JAL-1483 check dataset for features if none found on local sequence

[jalview.git] / src / jalview / analysis / NJTree.java

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 41d599e..ec5b79b 100644 (file)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -1,30 +1,40 @@
 /*
- * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
 
-import java.util.*;
-
 import jalview.api.analysis.ScoreModelI;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.CigarArray;
+import jalview.datamodel.NodeTransformI;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.io.NewickFile;
+import jalview.schemes.ResidueProperties;
+
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -722,19 +732,18 @@ 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;
 
-
   }
 
   /**