From: cmzmasek@gmail.com Date: Tue, 11 Mar 2014 20:42:35 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d1b2792049bf212f8a1898ddf7e552ab800d4397;p=jalview.git inprogress --- diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java index c71ad7d..6ebcbbf 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java @@ -38,7 +38,7 @@ import org.forester.util.ForesterUtil; public final class NeighborJoiningR { - private final static DecimalFormat DF = new DecimalFormat( "0.00" ); + private final static DecimalFormat DF = new DecimalFormat( "0.00000" ); private BasicSymmetricalDistanceMatrix _d; private double[][] _d_values; private final DecimalFormat _df; @@ -50,7 +50,7 @@ public final class NeighborJoiningR { private int _min_i; private int _min_j; private S _s; - private double _d_min; //TODO remove me + private double _d_min; //TODO remove me private NeighborJoiningR() { _verbose = false; @@ -81,9 +81,6 @@ 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 ) ) ); @@ -100,13 +97,16 @@ public final class NeighborJoiningR { node.addAsChild( getExternalPhylogenyNode( otu1 ) ); node.addAsChild( getExternalPhylogenyNode( otu2 ) ); if ( _verbose ) { - printProgress( otu1, otu2 ); + printProgress( otu1, otu2, node ); } + System.out.println( "otu1=" + otu1 ); + System.out.println( "otu2=" + otu2 ); calculateDistancesFromNewNode( otu1, otu2, d ); _external_nodes[ _mappings[ otu1 ] ] = node; updateMappings( otu2 ); --_n; - System.out.println( "-------------------------------------------------------------" ); + System.out.println( "" ); + System.out.println( "----------------------------------------------------------------------------------" ); System.out.println( "" ); } final double d = getDvalue( 0, 1 ) / 2; @@ -123,7 +123,7 @@ public final class NeighborJoiningR { root.addAsChild( getExternalPhylogenyNode( 0 ) ); root.addAsChild( getExternalPhylogenyNode( 1 ) ); if ( _verbose ) { - printProgress( 0, 1 ); + printProgress( 0, 1, root ); } phylogeny.setRoot( root ); phylogeny.setRooted( false ); @@ -139,18 +139,25 @@ public final class NeighborJoiningR { } private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) { - for( int i = 0; i < _n; ++i ) { - if ( ( i == otu1 ) || ( i == otu2 ) ) { + System.out.print( "new D values: " ); + for( int j = 0; j < _n; ++j ) { + if ( ( j == otu1 ) || ( j == otu2 ) ) { continue; } - updateDvalue( otu1, otu2, i, d ); + updateDvalue( otu1, otu2, j, d ); } + System.out.println(); } - private final void updateDvalue( final int otu1, final int otu2, final int i, final double d ) { - final double new_d = ( getDvalue( otu1, i ) + getDvalue( i, otu2 ) - d ) / 2; - _s.addPairing( new_d, otu1, i ); - setDvalue( otu1, i, new_d ); + private final void updateDvalue( final int otu1, final int otu2, final int j, final double d ) { + final double new_d = ( getDvalue( otu1, j ) + getDvalue( j, otu2 ) - d ) / 2; + System.out.print( DF.format( new_d ) + " " ); + System.out.println( "going to remove: " + getDvalue( otu1, j ) + ", " + otu1 + ", " + _mappings[ j ] ); + _s.removePairing( getDvalue( otu1, j ), _mappings[ otu1 ], _mappings[ j ] ); + System.out.println( "going to remove: " + getDvalue( j, otu2 ) + ", " + otu2 + ", " + _mappings[ j ] ); + _s.removePairing( getDvalue( j, otu2 ), _mappings[ otu2 ], _mappings[ j ] ); + _s.addPairing( new_d, otu1, _mappings[ j ] ); + setDvalue( otu1, j, new_d ); } private void setDvalue( final int i, final int j, final double d ) { @@ -210,9 +217,10 @@ public final class NeighborJoiningR { } } - private final void printProgress( final int otu1, final int otu2 ) { + private final void printProgress( final int otu1, final int otu2, final PhylogenyNode node ) { System.out.println( "Node " + printProgressNodeToString( getExternalPhylogenyNode( otu1 ) ) + " joins " - + ( printProgressNodeToString( getExternalPhylogenyNode( otu2 ) ) ) ); + + ( printProgressNodeToString( getExternalPhylogenyNode( otu2 ) ) ) + " [resulting in node " + + ( printProgressNodeToString( node ) ) + "]" ); } private final String printProgressNodeToString( final PhylogenyNode n ) { @@ -242,22 +250,26 @@ public final class NeighborJoiningR { _s = new S(); _s.initialize( distances ); initExternalNodes(); + System.out.println(); printM(); + System.out.println( "----------------------------------------------------------------------------------" ); + System.out.println(); + System.out.println(); } final private void printM() { - for( int j = 1; j < _n; ++j ) { + for( int j = 0; j < _n; ++j ) { + System.out.print( getExternalPhylogenyNode( j ) ); + System.out.print( "\t\t" ); for( int i = 0; i < _n; ++i ) { System.out.print( DF.format( _d_values[ _mappings[ i ] ][ _mappings[ j ] ] ) ); System.out.print( " " ); } - System.out.print( " " ); + System.out.print( "\t\t" ); for( final Entry> entry : _s.getSentrySet( _mappings[ j ] ) ) { - final double key = entry.getKey(); - final SortedSet value = entry.getValue(); - System.out.print( DF.format( key / S.FACTOR ) + "=" ); + System.out.print( DF.format( ( double ) entry.getKey() / S.FACTOR ) + "=" ); boolean first = true; - for( final Integer v : value ) { + for( final int v : entry.getValue() ) { if ( !first ) { System.out.print( "," ); } @@ -271,35 +283,26 @@ public final class NeighborJoiningR { } private final double updateM() { - printM(); calculateNetDivergences(); Double min = Double.MAX_VALUE; _min_i = -1; _min_j = -1; final int n_minus_2 = _n - 2; + printM(); for( int j = 1; j < _n; ++j ) { final double r_j = _r[ j ]; final int m_j = _mappings[ j ]; - int counter = 0; - int counter_all = 0; for( final Entry> 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( 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; - } - ++counter; + System.out.print( sorted_i + " " ); + System.out.print( "(" + DF.format( getDvalueUnmapped( sorted_i, m_j ) ) + ") " ); + final double m = getDvalue( sorted_i, j ) - ( ( _r[ sorted_i ] + r_j ) / n_minus_2 ); + if ( ( m < min ) && ( sorted_i != j ) ) { + _d_min = getDvalueUnmapped( sorted_i, m_j ); + min = m; + _min_i = sorted_i; + _min_j = j; } - ++counter_all; } } System.out.println(); diff --git a/forester/java/src/org/forester/evoinference/distance/S.java b/forester/java/src/org/forester/evoinference/distance/S.java index 842f59a..fe70cd6 100644 --- a/forester/java/src/org/forester/evoinference/distance/S.java +++ b/forester/java/src/org/forester/evoinference/distance/S.java @@ -66,6 +66,9 @@ public final class S { final SortedSet x = m.get( key ); if ( DEBUG ) { if ( x == null ) { + System.out.println(); + System.out + .println( "________________________________________________________________________________________" ); System.out.println( toString() ); throw new IllegalArgumentException( "key " + key + " (->" + value + ") does not exist for row " + j ); } @@ -73,6 +76,10 @@ public final class S { if ( x.size() == 1 ) { if ( DEBUG ) { if ( !x.contains( value ) ) { + System.out.println(); + System.out + .println( "________________________________________________________________________________________" ); + System.out.println( toString() ); throw new IllegalArgumentException( "pairing " + key + "->" + value + " does not exist for row " + j ); } @@ -107,9 +114,11 @@ public final class S { @Override final public String toString() { - final DecimalFormat df = new DecimalFormat( "0.00" ); + final DecimalFormat df = new DecimalFormat( "0.0000" ); final StringBuilder sb = new StringBuilder(); for( int j = 0; j < size(); ++j ) { + sb.append( j ); + sb.append( ": " ); for( final Entry> entry : getSentrySet( j ) ) { final double key = entry.getKey(); final SortedSet values = entry.getValue();