Changed more concrete DistanceMatrix references to reference interface

diff --git a/forester/java/src/org/forester/application/nj.java b/forester/java/src/org/forester/application/nj.java
index dca5d08..f210058 100644 (file)
--- a/forester/java/src/org/forester/application/nj.java
+++ b/forester/java/src/org/forester/application/nj.java
@@ -33,7 +33,6 @@ import java.util.Date;
 import java.util.List;
 
 import org.forester.evoinference.distance.NeighborJoining;
-import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.io.parsers.SymmetricalDistanceMatrixParser;
 import org.forester.io.writers.PhylogenyWriter;
@@ -122,7 +121,7 @@ public class nj {
         final NeighborJoining nj = NeighborJoining.createInstance( verbose, 6 );
         final long start_time = new Date().getTime();
         for( final DistanceMatrix matrix : matrices ) {
-            ps.add( nj.execute( ( BasicSymmetricalDistanceMatrix ) matrix ) );
+            ps.add( nj.execute( ( DistanceMatrix ) matrix ) );
         }
         final long end_time = new Date().getTime();
         final PhylogenyWriter w = new PhylogenyWriter();

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
index 1e8f3fc..cc62751 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
@@ -37,6 +37,7 @@ import org.forester.archaeopteryx.MainFrameApplication;
 import org.forester.evoinference.distance.NeighborJoiningF;
 import org.forester.evoinference.distance.PairwiseDistanceCalculator;
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
+import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.evoinference.tools.BootstrapResampler;
 import org.forester.msa.BasicMsa;
 import org.forester.msa.Mafft;
@@ -116,7 +117,7 @@ public class PhylogeneticInferrer extends RunnableProcess {
     }
 
     private Phylogeny inferPhylogeny( final Msa msa ) {
-        BasicSymmetricalDistanceMatrix m = null;
+        DistanceMatrix m = null;
         switch ( _options.getPwdDistanceMethod() ) {
             case KIMURA_DISTANCE:
                 m = PairwiseDistanceCalculator.calcKimuraDistances( msa );
@@ -274,7 +275,7 @@ public class PhylogeneticInferrer extends RunnableProcess {
         return msa;
     }
 
-    private void writeToFiles( final BasicSymmetricalDistanceMatrix m ) {
+    private void writeToFiles( final DistanceMatrix m ) {
         if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
             try {
                 final BufferedWriter msa_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()

diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
index 5b7b99c..a9c16e9 100644 (file)
--- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
+++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
@@ -439,7 +439,7 @@ public class TestPhylogenyReconstruction {
         try {
             final Msa msa0 = GeneralMsaParser.parseMsa( new FileInputStream( test_dir + ForesterUtil.FILE_SEPARATOR
                     + "bcl.aln" ) );
-            final BasicSymmetricalDistanceMatrix pwd0 = PairwiseDistanceCalculator.calcKimuraDistances( msa0 );
+            final DistanceMatrix pwd0 = PairwiseDistanceCalculator.calcKimuraDistances( msa0 );
             if ( pwd0.getSize() != 120 ) {
                 return false;
             }

diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java
index f13e520..2f10c40 100644 (file)
--- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java
+++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java
@@ -29,7 +29,6 @@ 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;
@@ -118,9 +117,9 @@ public final class NeighborJoiningF {
         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;

diff --git a/forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java b/forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java
index 39a446f..2e1dbbc 100644 (file)
--- a/forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java
+++ b/forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java
@@ -26,6 +26,8 @@
 package org.forester.evoinference.distance;
 
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
+import org.forester.evoinference.matrix.distance.DistanceMatrix;
+import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.msa.Msa;
 
 public final class PairwiseDistanceCalculator {
@@ -82,31 +84,31 @@ public final class PairwiseDistanceCalculator {
         return -Math.log( dp );
     }
 
