JAL-2795 Added get and set values to the converted matrix

diff --git a/forester b/forester
index 26d8d47..d62c120 160000 (submodule)
--- a/forester
+++ b/forester
@@ -1 +1 @@
-Subproject commit 26d8d47ed32a0eb9bd43c409d0e26ff13570b246
+Subproject commit d62c120f4c6fb10f20abaa929514d980fcea9671

diff --git a/src/jalview/ext/archaeopteryx/MergedMatrix.java b/src/jalview/ext/archaeopteryx/ForesterMatrix.java
similarity index 72%
rename from src/jalview/ext/archaeopteryx/MergedMatrix.java
rename to src/jalview/ext/archaeopteryx/ForesterMatrix.java
index 41855de..b7b3030 100644 (file)
--- a/src/jalview/ext/archaeopteryx/MergedMatrix.java
+++ b/src/jalview/ext/archaeopteryx/ForesterMatrix.java
@@ -1,9 +1,18 @@
 package jalview.ext.archaeopteryx;
 
+import jalview.math.MatrixI;
+
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 
-public class MergedMatrix implements DistanceMatrix
+public class ForesterMatrix implements DistanceMatrix
 {
+  private MatrixI jalviewMatrix;
+
+  public ForesterMatrix(MatrixI jalviewInputMatrix)
+  {
+    this.jalviewMatrix = jalviewInputMatrix;
+
+  }
 
   @Override
   public String getIdentifier(int i)
@@ -15,22 +24,19 @@ public class MergedMatrix implements DistanceMatrix
   @Override
   public int getIndex(String identifier)
   {
-    // TODO Auto-generated method stub
     return 0;
   }
 
   @Override
   public int getSize()
   {
-    // TODO Auto-generated method stub
     return 0;
   }
 
   @Override
   public double getValue(int col, int row)
   {
-    // TODO Auto-generated method stub
-    return 0;
+    return jalviewMatrix.getValue(row, col);
   }
 
   @Override
@@ -43,7 +49,7 @@ public class MergedMatrix implements DistanceMatrix
   @Override
   public void setValue(int col, int row, double distance)
   {
-    // TODO Auto-generated method stub
+    jalviewMatrix.setValue(row, col, distance);
 
   }