X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=ad1fe4e9b7911137ac7fd5e086d47b135b0c9a7b;hb=f24dacb1da56fccf05d684e2f4899facec2aecf7;hp=4ef250b2cf6b10d564fd938b9b85557144eae437;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 4ef250b..ad1fe4e 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -18,8 +18,6 @@
 */
 package jalview.analysis;
 
-import jalview.analysis.*;
-
 import jalview.datamodel.*;
 
 import java.util.*;
@@ -43,39 +41,41 @@ public class AAFrequency
     * the values being the count of each residue in that column.
     * 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)
+    public static final Vector calculate(Vector sequences, int start, int end)
     {
-        Vector result = new Vector();
+      Vector result = new Vector();
+      Hashtable residueHash;
+      int count, maxCount, nongap, i, j, jSize = sequences.size();
+      String maxResidue, sequence, res;
+      float percentage;
 
-        for (int i = start; i <= end; i++)
+        for (i = start; i <= end; i++)
         {
-            Hashtable residueHash = new Hashtable();
-            int maxCount = 0;
-            String maxResidue = "-";
-            int nongap = 0;
+            residueHash = new Hashtable();
+            maxCount = 0;
+            maxResidue = "-";
+            nongap = 0;
 
-            for (int j = 0; j < sequences.size(); j++)
+            for (j = 0; j < jSize; j++)
             {
                 if (sequences.elementAt(j) instanceof Sequence)
                 {
-                    Sequence s = (Sequence) sequences.elementAt(j);
+                    sequence = ((Sequence) sequences.elementAt(j)).getSequence();
 
-                    if (s.getSequence().length() > i)
+                    if (sequence.length() > i)
                     {
-                        String res = s.getSequence().charAt(i) + "";
+                        res = String.valueOf(Character.toUpperCase(sequence.charAt(i)));
 
-                        if (!jalview.util.Comparison.isGap(res.charAt(0)))
-                        {
-                            nongap++;
-                        }
-                        else
+                        if (jalview.util.Comparison.isGap(res.charAt(0)))
                         {
                             res = "-"; // we always use this for gaps in the property vectors
                         }
+                        else
+                        {   nongap++;    }
 
                         if (residueHash.containsKey(res))
                         {
-                            int count = ((Integer) residueHash.get(res)).intValue();
+                            count = ((Integer) residueHash.get(res)).intValue();
                             count++;
 
                             if (!jalview.util.Comparison.isGap(res.charAt(0)) &&
@@ -104,7 +104,7 @@ public class AAFrequency
                     {
                         if (residueHash.containsKey("-"))
                         {
-                            int count = ((Integer) residueHash.get("-")).intValue();
+                            count = ((Integer) residueHash.get("-")).intValue();
                             count++;
                             residueHash.put("-", new Integer(count));
                         }
@@ -117,18 +117,23 @@ public class AAFrequency
             }
 
             residueHash.put("maxCount", new Integer(maxCount));
+            residueHash.put("maxResidue", maxResidue);
 
-            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));
+            //Size is redundant at present if we calculate percentage here
+            //residueHash.put("size", new Integer(jSize));
+            //residueHash.put("nogaps", new Integer(nongap));
+
+            percentage = ((float)maxCount*100) / (float)jSize;
+            residueHash.put("pid_gaps", new Float(percentage) );
+
+            percentage = ((float)maxCount*100) / (float)nongap;
+            residueHash.put("pid_nogaps", new Float(percentage) );
             result.addElement(residueHash);
         }
 
+
+
         return result;
     }
 }