1b5e64c40e2a2785790edeaf8c54de55d89998a8
fanhsu
  Fri Mar 4 08:17:57 2011 -0800
Added 'X' to aminoAcidTable and to functions to get AA abbrev and letter.
diff --git src/lib/dnautil.c src/lib/dnautil.c
index 7aabeee..7a6e5f0 100644
--- src/lib/dnautil.c
+++ src/lib/dnautil.c
@@ -1027,31 +1027,31 @@
     return FALSE;
 dnaUtilOpen();
 for (i=0; i<size-1; ++i)
     {
     if (ntChars[(int)poly[i]] == 0) 
 	return FALSE;
     }
 return TRUE;
 }
 
 
 
 /* Tables to convert from 0-20 to ascii single letter representation
  * of proteins. */
 int aaVal[256];
-AA valToAa[20];
+AA valToAa[21];
 
 AA aaChars[256];	/* 0 except for value aa characters.  Converts to upper case rest. */
 
 struct aminoAcidTable
 /* A little info about each amino acid. */
     {
     int ix;
     char letter;
     char abbreviation[3];
     char *name;
     };
 
 struct aminoAcidTable aminoAcidTable[] = 
 {
     {0, 'A', "ala", "alanine"},
@@ -1060,34 +1060,47 @@
     {3, 'E', "glu",  "glutamic acid"},
     {4, 'F', "phe",  "phenylalanine"},
     {5, 'G', "gly",  "glycine"},
     {6, 'H', "his",  "histidine"},
     {7, 'I', "ile",  "isoleucine"},
     {8, 'K', "lys",  "lysine"},
     {9, 'L', "leu",  "leucine"},
     {10, 'M',  "met", "methionine"},
     {11, 'N',  "asn", "asparagine"},
     {12, 'P',  "pro", "proline"},
     {13, 'Q',  "gln", "glutamine"},
     {14, 'R',  "arg", "arginine"},
     {15, 'S',  "ser", "serine"},
     {16, 'T',  "thr", "threonine"},
     {17, 'V',  "val", "valine"},
-    {18, 'W',  "try", "tryptophan"},
+    {18, 'W',  "trp", "tryptophan"},
     {19, 'Y',  "tyr", "tyrosine"},
+    {20, 'X',  "ter", "termination"},
 };
 
+char *aaAbbr(int i)
+/* return pointer to AA abbrevation */
+{
+return(aminoAcidTable[i].abbreviation);
+}
+
+char aaLetter(int i)
+/* return AA letter */
+{
+return(aminoAcidTable[i].letter);
+}
+
 static void initAaVal()
 /* Initialize aaVal and valToAa tables. */
 {
 int i;
 char c, lowc;
 
 for (i=0; i<ArraySize(aaVal); ++i)
     aaVal[i] = -1;
 for (i=0; i<ArraySize(aminoAcidTable); ++i)
     {
     c = aminoAcidTable[i].letter;
     lowc = tolower(c);
     aaVal[(int)c] = aaVal[(int)lowc] = i;
     aaChars[(int)c] = aaChars[(int)lowc] = c;
     valToAa[i] = c;