inprogress

diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
index 281861c..44423b1 100644 (file)
--- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
+++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
@@ -67,13 +67,13 @@ public class TestPhylogenyReconstruction {
     }
 
     public static void main( final String[] args ) {
-        System.out.println( "NJ" );
-        if ( testNeighborJoining() ) {
-            System.out.println( "  OK." );
-        }
-        else {
-            System.out.println( "  failed." );
-        }
+        //        System.out.println( "NJ" );
+        //        if ( testNeighborJoining() ) {
+        //            System.out.println( "  OK." );
+        //        }
+        //        else {
+        //            System.out.println( "  failed." );
+        //        }
         System.out.println( "NJR" );
         if ( testNeighborJoiningR() ) {
             System.out.println( "  OK." );
@@ -2055,8 +2055,10 @@ 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 );
-            nj = NeighborJoining.createInstance( false, 6 );
+            //NeighborJoiningR njr = NeighborJoiningR.createInstance( true, 6 );
+            nj = NeighborJoining.createInstance( true, 6 );
             final Phylogeny p2 = nj.execute( m );
+            //  Archaeopteryx.createApplication( p2 );
             p2.reRoot( p2.getNode( "Bovine" ) );
             if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.151675 ) ) {
                 return false;
@@ -2229,83 +2231,147 @@ public class TestPhylogenyReconstruction {
     private static boolean testNeighborJoiningR() {
         try {
             NeighborJoiningR nj = NeighborJoiningR.createInstance();
-            final BasicSymmetricalDistanceMatrix m0 = new BasicSymmetricalDistanceMatrix( 4 );
-            m0.setIdentifier( 0, "A" );
-            m0.setIdentifier( 1, "B" );
-            m0.setIdentifier( 2, "C" );
-            m0.setIdentifier( 3, "D" );
-            m0.setRow( "5 ", 1 );
-            m0.setRow( "3 6 ", 2 );
-            m0.setRow( "7.5 10.5 5.5", 3 );
-            final Phylogeny p0 = nj.execute( m0 );
-            p0.reRoot( p0.getNode( "D" ) );
-            if ( isUnequal( p0.getNode( "A" ).getDistanceToParent(), 1 ) ) {
-                return false;
-            }
-            if ( isUnequal( p0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
-                return false;
-            }
-            if ( isUnequal( p0.getNode( "C" ).getDistanceToParent(), 0.5 ) ) {
-                return false;
-            }
-            if ( isUnequal( p0.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
-                return false;
-            }
-            if ( isUnequal( p0.getNode( "A" ).getParent().getDistanceToParent(), 1.5 ) ) {
-                return false;
-            }
-            if ( isUnequal( p0.getNode( "A" ).getParent().getParent().getDistanceToParent(), 2.5 ) ) {
+            //            final BasicSymmetricalDistanceMatrix m0 = new BasicSymmetricalDistanceMatrix( 4 );
+            //            m0.setIdentifier( 0, "A" );
+            //            m0.setIdentifier( 1, "B" );
+            //            m0.setIdentifier( 2, "C" );
+            //            m0.setIdentifier( 3, "D" );
+            //            m0.setRow( "5 ", 1 );
+            //            m0.setRow( "3 6 ", 2 );
+            //            m0.setRow( "7.5 10.5 5.5", 3 );
+            //            final Phylogeny p0 = nj.execute( m0 );
+            //            p0.reRoot( p0.getNode( "D" ) );
+            //            //  Archaeopteryx.createApplication( p0 );
+            //            if ( isUnequal( p0.getNode( "A" ).getDistanceToParent(), 1 ) ) {
+            //                return false;
+            //            }
+            //            if ( isUnequal( p0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
+            //                return false;
+            //            }
+            //            if ( isUnequal( p0.getNode( "C" ).getDistanceToParent(), 0.5 ) ) {
+            //                return false;
+            //            }
+            //            if ( isUnequal( p0.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
+            //                return false;
+            //            }
+            //            if ( isUnequal( p0.getNode( "A" ).getParent().getDistanceToParent(), 1.5 ) ) {
+            //                return false;
+            //            }
+            //            if ( isUnequal( p0.getNode( "A" ).getParent().getParent().getDistanceToParent(), 2.5 ) ) {
+            //                return false;
+            //            }
+            BasicSymmetricalDistanceMatrix m = new BasicSymmetricalDistanceMatrix( 6 );
+            //            m.setRow( "5", 1 );
+            //            m.setRow( "4 7", 2 );
+            //            m.setRow( "7 10 7", 3 );
+            //            m.setRow( "6 9 6 5", 4 );
+            //            m.setRow( "8 11 8 9 8", 5 );
+            //            m.setIdentifier( 0, "A" );
+            //            m.setIdentifier( 1, "B" );
+            //            m.setIdentifier( 2, "C" );
+            //            m.setIdentifier( 3, "D" );
+            //            m.setIdentifier( 4, "E" );
+            //            m.setIdentifier( 5, "F" );
+            //            nj = NeighborJoiningR.createInstance();
+            //            final Phylogeny p1 = nj.execute( m );
+            //            p1.reRoot( p1.getNode( "F" ) );
+            //            Archaeopteryx.createApplication( p1 );
+            //            if ( isUnequal( p1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
+            //                return false;
+            //            }
+            //            if ( isUnequal( p1.getNode( "B" ).getDistanceToParent(), 4 ) ) {
