in progress

diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
index 6db6453..c545f59 100644 (file)
--- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
+++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
@@ -32,6 +32,7 @@ import java.io.FileInputStream;
 import java.io.StringWriter;
 import java.util.Date;
 import java.util.List;
+import java.util.Set;
 import java.util.SortedSet;
 
 import org.forester.evoinference.distance.NeighborJoining;
@@ -2350,7 +2351,7 @@ public class TestPhylogenyReconstruction {
             }
             s0.addPairing( 2, 33, 0 );
             s0.addPairing( 2, 333, 0 );
-            final SortedSet<Integer>[] a = s0.toArray( 0 );
+            final Set<Integer>[] a = s0.toArray( 0 );
             if ( !a[ 0 ].contains( 1 ) ) {
                 return false;
             }
@@ -2522,6 +2523,7 @@ public class TestPhylogenyReconstruction {
                 return false;
             }
             //
+            System.exit(1);
             final BasicSymmetricalDistanceMatrix m3 = new BasicSymmetricalDistanceMatrix( 20 );
             m3.setIdentifier( 0, "F_MOUSE" );
             m3.setIdentifier( 1, "11_RAT" );

diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
index ef7e49b..2149f8a 100644 (file)
--- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
+++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
@@ -29,7 +29,7 @@ import java.text.DecimalFormat;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map.Entry;
-import java.util.SortedSet;
+import java.util.Set;
 
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 import org.forester.phylogeny.Phylogeny;
@@ -205,7 +205,7 @@ public final class NeighborJoiningR {
         _umax = -1000;
         for( int i = 0; i < _n; ++i ) {
             _r[ i ] = calculateNetDivergence( i );
-            if ( _r[i  ] > _umax ) {
+            if ( _r[ i ] > _umax ) {
                 _umax = _r[i ];
             }
         }
@@ -304,7 +304,7 @@ public final class NeighborJoiningR {
                 System.out.print( " " );
             }
             System.out.print( "\t\t" );
-            for( final Entry<Integer, SortedSet<Integer>> entry : _s.getSentrySet( _mappings[ j ] ) ) {
+            for( final Entry<Integer, Set<Integer>> entry : _s.getSentrySet( _mappings[ j ] ) ) {
                 System.out.print( DF.format( ( double ) entry.getKey() / S.FACTOR ) + "=" );
                 boolean first = true;
                 for( final int v : entry.getValue() ) {
@@ -329,22 +329,27 @@ public final class NeighborJoiningR {
         if ( _verbose ) {
             printM();
         }
-        for( int j = 1; j < _n; ++j ) {
+        J: for( int j = 1; j < _n; ++j ) {
             final double r_j = _r[ j ];
             final int m_j = _mappings[ j ];
             if ( _verbose ) {
                 System.out.print( "j=" + j + "  mj=" + m_j + ":  " );
             }
-            X: for( final Entry<Integer, SortedSet<Integer>> entry : _s.getSentrySet( m_j ) ) {
+            for( final Entry<Integer, Set<Integer>> entry : _s.getSentrySet( m_j ) ) {
                 for( final int sorted_i : entry.getValue() ) {
                     final double m = _d_values[ sorted_i ][ m_j ]
                             - ( ( _r[ _rev_mappings[ sorted_i ] ] + r_j ) / n_minus_2 );
                     //final double m = getDvalueUnmapped( sorted_i, m_j )
                     //        - ( ( _r[ _rev_mappings[ sorted_i ] ] + r_j ) / n_minus_2 );
                     
-                    if ( m  - r_j - _umax >  min_m  ) {
-                        System.out.println( m );
-                        continue X;
+                    System.out.println( "m=" + m );
+                    System.out.println( "r_j=" + r_j );
+                    System.out.println( "umax=" + _umax );
+                    System.out.println( "  =" + (  m  - r_j - _umax  ) );
+                    System.out.println( "  min_m=" + min_m );
+                    if ( ( m  - r_j - _umax ) >  min_m  ) {
+                        System.out.println(">>>>>>>>>>>>>>>>>>>>>>" +  m );
+                        continue J;
                     }
                     
                     
@@ -358,7 +363,7 @@ public final class NeighborJoiningR {
             }
             if ( _verbose ) {
                 System.out.println();
-                for( final Entry<Integer, SortedSet<Integer>> entry : _s.getSentrySet( m_j ) ) {
+                for( final Entry<Integer, Set<Integer>> entry : _s.getSentrySet( m_j ) ) {
                     for( final int sorted_i : entry.getValue() ) {
                         System.out.print( sorted_i );
                         System.out.print( "->" );

diff --git a/forester/java/src/org/forester/evoinference/distance/S.java b/forester/java/src/org/forester/evoinference/distance/S.java
index b510a61..2c3de8c 100644 (file)
--- a/forester/java/src/org/forester/evoinference/distance/S.java
+++ b/forester/java/src/org/forester/evoinference/distance/S.java
@@ -3,13 +3,13 @@ package org.forester.evoinference.distance;
 
 import java.text.DecimalFormat;
 import java.util.ArrayList;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map.Entry;
 import java.util.Set;
 import java.util.SortedMap;
 import java.util.SortedSet;
 import java.util.TreeMap;
-import java.util.TreeSet;
 
