From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Wed, 11 Oct 2017 20:12:19 +0000 (+0100)
Subject: More generic uses of DistanceMatrix instead of concrete implementations
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=25c731fbc8a993c2084d364e6c6c8ca9e662ad73;p=jalview.git

More generic uses of DistanceMatrix instead of concrete implementations
---

diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
index f63af04..9860c1a 100644
--- a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
+++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
@@ -29,7 +29,7 @@ import java.text.DecimalFormat;
 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;
@@ -37,7 +37,7 @@ import org.forester.util.ForesterUtil;
 public final class NeighborJoining {
 
     private final static DecimalFormat     DF = new DecimalFormat( "0.00000" );
-    private BasicSymmetricalDistanceMatrix _d;
+    private DistanceMatrix _d;
     private double[][]                     _d_values;
     private final DecimalFormat            _df;
     private PhylogenyNode[]                _external_nodes;
@@ -64,7 +64,7 @@ public final class NeighborJoining {
         _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 ) {
@@ -119,9 +119,9 @@ public final class NeighborJoining {
         return phylogeny;
     }
 
-    public final List<Phylogeny> execute( final List<BasicSymmetricalDistanceMatrix> distances_list ) {
+    public final List<Phylogeny> execute( final List<DistanceMatrix> distances_list ) {
         final List<Phylogeny> pl = new ArrayList<Phylogeny>();
-        for( final BasicSymmetricalDistanceMatrix distances : distances_list ) {
+        for( final DistanceMatrix distances : distances_list ) {
             pl.add( execute( distances ) );
         }
         return pl;
@@ -221,7 +221,7 @@ public final class NeighborJoining {
 
     // only the values in the lower triangle are used.
     // !matrix values will be changed!
-    private final void reset( final BasicSymmetricalDistanceMatrix distances ) {
+    private final void reset( final DistanceMatrix distances ) {
         _n = distances.getSize();
         _d = distances;
         _r = new double[ _n ];
diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
index 209b93f..050885d 100644
--- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
+++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
@@ -30,7 +30,7 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Map.Entry;
 
-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;
@@ -38,7 +38,7 @@ import org.forester.util.ForesterUtil;
 public final class NeighborJoiningR {
 
     private final static DecimalFormat     DF = new DecimalFormat( "0.00000" );
-    private BasicSymmetricalDistanceMatrix _d;
+    private DistanceMatrix _d;
     private double[][]                     _d_values;
     private final DecimalFormat            _df;
     private PhylogenyNode[]                _external_nodes;
@@ -70,7 +70,7 @@ public final class NeighborJoiningR {
         _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 ) {
@@ -145,9 +145,9 @@ public final class NeighborJoiningR {
         return phylogeny;
     }
 
-    public final List<Phylogeny> execute( final List<BasicSymmetricalDistanceMatrix> distances_list ) {
+    public final List<Phylogeny> execute( final List<DistanceMatrix> distances_list ) {
         final List<Phylogeny> pl = new ArrayList<Phylogeny>();
-        for( final BasicSymmetricalDistanceMatrix distances : distances_list ) {
+        for( final DistanceMatrix distances : distances_list ) {
             pl.add( execute( distances ) );
         }
         return pl;
@@ -266,7 +266,7 @@ public final class NeighborJoiningR {
 
     // only the values in the lower triangle are used.
     // !matrix values will be changed!
-    private final void reset( final BasicSymmetricalDistanceMatrix distances ) {
+    private final void reset( final DistanceMatrix distances ) {
         _n = distances.getSize();
         _d = distances;
         _r = new double[ _n ];
diff --git a/forester/java/src/org/forester/evoinference/distance/Sarray.java b/forester/java/src/org/forester/evoinference/distance/Sarray.java
index 2e961b8..0232363 100644
--- a/forester/java/src/org/forester/evoinference/distance/Sarray.java
+++ b/forester/java/src/org/forester/evoinference/distance/Sarray.java
@@ -10,6 +10,7 @@ import java.util.SortedMap;
 import java.util.TreeMap;
 
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
+import org.forester.evoinference.matrix.distance.DistanceMatrix;
 
 public final class Sarray {
 
@@ -37,7 +38,7 @@ public final class Sarray {
         return getS( j ).get( key );
     }
 
-    final public void initialize( final BasicSymmetricalDistanceMatrix d ) {
+    final public void initialize( final DistanceMatrix d ) {
         for( int j = 0; j < d.getSize(); ++j ) {
             final TreeMap<Integer, int[]> map = new TreeMap<Integer, int[]>();
             _data.add( map );
diff --git a/forester/java/src/org/forester/evoinference/matrix/distance/DistanceMatrix.java b/forester/java/src/org/forester/evoinference/matrix/distance/DistanceMatrix.java
index 2eeaca9..0a332b2 100644
--- a/forester/java/src/org/forester/evoinference/matrix/distance/DistanceMatrix.java
+++ b/forester/java/src/org/forester/evoinference/matrix/distance/DistanceMatrix.java
@@ -44,4 +44,6 @@ public interface DistanceMatrix {
     public static enum Format {
         PHYLIP
     }
+
+    public double[][] getValues();
 }