inprogress

diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
index b9d2bb1..2fe3a4c 100644 (file)
--- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
+++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
@@ -2480,6 +2480,25 @@ public class TestPhylogenyReconstruction {
             m.setRow( "1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830", 4 );
             m.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 );
             m.setRow( "1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000", 6 );
+            final NeighborJoining nj = NeighborJoining.createInstance( true, 6 );
+            //nj = NeighborJoining.createInstance( true, 6 );
+            final Phylogeny pnj = nj.execute( m );
+            //
+            m = new BasicSymmetricalDistanceMatrix( 7 );
+            m.setIdentifier( 0, "Bovine" );
+            m.setIdentifier( 1, "Mouse" );
+            m.setIdentifier( 2, "Gibbon" );
+            m.setIdentifier( 3, "Orang" );
+            m.setIdentifier( 4, "Gorilla" );
+            m.setIdentifier( 5, "Chimp" );
+            m.setIdentifier( 6, "Human" );
+            m.setRow( "0.00000 1.68660 1.71980 1.66060 1.52430 1.60430 1.59050", 0 );
+            m.setRow( "1.68660 0.00000 1.52320 1.48410 1.44650 1.43890 1.46290", 1 );
+            m.setRow( "1.71980 1.52320 0.00000 0.71150 0.59580 0.61790 0.55830", 2 );
+            m.setRow( "1.66060 1.48410 0.71150 0.00000 0.46310 0.50610 0.47100", 3 );
+            m.setRow( "1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830", 4 );
+            m.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 );
+            m.setRow( "1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000", 6 );
             final NeighborJoiningR nj2 = NeighborJoiningR.createInstance( true, 6 );
             //nj = NeighborJoining.createInstance( true, 6 );
             final Phylogeny p2 = nj2.execute( m );
@@ -2895,6 +2914,15 @@ public class TestPhylogenyReconstruction {
     }
 
     private static void timeNeighborJoining() {
+        final NeighborJoiningR njr = NeighborJoiningR.createInstance();
+        for( int n = 3; n <= 9; ++n ) {
+            final int x = ( int ) Math.pow( 2, n );
+            final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x );
+            mt.randomize( new Date().getTime() );
+            final long start_time = new Date().getTime();
+            njr.execute( mt );
+            System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" );
+        }
         final NeighborJoiningF njf = NeighborJoiningF.createInstance();
         for( int n = 3; n <= 9; ++n ) {
             final int x = ( int ) Math.pow( 2, n );

diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
index 1bce7bc..14553ce 100644 (file)
--- a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
+++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
@@ -36,6 +36,7 @@ import org.forester.util.ForesterUtil;
 
 public final class NeighborJoining {
 
+    private final static DecimalFormat     DF = new DecimalFormat( "0.00000" );
     private BasicSymmetricalDistanceMatrix _d;
     private double[][]                     _d_values;
     private final DecimalFormat            _df;
@@ -242,12 +243,28 @@ public final class NeighborJoining {
                 }
             }
         }
+        for( int j = 1; j < _n; ++j ) {
+            final double r_j = _r[ j ];
+            final int m_j = _mappings[ j ];
+            for( int i = 0; i < j; ++i ) {
+                System.out.print( i );
+                System.out.print( "->" );
+                System.out.print( DF.format( _r[ i ] ) );
+                System.out.print( "  " );
+            }
+            System.out.println();
+        }
     }
 
     // otu2 will, in effect, be "deleted" from the matrix.
     private final void updateMappings( final int otu2 ) {
         for( int i = otu2; i < ( _mappings.length - 1 ); ++i ) {
+            System.out.print( _mappings[ i ] );
             _mappings[ i ] = _mappings[ i + 1 ];
+            System.out.println( "----->" + _mappings[ i ] );
+        }
+        for( int i = 0; i < _mappings.length; ++i ) {
+            System.out.println( i + "-->" + _mappings[ i ] );
         }
     }
 

diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
index bdc80be..0db013a 100644 (file)
--- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
+++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
@@ -81,10 +81,11 @@ public final class NeighborJoiningR {
             final int otu2 = _min_j;
             System.out.println( _min_i + " " + _min_j + " => " + DF.format( m ) + " (" + DF.format( _d_min ) + ")" );
             // It is a condition that otu1 < otu2.
-            System.out.println( "mapped 1 " + _mappings[ otu1 ] );
-            System.out.println( "mapped 2 " + _mappings[ otu2 ] );
+            //System.out.println( "mapped 1 " + _mappings[ otu1 ] );
+            System.out.println( "mapped otu 2 " + _mappings[ otu2 ] );
             final PhylogenyNode node = new PhylogenyNode();
-            final double d = getDvalueUnmapped( otu1, _mappings[ otu2 ] );
+            //final double d = getDvalueUnmapped( otu1, _mappings[ otu2 ] );
+            final double d = _d_values[ otu1 ][ _mappings[ otu2 ] ];
             final double d1 = ( d / 2 ) + ( ( _r[ otu1 ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) );
             final double d2 = d - d1;
             if ( _df == null ) {
@@ -104,7 +105,8 @@ public final class NeighborJoiningR {
             System.out.println( "otu1=" + otu1 );
             System.out.println( "otu2=" + otu2 );
             calculateDistancesFromNewNode( otu1, otu2, d );
-            _external_nodes[ _mappings[ otu1 ] ] = node;
+            // _external_nodes[ _mappings[ otu1 ] ] = node;
+            _external_nodes[ otu1 ] = node;
             updateMappings( otu2 );
             --_n;
             System.out.println( "" );
@@ -313,7 +315,7 @@ public final class NeighborJoiningR {
                     System.out.print( sorted_i + " " );
                     System.out.print( "(" + DF.format( getDvalueUnmapped( sorted_i, m_j ) ) + ") " );
                     final double m = getDvalueUnmapped( sorted_i, m_j ) - ( ( _r[ sorted_i ] + r_j ) / n_minus_2 );
-                    if ( ( m < min_m ) && ( sorted_i != j ) ) {
+                    if ( ( m < min_m ) ) {
                         _d_min = getDvalueUnmapped( sorted_i, m_j );
                         min_m = m;
                         _min_i = sorted_i;
@@ -322,6 +324,15 @@ public final class NeighborJoiningR {
                 }
             }
             System.out.println();
+            for( final Entry<Integer, SortedSet<Integer>> entry : _s.getSentrySet( m_j ) ) {
+                for( final int sorted_i : entry.getValue() ) {
+                    System.out.print( sorted_i );
+                    System.out.print( "->" );
+                    System.out.print( DF.format( _r[ sorted_i ] ) );
+                    System.out.print( "  " );
+                }
+            }
+            System.out.println();
             /*
             for( int i = 0; i < j; ++i ) {
                 final double m = getDvalue( i, j ) - ( ( _r[ i ] + r_j ) / n_minus_2 );

diff --git a/forester/java/src/org/forester/evoinference/distance/S.java b/forester/java/src/org/forester/evoinference/distance/S.java
index f1d94db..fe70cd6 100644 (file)
--- a/forester/java/src/org/forester/evoinference/distance/S.java
+++ b/forester/java/src/org/forester/evoinference/distance/S.java
@@ -73,20 +73,20 @@ public final class S {
                 throw new IllegalArgumentException( "key " + key + " (->" + value + ") does not exist for row " + j );
             }
         }
-        //        if ( x.size() == 1 ) {
-        //            if ( DEBUG ) {
-        //                if ( !x.contains( value ) ) {
-        //                    System.out.println();
-        //                    System.out
-        //                            .println( "________________________________________________________________________________________" );
-        //                    System.out.println( toString() );
-        //                    throw new IllegalArgumentException( "pairing " + key + "->" + value + " does not exist for row "
-        //                            + j );
-        //                }
-        //            }
-        //            m.remove( key );
-        //        }
-        else if ( x.size() >= 1 ) {
+        if ( x.size() == 1 ) {
+            if ( DEBUG ) {
+                if ( !x.contains( value ) ) {
+                    System.out.println();
+                    System.out
+                            .println( "________________________________________________________________________________________" );
+                    System.out.println( toString() );
+                    throw new IllegalArgumentException( "pairing " + key + "->" + value + " does not exist for row "
+                            + j );
+                }
+            }
+            m.remove( key );
+        }
+        else if ( x.size() > 1 ) {
             if ( DEBUG ) {
                 if ( !x.remove( value ) ) {
                     throw new IllegalArgumentException( "pairing " + key + "->" + value