0f86f30893b5f0b45e7ef457ac5120bbb0e39ce7
cline
  Sat Aug 27 16:30:53 2011 -0700
(1) Various updates on the proteome browser code, addressing this week's code review feedback from Jim to ensure that all arrays have all cells initialized (and in the process, guesstimating some hydrophobicity numbers of amino acids such as pyrrolysine and selenocystine), and getting rid of some magic numbers that were doing nothing good to the code.  (2) Now that I've learned that there is a FAQ for formats, I've added an entry for peptideMapping, used by wgEncodeUncBsuProt
diff --git src/hg/inc/pbCommon.h src/hg/inc/pbCommon.h
index 2c466b2..0ee71c3 100644
--- src/hg/inc/pbCommon.h
+++ src/hg/inc/pbCommon.h
@@ -1,18 +1,14 @@
 /* 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"
 
-char *txAccFromTempName(char *tempName);
-/* Given name in this.that.acc.version format, return
- * just acc.version. */
-
-void txGeneAccFromId(int id, char acc[16]);
-/* Convert ID to accession in uc123ABC format. */
+/* define the size of the standard amino acid alphabet */
+#define NUM_STANDARD_AAS 20
 
 #endif /* PBCOMMON_H */