X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=eed6d0af8785119d8f94719047301ed72e064e78;hb=bf7d2036d80b4c31fa4fe0ee2e8ecb27023970ab;hp=db572ac8f8f6c1aefdefcf91c1ff48d50d1a08a1;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index db572ac..eed6d0a 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -35,13 +35,11 @@ public class Conservation {
   DrawableSequence consSequence;
   Hashtable        propHash;
   int              threshold;
-  Hashtable[]      freqs;
 
   String name = "";
 
-  public Conservation(String name,Hashtable[] freqs,Hashtable propHash, int threshold, Vector sequences, int start, int end) {
+  public Conservation(String name,Hashtable propHash, int threshold, Vector sequences, int start, int end) {
     this.name      = name;
-    this.freqs     = freqs;
     this.propHash  = propHash;
     this.threshold = threshold;
     this.sequences = sequences;
@@ -64,7 +62,7 @@ public class Conservation {
         if (sequences.elementAt(j) instanceof Sequence) {
           Sequence s = (Sequence)sequences.elementAt(j);
 
-          if (s.getSequence().length() > i) {
+          if (s.getLength() > i) {
             String res = s.getSequence().substring(i,i+1);
 
             if (residueHash.containsKey(res)) {
@@ -121,14 +119,19 @@ public class Conservation {
     }
   }
 
-  public int countGaps(int j) {
+  public int countGaps(int j)
+  {
     int count = 0;
 
-    for (int i = 0; i < sequences.size();i++) {
-      String tmp = ((Sequence)sequences.elementAt(i)).getSequence().substring(j,j+1);
-      if (tmp.equals(" ") || tmp.equals(".") || tmp.equals("-")) {
+    for (int i = 0; i < sequences.size();i++)
+    {
+      if( j+1 > ((Sequence)sequences.elementAt(i)).getSequence().length())
+      {  count++; continue;}
+
+      char c = ((Sequence)sequences.elementAt(i)).getSequence().charAt(j);
+      if (jalview.util.Comparison.isGap((c)))
         count++;
-      }
+
     }
     return count;
   }
@@ -140,42 +143,46 @@ public class Conservation {
       int totGaps = countGaps(i);
       float pgaps = (float)totGaps*100/(float)sequences.size();
 
-      if (percentageGaps > pgaps) {
-        Hashtable resultHash = (Hashtable)total.elementAt(i);
+      if (percentageGaps > pgaps)
+      {
+        Hashtable resultHash = (Hashtable)total.elementAt(i-start);
 
         //Now find the verdict
         int         count = 0;
         Enumeration e3    = resultHash.keys();
 
-        while (e3.hasMoreElements()) {
+        while (e3.hasMoreElements())
+        {
           String type    = (String)e3.nextElement();
           Integer result = (Integer)resultHash.get(type);
 
           //Do we want to count +ve conservation or +ve and -ve cons.?
 
-          if (consflag) {
-            if (result.intValue() == 1) {
+          if (consflag)
+          {
+            if (result.intValue() == 1)
               count++;
-            }
-          } else {
-            if (result.intValue() != -1) {
+          }
+          else
+          {
+            if (result.intValue() != -1)
               count++;
-            }
           }
         }
 
-        if (count < 10) {
+        if (count < 10)
           consString = consString + String.valueOf(count);
-        } else {
+        else
           consString = consString + "*";
-        }
-      } else {
+
+      }
+      else
+      {
         consString = consString + "-";
       }
     }
 
     consSequence = new DrawableSequence(name,consString,start,end);
-
   }
 
   public jalview.gui.DrawableSequence getConsSequence() {