X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FConsensus.java;h=9d2c7384500332292ee632e5e26a16baab381975;hb=4ad2441df1220e3b1133feb3f70f00ba8b28392f;hp=5cd7b52612e019578a0bc8c5ef4f1f5ac339f146;hpb=067a6494124d4f1d0fe8b6d758b593145393b7dd;p=jalview.git

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 5cd7b52..9d2c738 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,37 +1,41 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3
  * 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.
- *
+ *  
+ * Jalview 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
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
-////////////////////////////////////////////
+// //////////////////////////////////////////
 // This does nothing at all at the moment!!!!!!!!!!
 // AW 15th Dec 2004
-/////////////////////////////////////////
+// ///////////////////////////////////////
 public class Consensus
 {
   int[] mask;
+
   double threshold;
+
   String maskstr;
 
   public Consensus(String mask, double threshold)
   {
     // this.id = id;
-    //    this.mask = mask;
+    // this.mask = mask;
     this.maskstr = mask;
     setMask(mask);
     this.threshold = threshold;
@@ -41,34 +45,38 @@ public class Consensus
   {
     this.mask = setNums(s);
 
-    //   for (int i=0; i < mask.length; i++) {
-    //  System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
+    // for (int i=0; i < mask.length; i++) {
+    // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
     // }
   }
 
   /**
    * @deprecated Use {@link #isConserved(int[][],int,int,boolean)} instead
    */
+  @Deprecated
   public boolean isConserved(int[][] cons2, int col, int size)
   {
+    System.out.println("DEPRECATED!!!!");
     return isConserved(cons2, col, size, true);
   }
 
-  public boolean isConserved(int[][] cons2, int col, int size, boolean includeGaps)
+  public boolean isConserved(int[][] cons2, int col, int size,
+          boolean includeGaps)
   {
     int tot = 0;
     if (!includeGaps)
     {
-      size -= cons2[col][cons2[col].length-1]; 
+      size -= cons2[col][cons2[col].length - 1];
     }
     for (int i = 0; i < mask.length; i++)
     {
       tot += cons2[col][mask[i]];
     }
 
-    if ( (double) tot > ( (threshold * size) / 100))
+    if (tot > ((threshold * size) / 100))
     {
-        // System.out.println("True conserved "+tot+" from "+threshold+" out of "+size+" : "+maskstr);
+      // System.out.println("True conserved "+tot+" from "+threshold+" out of
+      // "+size+" : "+maskstr);
       return true;
     }