, or NULL */
     unsigned highlightColor;            /* highlight color,0 if no highlight */
     enum highlightMode highlightMode;   /* highlight mode,0 if no highlight */
     char* mouseOver;                    /* mouse over text */
+#ifdef USE_HAL
+    boolean isHalSnake;
+    struct hal_target_dupe_list_t *dupeList;
+#endif
     };
 
 struct linkedFeaturesSeries
 /* series of linked features that are comprised of multiple linked features */
 {
     struct linkedFeaturesSeries *next;
     char *name;                      /* name for series of linked features */
     int start, end;                     /* Start/end in browser coordinates. */
     int orientation;                    /* Orientation. */
     int grayIx;				/* Gray index (average of features) */
     boolean noLine;                     /* if true don't draw line connecting features */
     struct linkedFeatures *features;    /* linked features for a series */
 };
 
 struct knownGenesExtra