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 
@@ -17,10 +17,10 @@ public final class S {
 
     public final static int                                    FACTOR = 1000000;
     private final static boolean                               DEBUG  = true;
-    private final List<SortedMap<Integer, SortedSet<Integer>>> _data;
+    private final List<SortedMap<Integer, Set<Integer>>> _data;
 
     public S() {
-        _data = new ArrayList<SortedMap<Integer, SortedSet<Integer>>>();
+        _data = new ArrayList<SortedMap<Integer, Set<Integer>>>();
     }
 
     final public void addPairing( final double key, final int value, final int j ) {
@@ -31,17 +31,17 @@ public final class S {
         addPairing( key, value, getS( j ) );
     }
 
-    final public SortedMap<Integer, SortedSet<Integer>> getS( final int j ) {
+    final public SortedMap<Integer, Set<Integer>> getS( final int j ) {
         return _data.get( j );
     }
 
-    final public SortedSet<Integer> getValues( final int key, final int j ) {
+    final public Set<Integer> getValues( final int key, final int j ) {
         return getS( j ).get( key );
     }
 
     final public void initialize( final BasicSymmetricalDistanceMatrix d ) {
         for( int j = 0; j < d.getSize(); ++j ) {
-            final TreeMap<Integer, SortedSet<Integer>> map = new TreeMap<Integer, SortedSet<Integer>>();
+            final TreeMap<Integer, Set<Integer>> map = new TreeMap<Integer, Set<Integer>>();
             _data.add( map );
             for( int i = 0; i < j; ++i ) {
                 addPairing( ( int ) ( FACTOR * d.getValues()[ i ][ j ] ), i, map );
@@ -52,7 +52,7 @@ public final class S {
 
     final public void initialize( final int size ) {
         for( int j = 0; j < size; ++j ) {
-            final TreeMap<Integer, SortedSet<Integer>> map = new TreeMap<Integer, SortedSet<Integer>>();
+            final TreeMap<Integer, Set<Integer>> map = new TreeMap<Integer, Set<Integer>>();
             _data.add( map );
         }
     }
@@ -62,8 +62,8 @@ public final class S {
     }
 
     final public void removePairing( final int key, final int value, final int j ) {
-        final SortedMap<Integer, SortedSet<Integer>> m = _data.get( j );
-        final SortedSet<Integer> x = m.get( key );
+        final SortedMap<Integer, Set<Integer>> m = _data.get( j );
+        final Set<Integer> x = m.get( key );
         if ( DEBUG ) {
             if ( x == null ) {
                 System.out.println();
@@ -108,8 +108,8 @@ public final class S {
 
     // Slow, only for testing
     @SuppressWarnings( "unchecked")
-    final public SortedSet<Integer>[] toArray( final int j ) {
-        return _data.get( j ).values().toArray( new SortedSet[ _data.get( j ).size() ] );
+    final public Set<Integer>[] toArray( final int j ) {
+        return _data.get( j ).values().toArray( new Set[ _data.get( j ).size() ] );
     }
 
     @Override
@@ -119,9 +119,9 @@ public final class S {
         for( int j = 0; j < size(); ++j ) {
             sb.append( j );
             sb.append( ": " );
-            for( final Entry<Integer, SortedSet<Integer>> entry : getSentrySet( j ) ) {
+            for( final Entry<Integer, Set<Integer>> entry : getSentrySet( j ) ) {
                 final double key = entry.getKey();
-                final SortedSet<Integer> values = entry.getValue();
+                final Set<Integer> values = entry.getValue();
                 sb.append( df.format( key / FACTOR ) + "->" );
                 boolean first = true;
                 for( final int v : values ) {
@@ -138,13 +138,13 @@ public final class S {
         return sb.toString();
     }
 
-    final Set<Entry<Integer, SortedSet<Integer>>> getSentrySet( final int j ) {
+    final Set<Entry<Integer, Set<Integer>>> getSentrySet( final int j ) {
         return getS( j ).entrySet();
     }
 
-    final private static void addPairing( final int key, final int value, final SortedMap<Integer, SortedSet<Integer>> m ) {
+    final private static void addPairing( final int key, final int value, final SortedMap<Integer, Set<Integer>> m ) {
         if ( !m.containsKey( key ) ) {
-            final TreeSet<Integer> x = new TreeSet<Integer>();
+            final HashSet<Integer> x = new HashSet<Integer>();
             x.add( value );
             m.put( key, x );
         }