3954f10138da8c61fe8422438e79927fc63ca973
cline
  Mon Aug 29 11:54:23 2011 -0700
Added define of pbCommon
diff --git src/hg/inc/pbCommon.h src/hg/inc/pbCommon.h
index 0ee71c3..734691e 100644
--- src/hg/inc/pbCommon.h
+++ src/hg/inc/pbCommon.h
@@ -1,14 +1,22 @@
 /* pbCommon - contains data shared within the pb* family of programs
  * (which are used in building the Proteome Browser and data */
 
 #ifndef PBCOMMON_H
 #define PBCOMMON_H
 
-/* define the expected amino acid residues */
-#define AA_ALPHABET "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
+/* define the number of expected amino acid residues, including wildcards */
+#define NUM_AMINO_ACIDS 26 
+
+/* define the expected amino acid residues, including wildcards and 
+ * nonstandard residues.  It's possible that the order is important*/
+#define AA_ALPHABET "WCMHYNFIDQKRTVPGEASLXZBJOU"
 
 /* define the size of the standard amino acid alphabet */
-#define NUM_STANDARD_AAS 20
+#define NUM_STANDARD_AMINO_ACIDS 20
+
+/* define the standard amino acid alphabet.  The order here _might_ be
+ * important (I'm guessing that the unusual order is there for a reason) */
+#define STNADARD_AA_ALPHABET "WCMHYNFIDQKRTVPGEASL"
 
 #endif /* PBCOMMON_H */