From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Sat, 8 Mar 2014 03:26:18 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8dbc83f2fcaa7e9cb0ebc88fa9205c8c385a6e08;p=jalview.git

inprogress
---

diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
index 7c78c5c..b525c29 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 {
-            final NeighborJoiningR nj = NeighborJoiningR.createInstance();
+            //            final NeighborJoiningR nj0 = NeighborJoiningR.createInstance();
             //            final BasicSymmetricalDistanceMatrix m0 = new BasicSymmetricalDistanceMatrix( 4 );
             //            m0.setIdentifier( 0, "A" );
             //            m0.setIdentifier( 1, "B" );
@@ -2239,7 +2239,7 @@ public class TestPhylogenyReconstruction {
             //            m0.setRow( "5 ", 1 );
             //            m0.setRow( "3 6 ", 2 );
             //            m0.setRow( "7.5 10.5 5.5", 3 );
-            //            final Phylogeny p0 = nj.execute( m0 );
+            //            final Phylogeny p0 = nj0.execute( m0 );
             //            p0.reRoot( p0.getNode( "D" ) );
             //            //  Archaeopteryx.createApplication( p0 );
             //            if ( isUnequal( p0.getNode( "A" ).getDistanceToParent(), 1 ) ) {
@@ -2272,8 +2272,8 @@ public class TestPhylogenyReconstruction {
             //            m.setIdentifier( 3, "D" );
             //            m.setIdentifier( 4, "E" );
             //            m.setIdentifier( 5, "F" );
-            //            nj = NeighborJoiningR.createInstance();
-            //            final Phylogeny p1 = nj.execute( m );
+            //            final NeighborJoiningR nj1 = NeighborJoiningR.createInstance();
+            //            final Phylogeny p1 = nj1.execute( m );
             //            p1.reRoot( p1.getNode( "F" ) );
             //            Archaeopteryx.createApplication( p1 );
             //            if ( isUnequal( p1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
@@ -2328,9 +2328,9 @@ 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 NeighborJoiningR njr = NeighborJoiningR.createInstance( true, 6 );
+            final NeighborJoiningR nj2 = NeighborJoiningR.createInstance( true, 6 );
             //nj = NeighborJoining.createInstance( true, 6 );
-            final Phylogeny p2 = njr.execute( m );
+            final Phylogeny p2 = nj2.execute( m );
             //  Archaeopteryx.createApplication( p2 );
             p2.reRoot( p2.getNode( "Bovine" ) );
             if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.151675 ) ) {
diff --git a/forester/java/src/org/forester/evoinference/distance/S.java b/forester/java/src/org/forester/evoinference/distance/S.java
index 6c84598..e1593f4 100644
--- a/forester/java/src/org/forester/evoinference/distance/S.java
+++ b/forester/java/src/org/forester/evoinference/distance/S.java
@@ -1,6 +1,7 @@
 
 package org.forester.evoinference.distance;
 
+import java.text.DecimalFormat;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map.Entry;
@@ -20,8 +21,32 @@ public class S {
         _data = new ArrayList<SortedMap<Double, SortedSet<Integer>>>();
     }
 
+    @Override
+    public String toString() {
+        final DecimalFormat df = new DecimalFormat( "0.00" );
+        final StringBuilder sb = new StringBuilder();
+        for( int j = 1; j < size(); ++j ) {
+            for( final Entry<Double, SortedSet<Integer>> entry : getSentrySet( j ) ) {
+                final double key = entry.getKey();
+                final SortedSet<Integer> values = entry.getValue();
+                sb.append( df.format( key ) + "->" );
+                boolean first = true;
+                for( final Integer v : values ) {
+                    if ( !first ) {
+                        sb.append( "," );
+                    }
+                    first = false;
+                    sb.append( v );
+                }
+                sb.append( "  " );
+            }
+            sb.append( "\n" );
+        }
+        return sb.toString();
+    }
+
     void addPairing( final double key, final int value, final int j ) {
-        final SortedMap<Double, SortedSet<Integer>> m = _data.get( j );
+        final SortedMap<Double, SortedSet<Integer>> m = getS( j );
         addPairing( key, value, m );
     }
 
@@ -30,7 +55,7 @@ public class S {
     }
 
     Set<Entry<Double, SortedSet<Integer>>> getSentrySet( final int j ) {
-        return _data.get( j ).entrySet();
+        return getS( j ).entrySet();
     }
 
     void initialize( final BasicSymmetricalDistanceMatrix d ) {
@@ -41,6 +66,7 @@ public class S {
                 addPairing( d.getValues()[ i ][ j ], i, map );
             }
         }
+        System.out.println( toString() );
     }
 
     void removePairing( final double key, final int value, final int j ) {
@@ -49,7 +75,7 @@ public class S {
         if ( x.size() == 1 ) {
             if ( !x.contains( value ) ) {
                 //TODO remove me later
-                throw new IllegalStateException( "!x.contains( value )" );
+                throw new IllegalStateException( "pairing " + key + " -> " + value + " does not exist" );
             }
             m.remove( key );
         }
@@ -57,7 +83,7 @@ public class S {
             final boolean removed = x.remove( value );
             if ( !removed ) {
                 //TODO remove me later
-                throw new IllegalStateException( value + " not found" );
+                throw new IllegalStateException( "pairing " + key + " -> " + value + " does not exist/was not removed" );
             }
         }
         else {
@@ -66,6 +92,10 @@ public class S {
         }
     }
 
+    int size() {
+        return _data.size();
+    }
+
     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>();