X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FConsensus.java;h=fe71d312f61acce371d4cf6ff523268bd82f4908;hb=155a17a423e980849fd4dc5f857da1a72b0010b9;hp=d3942df57c5104b97c701c9ca4c94f20fac554ea;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index d3942df..fe71d31 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 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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;
@@ -43,15 +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);
}
@@ -68,9 +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;
}