X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FConsensus.java;h=9d2c7384500332292ee632e5e26a16baab381975;hb=453fa24ab502aaca4ffccf3590f97c897b9580b3;hp=213621b36f436a27b9d875ca870b25d489ff9d3b;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 213621b..9d2c738 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
@@ -50,8 +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);
}
@@ -68,7 +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);