X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=11e7a3d8514be3d0e14e3c249278a64dce353c1e;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=fc8cb4c49431005a7c9863687434bea2fd1eb317;hpb=ae6a322ef448be046ec78410b26e512e1c780d96;p=jalview.git
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index fc8cb4c..11e7a3d 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,20 +1,19 @@
/*
- * 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 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * 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.
*
- * 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
+ * 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 .
*/
package jalview.analysis;
@@ -194,9 +193,9 @@ public class AAFrequency
boolean includeAllConsSymbols)
{
completeConsensus(consensus, hconsensus, iStart, width,
- ignoreGapsInConsensusCalculation, includeAllConsSymbols,
- null); //new char[]
- // { 'A', 'C', 'G', 'T', 'U' });
+ ignoreGapsInConsensusCalculation, includeAllConsSymbols, null); // new
+ // char[]
+ // { 'A', 'C', 'G', 'T', 'U' });
}
public static void completeConsensus(AlignmentAnnotation consensus,
@@ -205,8 +204,18 @@ public class AAFrequency
boolean includeAllConsSymbols, char[] alphabet)
{
float tval, value;
+ if (consensus==null || consensus.annotations==null || consensus.annotations.length=hconsensus.length) {
+ // happens if sequences calculated over were shorter than alignment width
+ consensus.annotations[i]=null;
+ continue;
+ }
value = 0;
if (ignoreGapsInConsensusCalculation)
{
@@ -230,7 +239,7 @@ public class AAFrequency
if (profile != null && includeAllConsSymbols)
{
mouseOver = "";
- if (alphabet!=null)
+ if (alphabet != null)
{
for (int c = 0; c < alphabet.length; c++)
{