X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FConsensus.java;h=17cb789355ff58c402230beb53bafd530e538fb6;hb=58ba1562a8a739699ce47a338803b2641f6d7913;hp=7b0dbbb034ccf033b9848e9315cdbb75c9d04e5f;hpb=9360a7970c15aacc7e53eb3bdd2732d2c7bef9c8;p=jalview.git

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 7b0dbbb..17cb789 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -18,8 +18,6 @@
 
 package jalview.schemes;
 
-import jalview.datamodel.*;
-import java.util.*;
 ////////////////////////////////////////////
 // This does nothing at all at the moment!!!!!!!!!!
 // AW 15th Dec 2004
@@ -28,25 +26,29 @@ public class Consensus {
 
   int[] mask;
   double threshold;
+   String maskstr;
 
-  public Consensus(String m, double threshold)
-  {
-    mask = setNums(m);
+  public Consensus(String mask, double threshold) {
+    // this.id = id;
+    //    this.mask = mask;
+        this.maskstr = mask;
+    setMask(mask);
     this.threshold = threshold;
   }
 
+  public void setMask(String s) {
+    this.mask = setNums(s);
+    //   for (int i=0; i < mask.length; i++) {
+    //  System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
+    // }
+  }
 
-  public boolean isConserved(int[][] cons2,int col, int res,int size)
-  {
+  public boolean isConserved(int[][] cons2,int col ,int size) {
     int tot = 0;
-
-try{
-    for (int i=0; i < mask.length; i++)
+    for (int i = 0; i < mask.length; i++)
       tot += cons2[col][mask[i]];
-}catch(Exception ex)
-{ return true; }
 
-    if ((double)tot > threshold*size/100)
+    if ( (double) tot > threshold * size / 100)
       return true;
 
     return false;
@@ -60,7 +62,9 @@ try{
     {
       out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i, i + 1))).intValue();
       i++;
+
     }
+
     return out;
   }