+            //                return false;
+            //            }
+            //            if ( isUnequal( p1.getNode( "C" ).getDistanceToParent(), 2 ) ) {
+            //                return false;
+            //            }
+            //            if ( isUnequal( p1.getNode( "D" ).getDistanceToParent(), 3 ) ) {
+            //                return false;
+            //            }
+            //            if ( isUnequal( p1.getNode( "E" ).getDistanceToParent(), 2 ) ) {
+            //                return false;
+            //            }
+            //            if ( isUnequal( p1.getNode( "F" ).getDistanceToParent(), 2.5 ) ) {
+            //                return false;
+            //            }
+            //            if ( isUnequal( p1.getNode( "A" ).getParent().getDistanceToParent(), 1 ) ) {
+            //                return false;
+            //            }
+            //            if ( isUnequal( p1.getNode( "A" ).getParent().getParent().getDistanceToParent(), 1 ) ) {
+            //                return false;
+            //            }
+            //            if ( isUnequal( p1.getNode( "A" ).getParent().getParent().getParent().getDistanceToParent(), 2.5 ) ) {
+            //                return false;
+            //            }
+            //            if ( isUnequal( p1.getNode( "B" ).getParent().getDistanceToParent(), 1 ) ) {
+            //                return false;
+            //            }
+            //            if ( isUnequal( p1.getNode( "D" ).getParent().getDistanceToParent(), 1 ) ) {
+            //                return false;
+            //            }
+            //            if ( isUnequal( p1.getNode( "E" ).getParent().getDistanceToParent(), 1 ) ) {
+            //                return false;
+            //            }
+            ///////////////
+            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 );
+            NeighborJoiningR njr = NeighborJoiningR.createInstance( true, 6 );
+            //nj = NeighborJoining.createInstance( true, 6 );
+            final Phylogeny p2 = njr.execute( m );
+            //  Archaeopteryx.createApplication( p2 );
+            p2.reRoot( p2.getNode( "Bovine" ) );
+            if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.151675 ) ) {
                 return false;
             }
-            BasicSymmetricalDistanceMatrix m = new BasicSymmetricalDistanceMatrix( 6 );
-            m.setRow( "5", 1 );
-            m.setRow( "4 7", 2 );
-            m.setRow( "7 10 7", 3 );
-            m.setRow( "6 9 6 5", 4 );
-            m.setRow( "8 11 8 9 8", 5 );
-            m.setIdentifier( 0, "A" );
-            m.setIdentifier( 1, "B" );
-            m.setIdentifier( 2, "C" );
-            m.setIdentifier( 3, "D" );
-            m.setIdentifier( 4, "E" );
-            m.setIdentifier( 5, "F" );
-            nj = NeighborJoiningR.createInstance();
-            final Phylogeny p1 = nj.execute( m );
-            p1.reRoot( p1.getNode( "F" ) );
-            if ( isUnequal( p1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
+            if ( isUnequal( p2.getNode( "Human" ).getDistanceToParent(), 0.117525 ) ) {
                 return false;
             }
-            if ( isUnequal( p1.getNode( "B" ).getDistanceToParent(), 4 ) ) {
+            if ( isUnequal( p2.getNode( "Gorilla" ).getDistanceToParent(), 0.153932 ) ) {
                 return false;
             }
-            if ( isUnequal( p1.getNode( "C" ).getDistanceToParent(), 2 ) ) {
+            if ( isUnequal( p2.getNode( "Orang" ).getDistanceToParent(), 0.284694 ) ) {
                 return false;
             }
-            if ( isUnequal( p1.getNode( "D" ).getDistanceToParent(), 3 ) ) {
+            if ( isUnequal( p2.getNode( "Gibbon" ).getDistanceToParent(), 0.357931 ) ) {
                 return false;
             }
-            if ( isUnequal( p1.getNode( "E" ).getDistanceToParent(), 2 ) ) {
+            if ( isUnequal( p2.getNode( "Mouse" ).getDistanceToParent(), 0.76891 ) ) {
                 return false;
             }
-            if ( isUnequal( p1.getNode( "F" ).getDistanceToParent(), 2.5 ) ) {
+            if ( isUnequal( p2.getNode( "Bovine" ).getDistanceToParent(), 0.458845 ) ) {
                 return false;
             }
-            if ( isUnequal( p1.getNode( "A" ).getParent().getDistanceToParent(), 1 ) ) {
+            if ( isUnequal( p2.getNode( "Chimp" ).getParent().getDistanceToParent(), 0.039819 ) ) {
                 return false;
             }
-            if ( isUnequal( p1.getNode( "A" ).getParent().getParent().getDistanceToParent(), 1 ) ) {
+            if ( isUnequal( p2.getNode( "Human" ).getParent().getDistanceToParent(), 0.039819 ) ) {
                 return false;
             }
-            if ( isUnequal( p1.getNode( "A" ).getParent().getParent().getParent().getDistanceToParent(), 2.5 ) ) {
+            if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getDistanceToParent(), 0.026956 ) ) {
                 return false;
             }
-            if ( isUnequal( p1.getNode( "B" ).getParent().getDistanceToParent(), 1 ) ) {
+            if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getDistanceToParent(), 0.046481 ) ) {
                 return false;
             }
-            if ( isUnequal( p1.getNode( "D" ).getParent().getDistanceToParent(), 1 ) ) {
+            if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getDistanceToParent(),
+                            0.420269 ) ) {
                 return false;
             }
-            if ( isUnequal( p1.getNode( "E" ).getParent().getDistanceToParent(), 1 ) ) {
+            if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent()
+                    .getDistanceToParent(), 0.458845 ) ) {
                 return false;
             }
         }

diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
index 3d28ab7..1bce7bc 100644 (file)
--- a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
+++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
@@ -72,6 +72,7 @@ public final class NeighborJoining {
             updateM();
             final int otu1 = _min_i;
             final int otu2 = _min_j;
+            System.out.println( _min_i + " " + _min_j );
             // It is a condition that otu1 < otu2.
             final PhylogenyNode node = new PhylogenyNode();
             final double d = _d_values[ _mappings[ otu1 ] ][ _mappings[ otu2 ] ];
@@ -192,10 +193,24 @@ public final class NeighborJoining {
     }
 
     private final void printProgress( final int otu1, final int otu2 ) {
-        final PhylogenyNode n1 = getExternalPhylogenyNode( otu1 );
-        final PhylogenyNode n2 = getExternalPhylogenyNode( otu2 );
-        System.out.println( "Node " + ( ForesterUtil.isEmpty( n1.getName() ) ? n1.getId() : n1.getName() ) + " joins "
-                + ( ForesterUtil.isEmpty( n2.getName() ) ? n2.getId() : n2.getName() ) );
+        System.out.println( "Node " + printProgressNodeToString( getExternalPhylogenyNode( otu1 ) ) + " joins "
+                + ( printProgressNodeToString( getExternalPhylogenyNode( otu2 ) ) ) );
+    }
+
+    private final String printProgressNodeToString( final PhylogenyNode n ) {
+        if ( n.isExternal() ) {
+            if ( ForesterUtil.isEmpty( n.getName() ) ) {
+                return Long.toString( n.getId() );
+            }
+            return n.getName();
+        }
+        return n.getId()
+                + " ("
+                + ( ForesterUtil.isEmpty( n.getChildNode1().getName() ) ? n.getChildNode1().getId() : n.getChildNode1()
+                        .getName() )
+                + "+"
+                + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2()
+                        .getName() ) + ")";
     }
 
