X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fevoinference%2Fdistance%2FNeighborJoiningR.java;h=384b6e9825c874a419c70df3a3399f8d0e35fcce;hb=0ccf8b41a889edccde310d55377e1db2351f46e6;hp=cfcd02410817ff0d0d30bf8cf9b76f2d4e02aefd;hpb=88af7c059e5f19aae3b5a43003961b8689788a4b;p=jalview.git diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java index cfcd024..384b6e9 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java @@ -29,10 +29,7 @@ import java.text.DecimalFormat; import java.util.ArrayList; import java.util.List; import java.util.Map.Entry; -import java.util.SortedMap; import java.util.SortedSet; -import java.util.TreeMap; -import java.util.TreeSet; import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix; import org.forester.phylogeny.Phylogeny; @@ -41,17 +38,20 @@ import org.forester.util.ForesterUtil; public final class NeighborJoiningR { - private BasicSymmetricalDistanceMatrix _d; - private double[][] _d_values; - private final DecimalFormat _df; - private PhylogenyNode[] _external_nodes; - private int[] _mappings; - private int _n; - private double[] _r; - private final boolean _verbose; - private int _min_i; - private int _min_j; - private List>> _s; + private final static DecimalFormat DF = new DecimalFormat( "0.00000" ); + private BasicSymmetricalDistanceMatrix _d; + private double[][] _d_values; + private final DecimalFormat _df; + private PhylogenyNode[] _external_nodes; + private int[] _mappings; + private int _n; + private double[] _r; + private final boolean _verbose; + private int _min_i; + private int _min_j; + private S _s; + private double _d_min; //TODO remove me + private int[] _rev_mappings; private NeighborJoiningR() { _verbose = false; @@ -73,34 +73,46 @@ public final class NeighborJoiningR { reset( distance ); final Phylogeny phylogeny = new Phylogeny(); while ( _n > 2 ) { + System.out.println( "N=" + _n ); + System.out.println(); // Calculates the minimal distance. // If more than one minimal distances, always the first found is used - updateM(); + final double m = updateM(); final int otu1 = _min_i; 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. + //System.out.println( "mapped 1 " + _mappings[ otu1 ] ); + System.out.println( "mapped otu 2 " + _mappings[ otu2 ] ); final PhylogenyNode node = new PhylogenyNode(); - final double d = getDvalue( otu1, otu2 ); - final double d1 = ( d / 2 ) + ( ( _r[ otu1 ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) ); + //final double d = getDvalueUnmapped( otu1, _mappings[ otu2 ] ); + final double d = _d_values[ otu1 ][ _mappings[ otu2 ] ]; + final double d1 = ( d / 2 ) + ( ( _r[ _rev_mappings[ otu1 ] ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) ); final double d2 = d - d1; if ( _df == null ) { - getExternalPhylogenyNode( otu1 ).setDistanceToParent( d1 ); + _external_nodes[ otu1 ].setDistanceToParent( d1 ); getExternalPhylogenyNode( otu2 ).setDistanceToParent( d2 ); } else { // yes, yes, slow but only grows with n (and not n^2 or worse)... - getExternalPhylogenyNode( otu1 ).setDistanceToParent( Double.parseDouble( _df.format( d1 ) ) ); + _external_nodes[ otu1 ].setDistanceToParent( Double.parseDouble( _df.format( d1 ) ) ); getExternalPhylogenyNode( otu2 ).setDistanceToParent( Double.parseDouble( _df.format( d2 ) ) ); } - node.addAsChild( getExternalPhylogenyNode( otu1 ) ); + node.addAsChild( _external_nodes[ 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; + // _external_nodes[ _mappings[ otu1 ] ] = node; + _external_nodes[ otu1 ] = node; updateMappings( otu2 ); --_n; + System.out.println( "" ); + System.out.println( "----------------------------------------------------------------------------------" ); + System.out.println( "" ); } final double d = getDvalue( 0, 1 ) / 2; if ( _df == null ) { @@ -116,7 +128,7 @@ 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 ); @@ -132,23 +144,52 @@ 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 == otu2 ) { continue; } - updateDvalue( otu1, otu2, i, d ); + if ( otu1 < _mappings[ j ] ) { + updateDvalue( otu1, otu2, j, d ); + } } + System.out.println(); } - 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 ); + private final void updateDvalue( final int otu1, final int otu2, final int j, final double d ) { + final double new_d = ( getDvalueUnmapped( otu1, _mappings[ j ] ) + getDvalue( j, otu2 ) - d ) / 2; + System.out.print( DF.format( new_d ) + " " ); + // System.out.println( "going to remove: " + getDvalueUnmapped( otu1, _mappings[ j ] ) + ", " + otu1 + ", " + // + _mappings[ j ] ); + + if ( otu1< _mappings[ j ] ) { + _s.removePairing( getDvalueUnmapped( otu1, _mappings[ j ] ), otu1, _mappings[ j ] ); + } + else { + _s.removePairing( getDvalueUnmapped( otu1, _mappings[ j ] ), _mappings[ j ] , otu1 ); + } + + + // System.out.println( "going to remove: " + getDvalue( j, otu2 ) + ", " +_mappings[ otu2 ] + ", " + // + _mappings[ j ] ); + + if ( _mappings[ otu2 ] < _mappings[ j ] ) { + _s.removePairing( getDvalue( j, otu2 ), _mappings[ otu2 ] , _mappings[ j ] ); + } + else { + _s.removePairing( getDvalue( j, otu2 ) , _mappings[ j ], _mappings[ otu2 ] ); + + } + + _s.addPairing( new_d, otu1, _mappings[ j ] ); + setDvalueU( otu1, j, new_d ); } - private void setDvalue( final int i, final int j, final double d ) { - if ( i < j ) { - _d_values[ _mappings[ i ] ][ _mappings[ j ] ] = d; + private void setDvalueU( final int i, final int j, final double d ) { + if ( i < _mappings[ j ] ) { + _d_values[ i ][ _mappings[ j ] ] = d; } - _d_values[ _mappings[ j ] ][ _mappings[ i ] ] = d; + _d_values[_mappings[ j] ][ i ] = d; } private double getDvalue( final int i, final int j ) { @@ -158,6 +199,13 @@ public final class NeighborJoiningR { return _d_values[ _mappings[ j ] ][ _mappings[ i ] ]; } + private double getDvalueUnmapped( final int i, final int j ) { + if ( i < j ) { + return _d_values[ i ][ j ]; + } + return _d_values[ j ][ i ]; + } + private final void calculateNetDivergences() { for( int i = 0; i < _n; ++i ) { _r[ i ] = calculateNetDivergence( i ); @@ -191,14 +239,30 @@ public final class NeighborJoiningR { _external_nodes[ i ].setName( Integer.toString( i ) ); } _mappings[ i ] = i; + _rev_mappings[ i ] = i; } } - 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() ) ); + private final void printProgress( final int otu1, final int otu2, final PhylogenyNode node ) { + System.out.println( "Node " + printProgressNodeToString( _external_nodes[ otu1 ] ) + " joins " + + ( printProgressNodeToString( getExternalPhylogenyNode( otu2 ) ) ) + " [resulting in node " + + ( printProgressNodeToString( node ) ) + "]" ); + } + + 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. @@ -208,35 +272,40 @@ public final class NeighborJoiningR { _d = distances; _r = new double[ _n ]; _mappings = new int[ _n ]; + _rev_mappings = new int[ _n ]; _d_values = _d.getValues(); - _s = new ArrayList>>(); - for( int j = 0; j < _n; ++j ) { - final TreeMap> map = new TreeMap>(); - for( int i = 0; i < j; ++i ) { - if ( !map.containsKey( _d_values[ i ][ j ] ) ) { - map.put( _d_values[ i ][ j ], new TreeSet() ); - } - map.get( _d_values[ i ][ j ] ).add( i ); - } - _s.add( map ); - } + _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 < _d_values.length; ++j ) { + System.out.print( _external_nodes[ j ] ); + System.out.print( "\t\t" ); + for( int i = 0; i < _d_values[ j ].length; ++i ) { + System.out.print( DF.format( _d_values[ i ][ j ] ) ); + System.out.print( " " ); + } + System.out.println(); + } + 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( _d_values[ i ][ j ] ); + System.out.print( DF.format( _d_values[ _mappings[ i ] ][ _mappings[ j ] ] ) ); System.out.print( " " ); } - System.out.print( " " ); - for( final Entry> entry : _s.get( j ).entrySet() ) { - final double key = entry.getKey(); - final SortedSet value = entry.getValue(); - System.out.print( key + "=" ); + System.out.print( "\t\t" ); + for( final Entry> entry : _s.getSentrySet( _mappings[ j ] ) ) { + 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( "," ); } @@ -249,46 +318,68 @@ public final class NeighborJoiningR { } } - private final void updateM() { + private final double updateM() { calculateNetDivergences(); - Double min = Double.MAX_VALUE; + Double min_m = 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 ]; - final SortedMap> s_j = _s.get( m_j ); - for( final Entry> entry : s_j.entrySet() ) { - //Double key = entry.getKey(); - final SortedSet value = entry.getValue(); - for( final Integer sorted_i : value ) { + System.out.print( "j=" + j + " mj=" + m_j + ": " ); + for( final Entry> entry : _s.getSentrySet( m_j ) ) { + for( final int sorted_i : entry.getValue() ) { System.out.print( sorted_i + " " ); - // final double m = _d_values[ _mappings[ sorted_i ] ][ m_j ] - // - ( ( _r[ sorted_i ] + r_j ) / n_minus_2 ); - // if ( m < min ) { - // min = m; - // _min_i = sorted_i; - // _min_j = j; - // } + System.out.print( "(" + DF.format( getDvalueUnmapped( sorted_i, m_j ) ) + ") " ); + final double m = getDvalueUnmapped( sorted_i, m_j ) + - ( ( _r[ _rev_mappings[ sorted_i ] ] + r_j ) / n_minus_2 ); + if ( ( m < min_m ) ) { + _d_min = getDvalueUnmapped( sorted_i, m_j ); + min_m = m; + _min_i = sorted_i; + _min_j = j; + } + } + } + System.out.println(); + for( final Entry> entry : _s.getSentrySet( m_j ) ) { + for( final int sorted_i : entry.getValue() ) { + System.out.print( sorted_i ); + System.out.print( "->" ); + System.out.print( DF.format( _r[ sorted_i ] ) ); + System.out.print( " " ); } } System.out.println(); + /* for( int i = 0; i < j; ++i ) { final double m = getDvalue( i, j ) - ( ( _r[ i ] + r_j ) / n_minus_2 ); if ( m < min ) { min = m; + _d_min = getDvalue( i, j ); _min_i = i; _min_j = j; } - } + }*/ } + System.out.println(); + return min_m; } // otu2 will, in effect, be "deleted" from the matrix. private final void updateMappings( final int otu2 ) { for( int i = otu2; i < ( _mappings.length - 1 ); ++i ) { + System.out.print( _mappings[ i ] ); _mappings[ i ] = _mappings[ i + 1 ]; + System.out.println( "----->" + _mappings[ i ] ); + } + for( int i = 0; i < _mappings.length; ++i ) { + System.out.println( i + "-->" + _mappings[ i ] ); + } + for( int i = 0; i < _n; ++i ) { + _rev_mappings[ _mappings[ i ] ] = i; } }