39e090676e60afcf302c046587af55b3f8926727
hiram
  Thu Jul 18 10:25:14 2013 -0700
checking in Robert's code refs #9741
diff --git src/hg/hgTracks/hgTracks.h src/hg/hgTracks/hgTracks.h
index 783f9e4..95ff496 100644
--- src/hg/hgTracks/hgTracks.h
+++ src/hg/hgTracks/hgTracks.h
@@ -854,30 +854,31 @@
 void repeatMethods(struct track *tg);
 /* Make track for repeats. */
 
 void affyTransfragsMethods(struct track *tg);
 /* Substitute a new load method that filters based on score. Also add
    a new itemColor() method that draws transfrags that overlap dups
    and pseudoGenes in a different color. */
 
 struct repeatItem
 /* A repeat track item. */
     {
     struct repeatItem *next;
     char *class;
     char *className;
     int yOffset;
+    Color color;
     };
 
 void pslMethods(struct track *track, struct trackDb *tdb,
 	int argc, char *argv[]);
 /* Load up psl type methods. */
 
 void loadXenoPsl(struct track *tg);
 /* Load a xeno psl */
 
 void loadProteinPsl(struct track *tg);
 /* Load a protein psl */
 
 struct linkedFeatures *lfFromPslx(struct psl *psl,
 	int sizeMul, boolean isXeno, boolean nameGetsPos, struct track *tg);
 /* Create a linked feature item from pslx.  Pass in sizeMul=1 for DNA,
@@ -1339,30 +1340,33 @@
 
 void pgSnpCtMethods (struct track *tg);
 /* Load pgSnp track from custom tracks */
 
 void pgSnpMapItem(struct track *tg, struct hvGfx *hvg, void *item, char *itemName,
 		  char *mapItemName, int start, int end, int x, int y, int width, int height);
 /* create a special map box item with different pop-up statusLine with allele counts */
 
 void gvfMethods(struct track *tg);
 /* Load GVF variant data. */
 
 void messageLineMethods(struct track *track);
 /* Methods for drawing a single-height message line instead of track items,
  * e.g. if source was compiled without a necessary library. */
 
+void jRepeatMethods(struct track *track);
+/* construct track for detailed repeat visualization */
+
 void parentChildCartCleanup(struct track *trackList,struct cart *newCart,struct hash *oldVars);
 /* When composite/view settings changes, remove subtrack specific vis
    When superTrackChild is found and selected, shape superTrack to match. */
 
 void dontLoadItems(struct track *tg);
 /* No-op loadItems when we aren't going to try. */
 
 //#define REMOTE_TRACK_AJAX_CALLBACK
 #ifdef REMOTE_TRACK_AJAX_CALLBACK
 #define REMOTE_TRACK_HEIGHT (tl.fontHeight*2)
 
 boolean trackShouldUseAjaxRetrieval(struct track *track);
 /* Tracks with remote data sources should berendered via an ajax callback */
 
 #else//ifndef