forester as submodule with InternalFrame + start of distance conversion

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

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index b290428..0948a65 100644 (file)
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -1,3 +1,23 @@
+/*
+ * 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.analysis;
 
 import jalview.api.analysis.ScoreModelI;
@@ -53,7 +73,7 @@ public abstract class TreeBuilder
 
   Vector<SequenceNode> node;
 
-  private AlignmentView seqStrings;
+  private AlignmentView seqStrings; // redundant? (see seqData)
 
   /**
    * Constructor
@@ -344,7 +364,7 @@ public abstract class TreeBuilder
 
   protected void init(AlignmentView seqView, int start, int end)
   {
-    this.node = new Vector<SequenceNode>();
+    this.node = new Vector<>();
     if (seqView != null)
     {
       this.seqData = seqView;
@@ -438,7 +458,7 @@ public abstract class TreeBuilder
    */
   void makeLeaves()
   {
-    clusters = new Vector<BitSet>();
+    clusters = new Vector<>();
 
     for (int i = 0; i < noseqs; i++)
     {
@@ -447,6 +467,7 @@ public abstract class TreeBuilder
       sn.setElement(sequences[i]);
       sn.setName(sequences[i].getName());
       node.addElement(sn);
+
       BitSet bs = new BitSet();
       bs.set(i);
       clusters.addElement(bs);
@@ -458,4 +479,9 @@ public abstract class TreeBuilder
     return seqStrings;
   }
 
+  public MatrixI getDistances()
+  {
+    return distances;
+  }
+
 }