From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Wed, 11 Oct 2017 20:03:44 +0000 (+0100)
Subject: Use DistanceMatrix interface instead of the concrete implementation
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=2dc2907ec279a0134c907e120c2c893396cbd5e2

Use DistanceMatrix interface instead of the concrete implementation
---

diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java
index 217cdba..f13e520 100644
--- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java
+++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java
@@ -30,13 +30,14 @@ import java.util.ArrayList;
 import java.util.List;
 
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
+import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.util.ForesterUtil;
 
 public final class NeighborJoiningF {
 
-    private BasicSymmetricalDistanceMatrix _d;
+    private DistanceMatrix _d;
     private float[][]                      _d_values;
     private final DecimalFormat            _df;
     private PhylogenyNode[]                _external_nodes;
@@ -63,7 +64,7 @@ public final class NeighborJoiningF {
         _df.setRoundingMode( RoundingMode.HALF_UP );
     }
 
-    public final Phylogeny execute( final BasicSymmetricalDistanceMatrix distance ) {
+    public final Phylogeny execute( final DistanceMatrix distance ) {
         reset( distance );
         final Phylogeny phylogeny = new Phylogeny();
         while ( _n > 2 ) {
@@ -213,7 +214,7 @@ public final class NeighborJoiningF {
     }
 
     // only the values in the lower triangle are used.
-    private final void reset( final BasicSymmetricalDistanceMatrix distances ) {
+    private final void reset( final DistanceMatrix distances ) {
         _n = distances.getSize();
         _d = distances;
         _r = new float[ _n ];