-    private BasicSymmetricalDistanceMatrix calcKimuraDistances() {
+    private DistanceMatrix calcKimuraDistances() {
         final int s = _msa.getNumberOfSequences();
-        final BasicSymmetricalDistanceMatrix d = new BasicSymmetricalDistanceMatrix( s );
+        final DistanceMatrix d = new BasicSymmetricalDistanceMatrix( s );
         copyIdentifiers( s, d );
         calcKimuraDistances( s, d );
         return d;
     }
 
-    private BasicSymmetricalDistanceMatrix calcPoissonDistances() {
+    private DistanceMatrix calcPoissonDistances() {
         final int s = _msa.getNumberOfSequences();
-        final BasicSymmetricalDistanceMatrix d = new BasicSymmetricalDistanceMatrix( s );
+        final DistanceMatrix d = new BasicSymmetricalDistanceMatrix( s );
         copyIdentifiers( s, d );
         calcPoissonDistances( s, d );
         return d;
     }
 
-    private BasicSymmetricalDistanceMatrix calcFractionalDissimilarities() {
+    private DistanceMatrix calcFractionalDissimilarities() {
         final int s = _msa.getNumberOfSequences();
-        final BasicSymmetricalDistanceMatrix d = new BasicSymmetricalDistanceMatrix( s );
+        final DistanceMatrix d = new BasicSymmetricalDistanceMatrix( s );
         copyIdentifiers( s, d );
         calcFractionalDissimilarities( s, d );
         return d;
     }
 
-    private void calcKimuraDistances( final int s, final BasicSymmetricalDistanceMatrix d ) {
+    private void calcKimuraDistances( final int s, final DistanceMatrix d ) {
         for( int i = 1; i < s; i++ ) {
             for( int j = 0; j < i; j++ ) {
                 d.setValue( i, j, calcKimuraDistance( i, j ) );
@@ -114,7 +116,7 @@ public final class PairwiseDistanceCalculator {
         }
     }
 
-    private void calcPoissonDistances( final int s, final BasicSymmetricalDistanceMatrix d ) {
+    private void calcPoissonDistances( final int s, final DistanceMatrix d ) {
         for( int i = 1; i < s; i++ ) {
             for( int j = 0; j < i; j++ ) {
                 d.setValue( i, j, calcPoissonDistance( i, j ) );
@@ -122,7 +124,7 @@ public final class PairwiseDistanceCalculator {
         }
     }
 
-    private void calcFractionalDissimilarities( final int s, final BasicSymmetricalDistanceMatrix d ) {
+    private void calcFractionalDissimilarities( final int s, final DistanceMatrix d ) {
         for( int i = 1; i < s; i++ ) {
             for( int j = 0; j < i; j++ ) {
                 d.setValue( i, j, calcFractionalDissimilarity( i, j ) );
@@ -135,28 +137,28 @@ public final class PairwiseDistanceCalculator {
         throw new CloneNotSupportedException();
     }
 
-    private void copyIdentifiers( final int s, final BasicSymmetricalDistanceMatrix d ) {
+    private void copyIdentifiers( final int s, final DistanceMatrix d ) {
         for( int i = 0; i < s; i++ ) {
             d.setIdentifier( i, _msa.getIdentifier( i ) );
         }
     }
 
-    public static BasicSymmetricalDistanceMatrix calcFractionalDissimilarities( final Msa msa ) {
+    public static DistanceMatrix calcFractionalDissimilarities( final Msa msa ) {
         return new PairwiseDistanceCalculator( msa, DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA )
         .calcFractionalDissimilarities();
     }
 
-    public static BasicSymmetricalDistanceMatrix calcPoissonDistances( final Msa msa ) {
+    public static DistanceMatrix calcPoissonDistances( final Msa msa ) {
         return new PairwiseDistanceCalculator( msa, DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA )
         .calcPoissonDistances();
     }
 
-    public static BasicSymmetricalDistanceMatrix calcKimuraDistances( final Msa msa ) {
+    public static DistanceMatrix calcKimuraDistances( final Msa msa ) {
         return new PairwiseDistanceCalculator( msa, DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA )
         .calcKimuraDistances();
     }
 
