inprogress

[jalview.git] / forester / java / src / org / forester / evoinference / distance / NeighborJoining.java

diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
index 3d28ab7..156d72e 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;
@@ -72,6 +73,7 @@ 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 ] ];
@@ -136,19 +138,24 @@ public final class NeighborJoining {
             if ( otu1 < i ) {
                 if ( otu2 > i ) {
                     _d_values[ m_otu1 ][ m_i ] = ( _d_values[ m_otu1 ][ m_i ] + _d_values[ m_i ][ m_otu2 ] - d ) / 2;
+                    //System.out.print( DF.format( _d_values[ m_otu1 ][ m_i ] ) );
                 }
                 else {
                     _d_values[ m_otu1 ][ m_i ] = ( _d_values[ m_otu1 ][ m_i ] + _d_values[ m_otu2 ][ m_i ] - d ) / 2;
+                    //System.out.print( DF.format( _d_values[ m_otu1 ][ m_i ] ) );
                 }
             }
             else {
                 if ( otu2 > i ) {
                     _d_values[ m_i ][ m_otu1 ] = ( _d_values[ m_i ][ m_otu1 ] + _d_values[ m_i ][ m_otu2 ] - d ) / 2;
+                    //System.out.print( DF.format( _d_values[ m_i ][ m_otu1 ] ) );
                 }
                 else {
                     _d_values[ m_i ][ m_otu1 ] = ( _d_values[ m_i ][ m_otu1 ] + _d_values[ m_otu2 ][ m_i ] - d ) / 2;
+                    // System.out.print( DF.format( _d_values[ m_otu1 ][ m_i ] ) );
                 }
             }
+            //System.out.print( " " );
         }
     }
 
@@ -192,10 +199,24 @@ 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.
@@ -227,6 +248,17 @@ 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.