X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FConsensus.java;h=520196f532f20b7e130bb938eb93950b0185964a;hb=a2299be0ebb414d06b12d6735312a1bb1147694f;hp=27c59066bca12a6f05b91bb8ba75f43993a318d8;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 27c5906..520196f 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,77 +1,79 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-
+ * 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.schemes;
 
 ////////////////////////////////////////////
 // This does nothing at all at the moment!!!!!!!!!!
 // AW 15th Dec 2004
 /////////////////////////////////////////
-public class Consensus {
-
+public class Consensus
+{
   int[] mask;
   double threshold;
-   String maskstr;
+  String maskstr;
 
-  public Consensus(String mask, double threshold) {
+  public Consensus(String mask, double threshold)
+  {
     // this.id = id;
     //    this.mask = mask;
-        this.maskstr = mask;
+    this.maskstr = mask;
     setMask(mask);
     this.threshold = threshold;
   }
 
-  public void setMask(String s) {
+  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 size) {
+  public boolean isConserved(int[][] cons2, int col, int size)
+  {
     int tot = 0;
+
     for (int i = 0; i < mask.length; i++)
+    {
       tot += cons2[col][mask[i]];
+    }
 
-    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;
   }
-
-
 }
-
-
-
-