-    public static BasicSymmetricalDistanceMatrix calcKimuraDistances( final Msa msa,
+    public static DistanceMatrix calcKimuraDistances( final Msa msa,
                                                                       final double value_for_too_large_distance_for_kimura_formula ) {
         return new PairwiseDistanceCalculator( msa, value_for_too_large_distance_for_kimura_formula )
         .calcKimuraDistances();

diff --git a/forester/java/src/org/forester/evoinference/distance/Sset.java b/forester/java/src/org/forester/evoinference/distance/Sset.java
index c8f912f..9af6ea0 100644 (file)
--- a/forester/java/src/org/forester/evoinference/distance/Sset.java
+++ b/forester/java/src/org/forester/evoinference/distance/Sset.java
@@ -10,7 +10,7 @@ import java.util.Set;
 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 Sset {
 
@@ -38,7 +38,7 @@ public final class Sset {
         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, Set<Integer>> map = new TreeMap<Integer, Set<Integer>>();
             _data.add( map );

diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
index 8a13b5c..950d8cb 100644 (file)
--- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
+++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
@@ -43,6 +43,7 @@ import org.forester.evoinference.distance.NeighborJoiningF;
 import org.forester.evoinference.distance.PairwiseDistanceCalculator;
 import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD;
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
+import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.evoinference.tools.BootstrapResampler;
 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
@@ -601,7 +602,7 @@ public class MsaCompactor {
     }
 
     private final Phylogeny collapse( final Msa msa, final int threshold ) {
-        final BasicSymmetricalDistanceMatrix m = PairwiseDistanceCalculator.calcFractionalDissimilarities( msa );
+        final DistanceMatrix m = PairwiseDistanceCalculator.calcFractionalDissimilarities( msa );
         //TODO
         return null;
     }
@@ -610,7 +611,7 @@ public class MsaCompactor {
                                               final Msa msa,
                                               final boolean write_matrix,
                                               final String matrix_name ) {
-        BasicSymmetricalDistanceMatrix m = null;
+        DistanceMatrix m = null;
         switch ( pwd_distance_method ) {
             case KIMURA_DISTANCE:
                 m = PairwiseDistanceCalculator.calcKimuraDistances( msa );

diff --git a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
index b23f82b..ed4eae7 100644 (file)
--- a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
+++ b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
@@ -96,9 +96,9 @@ public class PairwiseGenomeComparator {
                                             final boolean calc_similarity_scores,
                                             final Phylogeny phy ) {
         init();
-        final BasicSymmetricalDistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
-        final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
-        final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+        final DistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+        final DistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+        final DistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
         if ( verbose ) {
             System.out.println();
             System.out.println( "Pairwise genome distances:" );
@@ -264,8 +264,8 @@ public class PairwiseGenomeComparator {
             final SortedSet<String> domain_ids_to_ignore = randomlyPickDomainIds( all_unique_domain_ids,
                                                                                   jacknife_ratio,
                                                                                   generator );
-            final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
-            final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+            final DistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+            final DistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
             for( int i = 0; i < number_of_genomes; ++i ) {
                 final String species_i = species[ i ].getSpeciesId();
                 shared_domains_based_distances.setIdentifier( i, species_i );

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index 3b52234..05a9101 100644 (file)
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -60,7 +60,6 @@ import org.forester.evoinference.matrix.character.CharacterStateMatrix;
 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
 import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
 import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
-import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.go.GoId;
 import org.forester.go.GoNameSpace;
@@ -246,7 +245,7 @@ public final class SurfacingUtil {
                                                              final DistanceMatrix distance ) {
         checkForOutputFileWriteability( nj_tree_outfile );
         final NeighborJoining nj = NeighborJoining.createInstance();
-        final Phylogeny phylogeny = nj.execute( ( BasicSymmetricalDistanceMatrix ) distance );
+        final Phylogeny phylogeny = nj.execute( ( DistanceMatrix ) distance );
         phylogeny.setName( nj_tree_outfile.getName() );
         writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
         return phylogeny;