3c529301c2900f3b03ea89955426db75b9b631f9
angie
  Mon Feb 7 10:08:54 2011 -0800
Track #1684 (SNPs 132 (dbSNP)): Added coloring by allele frequency:items are shaded on a scale of red (rare) to blue (common), or black
when no frequencies were given.  Now I'm wondering if I should have
used a log scale, but this works so I'm checking it in.

diff --git src/hg/hgTracks/variation.h src/hg/hgTracks/variation.h
index 924cda7..fecc618 100644
--- src/hg/hgTracks/variation.h
+++ src/hg/hgTracks/variation.h
@@ -74,82 +74,39 @@
 
 void ldAddToDenseValueHash(struct hash *ldHash, unsigned a, char charValue);
 /* Add new values to LD hash or update existing values.
    Values are averaged along the diagonals. */
 
 void ldDrawDenseValueHash(struct hvGfx *hvg, struct track *tg, int xOff, int yOff, 
 			  double scale, Color outlineColor, struct hash *ldHash);
 /* Draw all dense LD values */
 
 
 void snpMapMethods(struct track *tg);
 /* Make track for snps. */
 
 /****** snp ******/
 
-void filterSnpItems(struct track *tg, boolean (*filter)(struct track *tg, void *item));
-/* Filter out items from track->itemList. */
-
-boolean snpSourceFilterItem(struct track *tg, void *item);
-/* Return TRUE if item passes filter. */
-
-boolean snpMolTypeFilterItem(struct track *tg, void *item);
-/* Return TRUE if item passes filter. */
-
-boolean snpClassFilterItem(struct track *tg, void *item);
-/* Return TRUE if item passes filter. */
-
-boolean snpValidFilterItem(struct track *tg, void *item);
-/* Return TRUE if item passes filter. */
-
-boolean snpFuncFilterItem(struct track *tg, void *item);
-/* Return TRUE if item passes filter. */
-
-void freeSnp(struct track *tg);
-/* Free up snp items. */
-
-Color snpColor(struct track *tg, void *item, struct hvGfx *hvg);
-Color snp125Color(struct track *tg, void *item, struct hvGfx *hvg);
-/* Return color of snp track item. */
-
-void snpDrawItemAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, 
-		   double scale, MgFont *font, Color color, enum trackVisibility vis);
-/* Draw a single snp item at position. */
-
 void snpMethods(struct track *tg);
 void snp125Methods(struct track *tg);
 /* Make track for snps. */
 
-struct orthoBed
-/* Browser extensible data - first four fields plus a chimp allele */
-    {
-    struct orthoBed *next;       /* Next in singly linked list. */
-    char            *chrom;      /* Human chromosome or FPC contig */
-    unsigned         chromStart; /* Start position in chromosome */
-    unsigned         chromEnd;   /* End position in chromosome */
-    char            *name;       /* Name of item */
-    char            *chimp;      /* Chimp allele */
-    };
-
 /***** haplotypes *****/
 
 char *perlegenName(struct track *tg, void *item);
 /* return the actual perlegen name, in form xx/yyyy cut off xx/ return yyyy */
 
-int haplotypeHeight(struct track *tg, struct linkedFeatures *lf, struct simpleFeature *sf);
-/* if the item isn't the first or the last make it smaller */
-
 void haplotypeMethods(struct track *tg);
 /* setup special methods for haplotype track */
 
 void perlegenMethods(struct track *tg);
 /* setup special methods for Perlegen haplotype track */
 
 
 /****** LD *****/
 
 /* 10 shades from black to fully saturated of red/green/blue */
 #define LD_DATA_SHADES 10
 extern Color ldShadesPos[LD_DATA_SHADES];
 extern Color ldHighLodLowDprime;
 extern Color ldHighDprimeLowLod;
 extern int colorLookup[256];