X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FConsensus.java;h=520196f532f20b7e130bb938eb93950b0185964a;hb=1b1a1007c534a02fdbae76df0c084f215c7c4c21;hp=7b0dbbb034ccf033b9848e9315cdbb75c9d04e5f;hpb=9360a7970c15aacc7e53eb3bdd2732d2c7bef9c8;p=jalview.git

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 7b0dbbb..520196f 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,5 +1,6 @@
-/* Jalview - a java multiple alignment editor
- * Copyright (C) 1998  Michele Clamp
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -13,60 +14,66 @@
  *
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemes;
 
-import jalview.datamodel.*;
-import java.util.*;
 ////////////////////////////////////////////
 // This does nothing at all at the moment!!!!!!!!!!
 // AW 15th Dec 2004
 /////////////////////////////////////////
-public class Consensus {
-
+public class Consensus
+{
   int[] mask;
   double threshold;
+  String maskstr;
 
-  public Consensus(String m, double threshold)
+  public Consensus(String mask, double threshold)
   {
-    mask = setNums(m);
+    // 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;
   }
 
   int[] setNums(String s)
   {
-    int [] out = new int[s.length()];
+    int[] out = new int[s.length()];
     int i = 0;
+
     while (i < s.length())
     {
-      out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i, i + 1))).intValue();
+      out[i] = ResidueProperties.aaIndex[s.charAt(i)];
       i++;
     }
+
     return out;
   }
-
-
 }
-
-
-
-