X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FConsensus.java;h=fe71d312f61acce371d4cf6ff523268bd82f4908;hb=432842b2544071500b05978f4e0e177f6819a0cb;hp=af2be8da76686ee6358bfad2d02a57619b0eed14;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index af2be8d..fe71d31 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,20 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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 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.
+ *  
+ * 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;
 
@@ -44,15 +46,17 @@ 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);
   }
 
@@ -69,9 +73,9 @@ 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;
     }