Index: src/hg/inc/hapmapSnps.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/inc/hapmapSnps.h,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 4 -r1.5 -r1.6
--- src/hg/inc/hapmapSnps.h	8 May 2007 21:54:33 -0000	1.5
+++ src/hg/inc/hapmapSnps.h	3 Mar 2009 01:07:24 -0000	1.6
@@ -68,15 +68,20 @@
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 /* items for trackUi options and filters */
 
-#define HAP_POP_MIXED "hapmapSnps.isMixed"
-#define HAP_POP_COUNT "hapmapSnps.popCount"
-#define HAP_TYPE "hapmapSnps.polyType"
-#define HAP_MIN_FREQ "hapmapSnps.minorAlleleFreqMinimum"
-#define HAP_MAX_FREQ "hapmapSnps.minorAlleleFreqMaximum"
-#define HAP_MIN_HET "hapmapSnps.hetMinimum"
-#define HAP_MAX_HET "hapmapSnps.hetMaximum"
+#define HAP_POP_MIXED "hapmapSnps_isMixed"
+#define HAP_POP_COUNT "hapmapSnps_popCount"
+#define HAP_TYPE "hapmapSnps_polyType"
+#define HAP_MIN_FREQ "hapmapSnps_minorAlleleFreqMinimum"
+#define HAP_MAX_FREQ "hapmapSnps_minorAlleleFreqMaximum"
+#define HAP_MIN_HET "hapmapSnps_hetMinimum"
+#define HAP_MAX_HET "hapmapSnps_hetMaximum"
+#define HAP_MONO_PREFIX "hapmapSnps_monomorphic"
+#define HAP_ORTHO_PREFIX "hapmapSnps_ortho"
+#define HAP_ORTHO_QUAL_PREFIX "hapmapSnps_orthoQual"
+
+/* OLD -- Keeping these until I can check in the changes to hgTracks/hapmapTrack.c. */
 #define HAP_MONO_CEU "hapmapSnps.monomorphic.ceu"
 #define HAP_MONO_CHB "hapmapSnps.monomorphic.chb"
 #define HAP_MONO_JPT "hapmapSnps.monomorphic.jpt"
 #define HAP_MONO_YRI "hapmapSnps.monomorphic.yri"
@@ -83,24 +88,36 @@
 #define HAP_CHIMP "hapmapSnps.chimp"
 #define HAP_CHIMP_QUAL "hapmapSnps.chimpQualScore"
 #define HAP_MACAQUE "hapmapSnps.macaque"
 #define HAP_MACAQUE_QUAL "hapmapSnps.macaqueQualScore"
-
 #define HAP_POP_MIXED_DEFAULT "no filter"
 #define HAP_POP_COUNT_DEFAULT "no filter"
 #define HAP_TYPE_DEFAULT      "no filter"
+#define HAP_MONO_DEFAULT      "no filter"
+#define HAP_CHIMP_DEFAULT     "no filter"
+#define HAP_CHIMP_QUAL_DEFAULT "0"
+#define HAP_MACAQUE_DEFAULT   "no filter"
+#define HAP_MACAQUE_QUAL_DEFAULT "0"
+/* End of old stuff. */
+
+#define HAP_FILTER_DEFAULT "no filter"
 
 #define HAP_MIN_FREQ_DEFAULT  "0.0"
 #define HAP_MAX_FREQ_DEFAULT  "0.5"
 #define HAP_MIN_HET_DEFAULT   "0.0"
 #define HAP_MAX_HET_DEFAULT   "0.5"
 
-#define HAP_MONO_DEFAULT      "no filter"
+#define HAP_ORTHO_QUAL_DEFAULT "0"
 
-#define HAP_CHIMP_DEFAULT     "no filter"
-#define HAP_CHIMP_QUAL_DEFAULT "0"
-#define HAP_MACAQUE_DEFAULT   "no filter"
-#define HAP_MACAQUE_QUAL_DEFAULT "0"
+#define HAP_PHASEII_POPCOUNT 4
+#define HAP_PHASEIII_POPCOUNT 11
+#define HAP_ORTHO_COUNT 2
+
+char *hapmapPhaseIIPops[HAP_PHASEII_POPCOUNT];
+char *hapmapPhaseIIIPops[HAP_PHASEIII_POPCOUNT];
+
+/* Someday this should come from a trackDb setting: */
+extern char *hapmapOrthoSpecies[HAP_ORTHO_COUNT+1];
 
 #endif /* HAPMAPSNPS_H */
 
 

