X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=eed6d0af8785119d8f94719047301ed72e064e78;hb=a2d2bfc9a2efd08446954c01dc5957560fdec9be;hp=520036edf8cbaf2566b2f500760a3012c23f3b29;hpb=ff75356cd448ad8bf24733c328054a53e87c242c;p=jalview.git

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 520036e..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;
@@ -121,17 +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++) {
+    for (int i = 0; i < sequences.size();i++)
+    {
       if( j+1 > ((Sequence)sequences.elementAt(i)).getSequence().length())
       {  count++; continue;}
 
-      String tmp = ((Sequence)sequences.elementAt(i)).getSequence().substring(j,j+1);
-      if (tmp.equals(" ") || tmp.equals(".") || tmp.equals("-")) {
+      char c = ((Sequence)sequences.elementAt(i)).getSequence().charAt(j);
+      if (jalview.util.Comparison.isGap((c)))
         count++;
-      }
+
     }
     return count;
   }