X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FConsensus.java;h=8295699365932c43d6a26d2a8db6b3e355003974;hb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;hp=cccc995cd68b15e59a382e8f2649a8904023ef7a;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index cccc995..8295699 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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.
  * 
@@ -46,15 +46,18 @@ public class Consensus
     this.mask = setNums(s);
 
     // for (int i=0; i < mask.length; i++) {
-    // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
+    // jalview.bin.Console.outPrintln(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)
   {
+    jalview.bin.Console.outPrintln("DEPRECATED!!!!");
     return isConserved(cons2, col, size, true);
   }
 
@@ -71,9 +74,10 @@ 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
+      // jalview.bin.Console.outPrintln("True conserved "+tot+" from
+      // "+threshold+" out of
       // "+size+" : "+maskstr);
       return true;
     }