inprogress

diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
index 534fe21..b9d2bb1 100644 (file)
--- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
+++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
@@ -2248,10 +2248,7 @@ public class TestPhylogenyReconstruction {
             final S s0 = new S();
             s0.initialize( 1 );
             s0.addPairing( 0, 1, 0 );
-            s0.addPairing( 7.0000001, 8, 0 );
-            s0.addPairing( 7.00000011, 9, 0 );
-            s0.addPairing( 7.000000111, 10, 0 );
-            s0.addPairing( 7.000000111, 101, 0 );
+            s0.addPairing( 7, 8, 0 );
             s0.addPairing( 4, 55, 0 );
             s0.addPairing( 2, 3, 0 );
             s0.addPairing( 4, 5, 0 );
@@ -2265,7 +2262,7 @@ public class TestPhylogenyReconstruction {
             if ( s0.size() != 1 ) {
                 return false;
             }
-            if ( s0.getS( 0 ).size() != 10 ) {
+            if ( s0.getS( 0 ).size() != 8 ) {
                 return false;
             }
             if ( s0.getValues( 0, 0 ).size() != 1 ) {
@@ -2289,13 +2286,7 @@ public class TestPhylogenyReconstruction {
             if ( s0.getValues( 6, 0 ).size() != 1 ) {
                 return false;
             }
-            if ( s0.getValues( 7.0000001, 0 ).size() != 1 ) {
-                return false;
-            }
-            if ( s0.getValues( 7.00000011, 0 ).size() != 1 ) {
-                return false;
-            }
-            if ( s0.getValues( 7.000000111, 0 ).size() != 2 ) {
+            if ( s0.getValues( 7, 0 ).size() != 1 ) {
                 return false;
             }
             if ( !s0.getValues( 0, 0 ).contains( 1 ) ) {
@@ -2328,15 +2319,15 @@ public class TestPhylogenyReconstruction {
             if ( s0.getValues( 5, 0 ).size() != 1 ) {
                 return false;
             }
-            if ( s0.getS( 0 ).size() != 10 ) {
+            if ( s0.getS( 0 ).size() != 8 ) {
                 return false;
             }
             s0.removePairing( 5, 6, 0 );
-            if ( s0.getS( 0 ).size() != 9 ) {
+            if ( s0.getS( 0 ).size() != 7 ) {
                 return false;
             }
             s0.addPairing( 5, 6, 0 );
-            if ( s0.getS( 0 ).size() != 10 ) {
+            if ( s0.getS( 0 ).size() != 8 ) {
                 return false;
             }
             if ( s0.getValues( 5, 0 ).size() != 1 ) {
@@ -2352,9 +2343,9 @@ public class TestPhylogenyReconstruction {
             if ( !s0.getValues( 5, 0 ).contains( 403 ) ) {
                 return false;
             }
-            s0.addPairing( 693.539324, 100, 0 );
-            s0.addPairing( 693.539324, 101, 0 );
-            if ( s0.getValues( 693.539324, 0 ).size() != 2 ) {
+            s0.addPairing( 693, 100, 0 );
+            s0.addPairing( 693, 101, 0 );
+            if ( s0.getValues( 693, 0 ).size() != 2 ) {
                 return false;
             }
             s0.addPairing( 2, 33, 0 );
@@ -2381,39 +2372,6 @@ public class TestPhylogenyReconstruction {
             if ( !a[ 2 ].contains( 333 ) ) {
                 return false;
             }
-            if ( a[ 2 ].size() != 3 ) {
-                return false;
-            }
-            if ( a[ 8 ].size() != 1 ) {
-                return false;
-            }
-            if ( !a[ 8 ].contains( 9 ) ) {
-                return false;
-            }
-            if ( a[ 9 ].size() != 2 ) {
-                return false;
-            }
-            if ( !a[ 9 ].contains( 10 ) ) {
-                return false;
-            }
-            if ( !a[ 9 ].contains( 101 ) ) {
-                return false;
-            }
-            if ( !a[ 10 ].contains( 100 ) ) {
-                return false;
-            }
-            if ( !a[ 10 ].contains( 101 ) ) {
-                return false;
-            }
-            if ( a[ 4 ].size() != 2 ) {
-                return false;
-            }
-            if ( !a[ 4 ].contains( 5 ) ) {
-                return false;
-            }
-            if ( !a[ 4 ].contains( 55 ) ) {
-                return false;
-            }
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );

diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
index 2a851b5..c71ad7d 100644 (file)
--- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
+++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
@@ -81,6 +81,9 @@ 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.
+            //for( int j = 0; j < _s.size(); ++j ) {
+            _s.removePairing( _d_min, _min_i, 1 );
+            // }
             final PhylogenyNode node = new PhylogenyNode();
             final double d = getDvalue( otu1, otu2 );
             final double d1 = ( d / 2 ) + ( ( _r[ otu1 ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) );
@@ -145,7 +148,9 @@ public final class NeighborJoiningR {
     }
 
     private final void updateDvalue( final int otu1, final int otu2, final int i, final double d ) {
-        setDvalue( otu1, i, ( getDvalue( otu1, i ) + getDvalue( i, otu2 ) - d ) / 2 );
+        final double new_d = ( getDvalue( otu1, i ) + getDvalue( i, otu2 ) - d ) / 2;
+        _s.addPairing( new_d, otu1, i );
+        setDvalue( otu1, i, new_d );
     }
 
     private void setDvalue( final int i, final int j, final double d ) {
@@ -247,10 +252,10 @@ public final class NeighborJoiningR {
                 System.out.print( " " );
             }
             System.out.print( "    " );
-            for( final Entry<Double, SortedSet<Integer>> entry : _s.getSentrySet( _mappings[ j ] ) ) {
+            for( final Entry<Integer, SortedSet<Integer>> entry : _s.getSentrySet( _mappings[ j ] ) ) {
                 final double key = entry.getKey();
                 final SortedSet<Integer> value = entry.getValue();
-                System.out.print( DF.format( key ) + "=" );
+                System.out.print( DF.format( key / S.FACTOR ) + "=" );
                 boolean first = true;
                 for( final Integer v : value ) {
                     if ( !first ) {
@@ -277,17 +282,17 @@ public final class NeighborJoiningR {
             final int m_j = _mappings[ j ];
             int counter = 0;
             int counter_all = 0;
-            X: for( final Entry<Double, SortedSet<Integer>> entry : _s.getSentrySet( m_j ) ) {
+            for( final Entry<Integer, 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 );
+                        System.out.print( "(" + DF.format( getDvalue( sorted_i, j ) ) + ") " );
+                        final double m = getDvalue( sorted_i, j ) - ( ( _r[ sorted_i ] + r_j ) / n_minus_2 );
+                        if ( ( m < min ) && ( sorted_i != j ) ) {
+                            _d_min = getDvalue( sorted_i, j );
                             min = m;
                             _min_i = sorted_i;
                             _min_j = j;

diff --git a/forester/java/src/org/forester/evoinference/distance/S.java b/forester/java/src/org/forester/evoinference/distance/S.java
index 8f3e994..842f59a 100644 (file)
--- a/forester/java/src/org/forester/evoinference/distance/S.java
+++ b/forester/java/src/org/forester/evoinference/distance/S.java
@@ -15,31 +15,36 @@ import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 
 public final class S {
 
-    private final static boolean                              DEBUG = true;
-    private final List<SortedMap<Double, SortedSet<Integer>>> _data;
+    public final static int                                    FACTOR = 1000000;
+    private final static boolean                               DEBUG  = true;
+    private final List<SortedMap<Integer, SortedSet<Integer>>> _data;
 
     public S() {
-        _data = new ArrayList<SortedMap<Double, SortedSet<Integer>>>();
+        _data = new ArrayList<SortedMap<Integer, SortedSet<Integer>>>();
     }
 
     final public void addPairing( final double key, final int value, final int j ) {
+        addPairing( ( int ) ( FACTOR * key ), value, getS( j ) );
+    }
+
+    final public void addPairing( final int key, final int value, final int j ) {
         addPairing( key, value, getS( j ) );
     }
 
-    final public SortedMap<Double, SortedSet<Integer>> getS( final int j ) {
+    final public SortedMap<Integer, SortedSet<Integer>> getS( final int j ) {
         return _data.get( j );
     }
 
