From ed6eee466c185fbc257e9228da41678c6d527b02 Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Mon, 30 Oct 2017 11:50:05 +0000
Subject: [PATCH] JAL-2795 foresterMatrix now stores distance values itself

---
 src/jalview/ext/forester/ForesterMatrix.java |   28 +++++++++++++++++---------
 1 file changed, 19 insertions(+), 9 deletions(-)

diff --git a/src/jalview/ext/forester/ForesterMatrix.java b/src/jalview/ext/forester/ForesterMatrix.java
index d4864cf..0500704 100644
--- a/src/jalview/ext/forester/ForesterMatrix.java
+++ b/src/jalview/ext/forester/ForesterMatrix.java
@@ -17,27 +17,37 @@ public class ForesterMatrix implements DistanceMatrix
   private final static NumberFormat PHYLIP_FORMATTER = new DecimalFormat(
           "0.000000"); // straight from forester
 
-  private final MatrixI jalviewMatrix;
 
-  private final Sequence[] sequences;
+  private Sequence[] sequences;
+
+  private int width;
+
+  private int height;
 
   private final double[][] values;
 
+  private String[] identifiers;
+
   public ForesterMatrix(MatrixI jalviewInputMatrix,
           Sequence[] matrixSequences)
   {
-    this.jalviewMatrix = jalviewInputMatrix;
+    width = jalviewInputMatrix.width();
+    height = jalviewInputMatrix.height();
+    values = new double[width][height];
+
     this.sequences = matrixSequences;
 
-    if (jalviewMatrix.width() != jalviewMatrix.height())
+
+    if (width != height)
     {
       // some kind of warning?
     }
 
-    values = new double[jalviewMatrix.width()][jalviewMatrix.height()];
+
 
   }
 
+
   @Override
   public String getIdentifier(int i)
   {
@@ -54,13 +64,13 @@ public class ForesterMatrix implements DistanceMatrix
   @Override
   public int getSize()
   {
-    return jalviewMatrix.width();
+    return values.length;
   }
 
   @Override
   public double getValue(int col, int row)
   {
-    return jalviewMatrix.getValue(row, col);
+    return values[row][col];
   }
 
   @Override
@@ -73,7 +83,7 @@ public class ForesterMatrix implements DistanceMatrix
   @Override
   public void setValue(int col, int row, double distance)
   {
-    jalviewMatrix.setValue(row, col, distance);
+    values[row][col] = distance;
 
   }
 
@@ -88,7 +98,7 @@ public class ForesterMatrix implements DistanceMatrix
   public double[][] getValues()
   {
 
-    return null;
+    return values;
   }
 
   @Override
-- 
1.7.10.2