X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=edcc50fa5cc9bb06890a3a5afa403161546a9330;hb=9d701bbe1b456aac498c5665cb3d7ac00a58db57;hp=c8e6388ab31b34836969cea706c957da0d4bcc30;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index c8e6388..edcc50f 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -20,6 +20,7 @@ public class AAFrequency {
     // This class is used extensively in calculating alignment colourschemes
     // that depend on the amount of conservation in each alignment column.
 
+
     public static Vector calculate(Vector sequences,int start,int end) {
 
     Vector result = new Vector();
@@ -28,7 +29,7 @@ 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++)
@@ -41,10 +42,12 @@ 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++;
+            else
+              res = "-"; // we always use this for gaps in the property vectors
 
             if (residueHash.containsKey(res))
             {
@@ -52,7 +55,7 @@ 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 +87,10 @@ 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));
@@ -130,26 +136,28 @@ public class AAFrequency {
 
 	    for (int k = winstart; k <= winend; k++) {
 		String refchar = refseq.getSequence().substring(k,k+1);
+                if (jalview.util.Comparison.isGap(refchar.charAt(0)))
+                  refchar="-";
+                else {
+                  for (int j = 0; j < sequences.size(); j++) {
 
-		for (int j = 0; j < sequences.size(); j++) {
+                    Sequence s = (Sequence)sequences.elementAt(j);
 
-		    if (refchar.equals("-") == false) {
+                    if (s.getSequence().length() > k) {
 
-			Sequence s = (Sequence)sequences.elementAt(j);
+                      String res = s.getSequence().substring(k,k+1); // no gapchar test needed
 
-			if (s.getSequence().length() > k) {
+                      if (res.equals(refchar)) {
+                        int val = ((Integer)values.elementAt(j)).intValue();
+                        val++;
+                        values.setElementAt(new Integer(val),j);
+                      }
+                    }
+                  }
+                }
 
-			    String res = s.getSequence().substring(k,k+1);
+              }
 
-			    if (res.equals(refchar)) {
-				int val = ((Integer)values.elementAt(j)).intValue();
-				val++;
-				values.setElementAt(new Integer(val),j);
-			    }
-			}
-		    }
-		}
-	    }
 	    prev = values;
 	} else {
 	    int winstart = i-window/2;
@@ -186,11 +194,13 @@ public class AAFrequency {
 
 		// Now substract 1 if the chars at winstart-1 match
 
-		if (pre_refchar.equals("-") == false && pre_char.equals(pre_refchar)) {
+                if (jalview.util.Comparison.isGap(pre_refchar.charAt(0)) == false
+                    && pre_char.equals(pre_refchar)) {
 		    val--;
 		}
 
-		if (pos_refchar.equals("-") == false && pos_char.equals(pos_refchar)) {
+                if (jalview.util.Comparison.isGap(pos_refchar.charAt(0)) == false
+                    && pos_char.equals(pos_refchar)) {
 		    val++;
 		}