-    final public SortedSet<Integer> getValues( final double key, final int j ) {
+    final public SortedSet<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<Double, SortedSet<Integer>> map = new TreeMap<Double, SortedSet<Integer>>();
+            final TreeMap<Integer, SortedSet<Integer>> map = new TreeMap<Integer, SortedSet<Integer>>();
             _data.add( map );
             for( int i = 0; i < j; ++i ) {
-                addPairing( d.getValues()[ i ][ j ], i, map );
+                addPairing( ( int ) ( FACTOR * d.getValues()[ i ][ j ] ), i, map );
             }
         }
         System.out.println( toString() );
@@ -47,18 +52,28 @@ public final class S {
 
     final public void initialize( final int size ) {
         for( int j = 0; j < size; ++j ) {
-            final TreeMap<Double, SortedSet<Integer>> map = new TreeMap<Double, SortedSet<Integer>>();
+            final TreeMap<Integer, SortedSet<Integer>> map = new TreeMap<Integer, SortedSet<Integer>>();
             _data.add( map );
         }
     }
 
     final public void removePairing( final double key, final int value, final int j ) {
-        final SortedMap<Double, SortedSet<Integer>> m = _data.get( j );
+        removePairing( ( int ) ( key * FACTOR ), value, j );
+    }
+
+    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 );
+        if ( DEBUG ) {
+            if ( x == null ) {
+                System.out.println( toString() );
+                throw new IllegalArgumentException( "key " + key + " (->" + value + ") does not exist for row " + j );
+            }
+        }
         if ( x.size() == 1 ) {
             if ( DEBUG ) {
                 if ( !x.contains( value ) ) {
-                    throw new IllegalArgumentException( "pairing " + key + " -> " + value + " does not exist for row "
+                    throw new IllegalArgumentException( "pairing " + key + "->" + value + " does not exist for row "
                             + j );
                 }
             }
@@ -67,7 +82,7 @@ public final class S {
         else if ( x.size() > 1 ) {
             if ( DEBUG ) {
                 if ( !x.remove( value ) ) {
-                    throw new IllegalArgumentException( "pairing " + key + " -> " + value
+                    throw new IllegalArgumentException( "pairing " + key + "->" + value
                             + " does not exist (could not be removed) for row " + j );
                 }
             }
@@ -95,12 +110,12 @@ public final class S {
         final DecimalFormat df = new DecimalFormat( "0.00" );
         final StringBuilder sb = new StringBuilder();
         for( int j = 0; j < size(); ++j ) {
-            for( final Entry<Double, SortedSet<Integer>> entry : getSentrySet( j ) ) {
+            for( final Entry<Integer, SortedSet<Integer>> entry : getSentrySet( j ) ) {
                 final double key = entry.getKey();
                 final SortedSet<Integer> values = entry.getValue();
-                sb.append( df.format( key ) + "->" );
+                sb.append( df.format( key / FACTOR ) + "->" );
                 boolean first = true;
-                for( final Integer v : values ) {
+                for( final int v : values ) {
                     if ( !first ) {
                         sb.append( "," );
                     }
@@ -114,13 +129,11 @@ public final class S {
         return sb.toString();
     }
 
-    final Set<Entry<Double, SortedSet<Integer>>> getSentrySet( final int j ) {
+    final Set<Entry<Integer, SortedSet<Integer>>> getSentrySet( final int j ) {
         return getS( j ).entrySet();
     }
 
-    final private static void addPairing( final double key,
-                                          final int value,
-                                          final SortedMap<Double, SortedSet<Integer>> m ) {
+    final private static void addPairing( final int key, final int value, final SortedMap<Integer, SortedSet<Integer>> m ) {
         if ( !m.containsKey( key ) ) {
             final TreeSet<Integer> x = new TreeSet<Integer>();
             x.add( value );
@@ -129,7 +142,7 @@ public final class S {
         else {
             if ( DEBUG ) {
                 if ( m.get( key ).contains( value ) ) {
-                    throw new IllegalArgumentException( "pairing " + key + " -> " + value + " already exists" );
+                    throw new IllegalArgumentException( "pairing " + key + "->" + value + " already exists" );
                 }
             }
             m.get( key ).add( value );