     // only the values in the lower triangle are used.

diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java
index fc39735..a696a38 100644 (file)
--- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java
+++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java
@@ -192,10 +192,24 @@ public final class NeighborJoiningF {
     }
 
     private final void printProgress( final int otu1, final int otu2 ) {
-        final PhylogenyNode n1 = getExternalPhylogenyNode( otu1 );
-        final PhylogenyNode n2 = getExternalPhylogenyNode( otu2 );
-        System.out.println( "Node " + ( ForesterUtil.isEmpty( n1.getName() ) ? n1.getId() : n1.getName() ) + " joins "
-                + ( ForesterUtil.isEmpty( n2.getName() ) ? n2.getId() : n2.getName() ) );
+        System.out.println( "Node " + printProgressNodeToString( getExternalPhylogenyNode( otu1 ) ) + " joins "
+                + ( printProgressNodeToString( getExternalPhylogenyNode( otu2 ) ) ) );
+    }
+
+    private final String printProgressNodeToString( final PhylogenyNode n ) {
+        if ( n.isExternal() ) {
+            if ( ForesterUtil.isEmpty( n.getName() ) ) {
+                return Long.toString( n.getId() );
+            }
+            return n.getName();
+        }
+        return n.getId()
+                + " ("
+                + ( ForesterUtil.isEmpty( n.getChildNode1().getName() ) ? n.getChildNode1().getId() : n.getChildNode1()
+                        .getName() )
+                + "+"
+                + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2()
+                        .getName() ) + ")";
     }
 
     // only the values in the lower triangle are used.

diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
index cfcd024..2a851b5 100644 (file)
--- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
+++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
@@ -29,10 +29,7 @@ import java.text.DecimalFormat;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map.Entry;
-import java.util.SortedMap;
 import java.util.SortedSet;
-import java.util.TreeMap;
-import java.util.TreeSet;
 
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 import org.forester.phylogeny.Phylogeny;
@@ -41,17 +38,19 @@ import org.forester.util.ForesterUtil;
 
 public final class NeighborJoiningR {
 
-    private BasicSymmetricalDistanceMatrix              _d;
-    private double[][]                                  _d_values;
-    private final DecimalFormat                         _df;
-    private PhylogenyNode[]                             _external_nodes;
-    private int[]                                       _mappings;
-    private int                                         _n;
-    private double[]                                    _r;
-    private final boolean                               _verbose;
-    private int                                         _min_i;
-    private int                                         _min_j;
-    private List<SortedMap<Double, SortedSet<Integer>>> _s;
+    private final static DecimalFormat     DF = new DecimalFormat( "0.00" );
+    private BasicSymmetricalDistanceMatrix _d;
+    private double[][]                     _d_values;
+    private final DecimalFormat            _df;
+    private PhylogenyNode[]                _external_nodes;
+    private int[]                          _mappings;
+    private int                            _n;
+    private double[]                       _r;
+    private final boolean                  _verbose;
+    private int                            _min_i;
+    private int                            _min_j;
+    private S                              _s;
+    private double                         _d_min;                          //TODO remove me
 
     private NeighborJoiningR() {
         _verbose = false;
@@ -73,11 +72,14 @@ public final class NeighborJoiningR {
         reset( distance );
         final Phylogeny phylogeny = new Phylogeny();
         while ( _n > 2 ) {
+            System.out.println( "N=" + _n );
+            System.out.println();
             // Calculates the minimal distance.
             // If more than one minimal distances, always the first found is used
-            updateM();
+            final double m = updateM();
             final int otu1 = _min_i;
             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.
             final PhylogenyNode node = new PhylogenyNode();
             final double d = getDvalue( otu1, otu2 );
@@ -101,6 +103,8 @@ public final class NeighborJoiningR {
             _external_nodes[ _mappings[ otu1 ] ] = node;
             updateMappings( otu2 );
             --_n;
+            System.out.println( "-------------------------------------------------------------" );
+            System.out.println( "" );
         }
         final double d = getDvalue( 0, 1 ) / 2;
         if ( _df == null ) {
@@ -158,6 +162,13 @@ public final class NeighborJoiningR {
         return _d_values[ _mappings[ j ] ][ _mappings[ i ] ];
     }
 
