From bec86286aeecc7008a006e56efe3816a509cc593 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 7 Apr 2005 13:17:34 +0000
Subject: [PATCH] checkfor gap characters

---
 src/jalview/analysis/AAFrequency.java |   11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index c8e6388..c61e7ef 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -28,7 +28,7 @@ public class AAFrequency {
     {
 
       Hashtable residueHash = new Hashtable();
-      int       maxCount    = -1;
+      int       maxCount    = 0;
       String    maxResidue  = "-";
       int       nongap      = 0;
       for (int j=0; j < sequences.size(); j++)
@@ -41,9 +41,9 @@ public class AAFrequency {
           if (s.getSequence().length() > i)
           {
 
-            String res = s.getSequence().substring(i,i+1);
+            String res = s.getSequence().charAt(i)+"";
 
-            if (!res.equals("-"))
+            if (!jalview.util.Comparison.isGap(res.charAt(0)))
               nongap++;
 
             if (residueHash.containsKey(res))
@@ -52,7 +52,7 @@ public class AAFrequency {
               int count = ((Integer)residueHash.get(res)).intValue() ;
               count++;
 
-	      if (!res.equals("-") && count >= maxCount)
+	      if (!jalview.util.Comparison.isGap(res.charAt(0)) && count >= maxCount)
               {
 
                   if(count>maxCount)
@@ -84,7 +84,10 @@ public class AAFrequency {
           }
         }
       }
+
       residueHash.put("maxCount",new Integer(maxCount));
+      if(maxCount<0)
+        System.out.println("asasa "+maxCount);
       residueHash.put("maxResidue", maxResidue);
       residueHash.put("size", new Integer(sequences.size()));
       residueHash.put("nongap", new Integer(nongap));
-- 
1.7.10.2