From 3dc1b0bab30025b34753df4325b60cb47ee5bdff Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Sat, 8 Mar 2014 02:49:03 +0000
Subject: [PATCH] inprogress

---
 .../evoinference/TestPhylogenyReconstruction.java  |    4 +--
 .../src/org/forester/evoinference/distance/S.java  |   35 +++++++++++++++++---
 2 files changed, 33 insertions(+), 6 deletions(-)

diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
index 44423b1..7c78c5c 100644
--- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
+++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
@@ -2230,7 +2230,7 @@ public class TestPhylogenyReconstruction {
 
     private static boolean testNeighborJoiningR() {
         try {
-            NeighborJoiningR nj = NeighborJoiningR.createInstance();
+            final NeighborJoiningR nj = NeighborJoiningR.createInstance();
             //            final BasicSymmetricalDistanceMatrix m0 = new BasicSymmetricalDistanceMatrix( 4 );
             //            m0.setIdentifier( 0, "A" );
             //            m0.setIdentifier( 1, "B" );
@@ -2328,7 +2328,7 @@ 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 );
-            NeighborJoiningR njr = NeighborJoiningR.createInstance( true, 6 );
+            final NeighborJoiningR njr = NeighborJoiningR.createInstance( true, 6 );
             //nj = NeighborJoining.createInstance( true, 6 );
             final Phylogeny p2 = njr.execute( m );
             //  Archaeopteryx.createApplication( p2 );
diff --git a/forester/java/src/org/forester/evoinference/distance/S.java b/forester/java/src/org/forester/evoinference/distance/S.java
index 1ea6f9b..6c84598 100644
--- a/forester/java/src/org/forester/evoinference/distance/S.java
+++ b/forester/java/src/org/forester/evoinference/distance/S.java
@@ -20,9 +20,9 @@ public class S {
         _data = new ArrayList<SortedMap<Double, SortedSet<Integer>>>();
     }
 
-    void addValue( final double key, final int value, final int j ) {
+    void addPairing( final double key, final int value, final int j ) {
         final SortedMap<Double, SortedSet<Integer>> m = _data.get( j );
-        addValue( key, value, m );
+        addPairing( key, value, m );
     }
 
     SortedMap<Double, SortedSet<Integer>> getS( final int j ) {
@@ -38,18 +38,45 @@ public class S {
             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 );
+                addPairing( d.getValues()[ i ][ j ], i, map );
             }
         }
     }
 
-    static void addValue( final double key, final int value, final SortedMap<Double, SortedSet<Integer>> m ) {
+    void removePairing( final double key, final int value, final int j ) {
+        final SortedMap<Double, SortedSet<Integer>> m = _data.get( j );
+        final SortedSet<Integer> x = m.get( key );
+        if ( x.size() == 1 ) {
+            if ( !x.contains( value ) ) {
+                //TODO remove me later
+                throw new IllegalStateException( "!x.contains( value )" );
+            }
+            m.remove( key );
+        }
+        else if ( x.size() > 1 ) {
+            final boolean removed = x.remove( value );
+            if ( !removed ) {
+                //TODO remove me later
+                throw new IllegalStateException( value + " not found" );
+            }
+        }
+        else {
+            //TODO remove me later
+            throw new IllegalStateException( "empty" );
+        }
+    }
+
+    private static void addPairing( final double key, final int value, final SortedMap<Double, SortedSet<Integer>> m ) {
         if ( !m.containsKey( key ) ) {
             final TreeSet<Integer> x = new TreeSet<Integer>();
             x.add( value );
             m.put( key, x );
         }
         else {
+            if ( m.get( key ).contains( value ) ) {
+                //TODO remove me later
+                throw new IllegalStateException( "pairing " + key + " -> " + value + " already exists" );
+            }
             m.get( key ).add( value );
         }
     }
-- 
1.7.10.2