+    private double getDvalueUnmapped( final int i, final int j ) {
+        if ( i < j ) {
+            return _d_values[ i ][ j ];
+        }
+        return _d_values[ j ][ i ];
+    }
+
     private final void calculateNetDivergences() {
         for( int i = 0; i < _n; ++i ) {
             _r[ i ] = calculateNetDivergence( i );
@@ -195,10 +206,24 @@ public final class NeighborJoiningR {
     }
 
     private final void printProgress( final int otu1, final int otu2 ) {
-        final PhylogenyNode n1 = getExternalPhylogenyNode( otu1 );
-        final PhylogenyNode n2 = getExternalPhylogenyNode( otu2 );
-        System.out.println( "Node " + ( ForesterUtil.isEmpty( n1.getName() ) ? n1.getId() : n1.getName() ) + " joins "
-                + ( ForesterUtil.isEmpty( n2.getName() ) ? n2.getId() : n2.getName() ) );
+        System.out.println( "Node " + printProgressNodeToString( getExternalPhylogenyNode( otu1 ) ) + " joins "
+                + ( printProgressNodeToString( getExternalPhylogenyNode( otu2 ) ) ) );
+    }
+
+    private final String printProgressNodeToString( final PhylogenyNode n ) {
+        if ( n.isExternal() ) {
+            if ( ForesterUtil.isEmpty( n.getName() ) ) {
+                return Long.toString( n.getId() );
+            }
+            return n.getName();
+        }
+        return n.getId()
+                + " ("
+                + ( ForesterUtil.isEmpty( n.getChildNode1().getName() ) ? n.getChildNode1().getId() : n.getChildNode1()
+                        .getName() )
+                + "+"
+                + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2()
+                        .getName() ) + ")";
     }
 
     // only the values in the lower triangle are used.
@@ -209,17 +234,8 @@ public final class NeighborJoiningR {
         _r = new double[ _n ];
         _mappings = new int[ _n ];
         _d_values = _d.getValues();
-        _s = new ArrayList<SortedMap<Double, SortedSet<Integer>>>();
-        for( int j = 0; j < _n; ++j ) {
-            final TreeMap<Double, SortedSet<Integer>> map = new TreeMap<Double, SortedSet<Integer>>();
-            for( int i = 0; i < j; ++i ) {
-                if ( !map.containsKey( _d_values[ i ][ j ] ) ) {
-                    map.put( _d_values[ i ][ j ], new TreeSet<Integer>() );
-                }
-                map.get( _d_values[ i ][ j ] ).add( i );
-            }
-            _s.add( map );
-        }
+        _s = new S();
+        _s.initialize( distances );
         initExternalNodes();
         printM();
     }
@@ -227,14 +243,14 @@ public final class NeighborJoiningR {
     final private void printM() {
         for( int j = 1; j < _n; ++j ) {
             for( int i = 0; i < _n; ++i ) {
-                System.out.print( _d_values[ i ][ j ] );
+                System.out.print( DF.format( _d_values[ _mappings[ i ] ][ _mappings[ j ] ] ) );
                 System.out.print( " " );
             }
             System.out.print( "    " );
-            for( final Entry<Double, SortedSet<Integer>> entry : _s.get( j ).entrySet() ) {
+            for( final Entry<Double, SortedSet<Integer>> entry : _s.getSentrySet( _mappings[ j ] ) ) {
                 final double key = entry.getKey();
                 final SortedSet<Integer> value = entry.getValue();
-                System.out.print( key + "=" );
+                System.out.print( DF.format( key ) + "=" );
                 boolean first = true;
                 for( final Integer v : value ) {
                     if ( !first ) {
@@ -249,7 +265,8 @@ public final class NeighborJoiningR {
         }
     }
 
