X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=a8ca3f7056c9f88e7e9c32283ebeaedc9ce8d0ce;hb=9493ac8f3b6a02d3cf9747ed6c0d6cf407d284e8;hp=41d599e8f4f961e568ea470499da5de2ac869ece;hpb=27b77d2219147d3741d4af7377e13918a8ae972a;p=jalview.git
diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 41d599e..a8ca3f7 100644
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 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.analysis;
@@ -722,19 +724,18 @@ public class NJTree
*/
public float[][] findDistances()
{
-
+
float[][] distance = new float[noseqs][noseqs];
- // Pairwise substitution score (with no gap penalties)
- ScoreModelI _pwmatrix = ResidueProperties.getScoreModel(pwtype);
- if (_pwmatrix == null)
- {
- _pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
- }
- distance = _pwmatrix.findDistances(seqData);
+ // Pairwise substitution score (with no gap penalties)
+ ScoreModelI _pwmatrix = ResidueProperties.getScoreModel(pwtype);
+ if (_pwmatrix == null)
+ {
+ _pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
+ }
+ distance = _pwmatrix.findDistances(seqData);
return distance;
-
}
/**