65479b434f3b7e556b78d1c75171fd3365e20272
angie
  Mon Oct 14 16:46:03 2013 -0700
isAllDna has a condition that surprised me (returns FALSE if size is 1),so I added isAllNt which has the behavior I expected.

diff --git src/lib/dnautil.c src/lib/dnautil.c
index 61ac692..d02806d 100644
--- src/lib/dnautil.c
+++ src/lib/dnautil.c
@@ -991,60 +991,65 @@
  * noise to be trimmed too, but skips last two tt for revcomp'd taa stop 
  * codon.  
  * It is less conservative in extending the polyA region than maskHeadPolyT. */
 {
 return findHeadPolyTMaybeMask(dna, size, FALSE, TRUE);
 }
 
 int maskHeadPolyT(DNA *dna, int size)
 /* Convert PolyT at start.  This allows a few non-T's as noise to be 
  * trimmed too.  Returns number of bases trimmed.  */
 {
 return findHeadPolyTMaybeMask(dna, size, TRUE, FALSE);
 }
 
 boolean isDna(char *poly, int size)
-/* Return TRUE if letters in poly are at least 90% ACGTU */
+/* Return TRUE if letters in poly are at least 90% ACGTNU- */
 {
 int i;
 int dnaCount = 0;
 
 dnaUtilOpen();
 for (i=0; i<size; ++i)
     {
     if (ntChars[(int)poly[i]])
 	dnaCount += 1;
     }
 return (dnaCount >= round(0.9 * size));
 }
 
-boolean isAllDna(char *poly, int size)
-/* Return TRUE if letters in poly are 100% ACGTU */
+boolean isAllNt(char *seq, int size)
+/* Return TRUE if all letters in seq are ACGTNU-. */
 {
 int i;
-
-if (size <= 1)
-    return FALSE;
 dnaUtilOpen();
 for (i=0; i<size-1; ++i)
     {
-    if (ntChars[(int)poly[i]] == 0) 
+    if (ntChars[(int)seq[i]] == 0)
 	return FALSE;
     }
 return TRUE;
 }
 
+boolean isAllDna(char *poly, int size)
+/* Return TRUE if size is great than 1 and letters in poly are 100% ACGTNU- */
+{
+if (size <= 1)
+    return FALSE;
+return isAllNt(poly, size);
+}
+
 
 
 /* Tables to convert from 0-20 to ascii single letter representation
  * of proteins. */
 int aaVal[256];
 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];