-    private final void updateM() {
+    private final double updateM() {
+        printM();
         calculateNetDivergences();
         Double min = Double.MAX_VALUE;
         _min_i = -1;
@@ -258,31 +275,42 @@ public final class NeighborJoiningR {
         for( int j = 1; j < _n; ++j ) {
             final double r_j = _r[ j ];
             final int m_j = _mappings[ j ];
-            final SortedMap<Double, SortedSet<Integer>> s_j = _s.get( m_j );
-            for( final Entry<Double, SortedSet<Integer>> entry : s_j.entrySet() ) {
-                //Double key = entry.getKey();
-                final SortedSet<Integer> value = entry.getValue();
-                for( final Integer sorted_i : value ) {
-                    System.out.print( sorted_i + " " );
-                    //                    final double m = _d_values[ _mappings[ sorted_i ] ][ m_j ]
-                    //                            - ( ( _r[ sorted_i ] + r_j ) / n_minus_2 );
-                    //                    if ( m < min ) {
-                    //                        min = m;
-                    //                        _min_i = sorted_i;
-                    //                        _min_j = j;
-                    //                    }
+            int counter = 0;
+            int counter_all = 0;
+            X: for( final Entry<Double, SortedSet<Integer>> entry : _s.getSentrySet( m_j ) ) {
+                for( final int sorted_i : entry.getValue() ) {
+                    //if ( counter_all >= j ) {
+                    //    break X;
+                    //}
+                    if ( _mappings[ counter ] == counter_all ) {
+                        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 ) {
+                            _d_min = getDvalueUnmapped( sorted_i, m_j );
+                            min = m;
+                            _min_i = sorted_i;
+                            _min_j = j;
+                        }
+                        ++counter;
+                    }
+                    ++counter_all;
                 }
             }
             System.out.println();
+            /*
             for( int i = 0; i < j; ++i ) {
                 final double m = getDvalue( i, j ) - ( ( _r[ i ] + r_j ) / n_minus_2 );
                 if ( m < min ) {
                     min = m;
+                    _d_min = getDvalue( i, j );
                     _min_i = i;
                     _min_j = j;
                 }
-            }
+            }*/
         }
+        System.out.println();
+        return min;
     }
 
     // otu2 will, in effect, be "deleted" from the matrix.

diff --git a/forester/java/src/org/forester/evoinference/distance/S.java b/forester/java/src/org/forester/evoinference/distance/S.java
new file mode 100644 (file)
index 0000000..4452ba3
--- /dev/null
+++ b/forester/java/src/org/forester/evoinference/distance/S.java
@@ -0,0 +1,56 @@
+
+package org.forester.evoinference.distance;
+
+import java.util.ArrayList;
+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;
+
+public class S {
+
+    private final List<SortedMap<Double, SortedSet<Integer>>> _data;
+
+    S() {
+        _data = new ArrayList<SortedMap<Double, SortedSet<Integer>>>();
+    }
+
+    void initialize( final BasicSymmetricalDistanceMatrix d ) {
+        for( int j = 0; j < d.getSize(); ++j ) {
+            final TreeMap<Double, SortedSet<Integer>> map = new TreeMap<Double, SortedSet<Integer>>();
+            _data.add( map );
+            for( int i = 0; i < j; ++i ) {
+                addValue( d.getValues()[ i ][ j ], i, map );
+            }
+        }
+    }
+
+    SortedMap<Double, SortedSet<Integer>> getS( final int j ) {
+        return _data.get( j );
+    }
+
+    Set<Entry<Double, SortedSet<Integer>>> getSentrySet( final int j ) {
+        return _data.get( j ).entrySet();
+    }
+
+    void addValue( double key, int value, int j ) {
+        SortedMap<Double, SortedSet<Integer>> m = _data.get( j );
+        addValue( key, value, m );
+    }
+
+    static void addValue( double key, int value, SortedMap<Double, SortedSet<Integer>> m ) {
+        if ( !m.containsKey( key ) ) {
+            TreeSet<Integer> x = new TreeSet<Integer>();
+            x.add( value );
+            m.put( key, x );
+        }
+        else {
+            m.get( key ).add( value );
+        }
+    }
+}