X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FConsensus.java;h=9d2c7384500332292ee632e5e26a16baab381975;hb=2eea4e73351d902cd88923d863e9780fa57a0ee7;hp=c8c99bf808e97238ed4211d564d0f24f3e5de19f;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index c8c99bf..9d2c738 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
@@ -51,8 +53,10 @@ public class Consensus
   /**
    * @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);
   }
 
@@ -69,7 +73,7 @@ public class Consensus
       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);