From 433c0001db1f1771ede8e2e6a010ba5a1aea06eb Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Mon, 30 Oct 2017 13:22:17 +0000
Subject: [PATCH] JAL-2795 add get for all matrix values to MatrixI (and
 concrete classes)

---
 src/jalview/ext/forester/ForesterMatrix.java |   37 ++++++++++++++++----------
 src/jalview/math/Matrix.java                 |    6 +++++
 src/jalview/math/MatrixI.java                |    3 +++
 3 files changed, 32 insertions(+), 14 deletions(-)

diff --git a/src/jalview/ext/forester/ForesterMatrix.java b/src/jalview/ext/forester/ForesterMatrix.java
index 0500704..9090d94 100644
--- a/src/jalview/ext/forester/ForesterMatrix.java
+++ b/src/jalview/ext/forester/ForesterMatrix.java
@@ -17,13 +17,10 @@ public class ForesterMatrix implements DistanceMatrix
   private final static NumberFormat PHYLIP_FORMATTER = new DecimalFormat(
           "0.000000"); // straight from forester
 
+  private final MatrixI jalviewMatrix;
 
   private Sequence[] sequences;
 
-  private int width;
-
-  private int height;
-
   private final double[][] values;
 
   private String[] identifiers;
@@ -31,22 +28,34 @@ public class ForesterMatrix implements DistanceMatrix
   public ForesterMatrix(MatrixI jalviewInputMatrix,
           Sequence[] matrixSequences)
   {
-    width = jalviewInputMatrix.width();
-    height = jalviewInputMatrix.height();
-    values = new double[width][height];
-
+    this.jalviewMatrix = jalviewInputMatrix;
     this.sequences = matrixSequences;
 
 
-    if (width != height)
+    if (jalviewMatrix.width() != jalviewMatrix.height())
     {
       // some kind of warning?
     }
 
-
+    values = new double[jalviewMatrix.width()][jalviewMatrix.height()];
 
   }
 
+  public ForesterMatrix(MatrixI jalviewInputMatrix,
+          String[] matrixIdentifiers)
+  {
+    this.jalviewMatrix = jalviewInputMatrix;
+    this.identifiers = matrixIdentifiers;
+
+
+    if (jalviewMatrix.width() != jalviewMatrix.height())
+    {
+      // some kind of warning?
+    }
+
+    values = new double[jalviewMatrix.width()][jalviewMatrix.height()];
+
+  }
 
   @Override
   public String getIdentifier(int i)
@@ -64,13 +73,13 @@ public class ForesterMatrix implements DistanceMatrix
   @Override
   public int getSize()
   {
-    return values.length;
+    return jalviewMatrix.width();
   }
 
   @Override
   public double getValue(int col, int row)
   {
-    return values[row][col];
+    return jalviewMatrix.getValue(row, col);
   }
 
   @Override
@@ -83,7 +92,7 @@ public class ForesterMatrix implements DistanceMatrix
   @Override
   public void setValue(int col, int row, double distance)
   {
-    values[row][col] = distance;
+    jalviewMatrix.setValue(row, col, distance);
 
   }
 
@@ -98,7 +107,7 @@ public class ForesterMatrix implements DistanceMatrix
   public double[][] getValues()
   {
 
-    return values;
+    return null;
   }
 
   @Override
diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 8910c67..21c5a4d 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -995,4 +995,10 @@ public class Matrix implements MatrixI
       }
     }
   }
+
+  @Override
+  public double[][] getValues()
+  {
+    return value;
+  }
 }
diff --git a/src/jalview/math/MatrixI.java b/src/jalview/math/MatrixI.java
index 5b93c76..f4d5030 100644
--- a/src/jalview/math/MatrixI.java
+++ b/src/jalview/math/MatrixI.java
@@ -63,6 +63,9 @@ public interface MatrixI
    */
   double[] getRow(int i);
 
+  double[][] getValues();
+
+
   MatrixI copy();
 
   MatrixI transpose();
-- 
1.7.10.2