X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FTreeBuilder.java;h=0948a65bebd43613a0c4d64e6f94ba2adf7d082a;hb=c21989bd32ddf92f7583578b66e3f491643ce775;hp=b290428de2fb630c8322f9fc75925cf5f5d7a03a;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git
diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index b290428..0948a65 100644
--- 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 .
+ * 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 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();
+ this.node = new Vector<>();
if (seqView != null)
{
this.seqData = seqView;
@@ -438,7 +458,7 @@ public abstract class TreeBuilder
*/
void makeLeaves()
{
- clusters = new Vector();
+ 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;
+ }
+
}