X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fevoinference%2Fdistance%2FNeighborJoiningR.java;h=209b93fd97788050086a8932f963b7e096ca639c;hb=c0439ed8b088887ffea2faf11bc7897333287cb3;hp=ee3b0148ecdab5c45056ff1e762d680b0503078a;hpb=e628c857be63e8d8a8698f536b3a56b9ba61e1f9;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 ee3b014..209b93f 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java @@ -29,10 +29,6 @@ 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 +37,22 @@ 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 Sarray _s; + private double _d_min; //TODO remove me + private int[] _rev_mappings; + private double _umax; + private double _rmax; private NeighborJoiningR() { _verbose = false; @@ -73,36 +74,57 @@ public final class NeighborJoiningR { reset( distance ); final Phylogeny phylogeny = new Phylogeny(); while ( _n > 2 ) { + if ( _verbose ) { + 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 int otu1 = _min_i; final int otu2 = _min_j; + //if ( _verbose ) { + // 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 = _d_values[ _mappings[ otu1 ] ][ _mappings[ 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 ); + } + if ( _verbose ) { + 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; + if ( _verbose ) { + System.out.println( "" ); + System.out + .println( "----------------------------------------------------------------------------------" ); + System.out.println( "" ); + } } - final double d = _d_values[ _mappings[ 0 ] ][ _mappings[ 1 ] ] / 2; + final double d = getDvalue( 0, 1 ) / 2; if ( _df == null ) { getExternalPhylogenyNode( 0 ).setDistanceToParent( d ); getExternalPhylogenyNode( 1 ).setDistanceToParent( d ); @@ -116,7 +138,7 @@ 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 ); @@ -132,49 +154,68 @@ public final class NeighborJoiningR { } private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) { - final int m_otu1 = _mappings[ otu1 ]; - final int m_otu2 = _mappings[ otu2 ]; - for( int i = 0; i < _n; ++i ) { - if ( ( i == otu1 ) || ( i == otu2 ) ) { + for( int j = 0; j < _n; ++j ) { + if ( ( j == otu2 ) || ( j == _rev_mappings[ otu1 ] ) ) { continue; } - final int m_i = _mappings[ i ]; - 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; - } - else { - _d_values[ m_otu1 ][ m_i ] = ( _d_values[ m_otu1 ][ m_i ] + _d_values[ m_otu2 ][ m_i ] - d ) / 2; - } - } - else { - if ( otu2 > i ) { - _d_values[ m_i ][ m_otu1 ] = ( _d_values[ m_i ][ m_otu1 ] + _d_values[ m_i ][ m_otu2 ] - d ) / 2; - } - else { - _d_values[ m_i ][ m_otu1 ] = ( _d_values[ m_i ][ m_otu1 ] + _d_values[ m_otu2 ][ m_i ] - d ) / 2; - } - } + updateDvalue( otu1, otu2, j, d ); + } + if ( _verbose ) { + System.out.println(); } } + private final void updateDvalue( final int otu1, final int otu2, final int j, final double d ) { + final int mj = _mappings[ j ]; + // final double new_d = ( getDvalueUnmapped( otu1, _mappings[ j ] ) + getDvalue( j, otu2 ) - d ) / 2; + // System.out.println( "\nnew d value: " + DF.format( new_d ) ); + if ( otu1 < mj ) { + _s.removePairing( _d_values[ otu1 ][ mj ], otu1, mj ); + } + else { + _s.removePairing( _d_values[ mj ][ otu1 ], mj, otu1 ); + } + if ( _mappings[ otu2 ] < mj ) { + _s.removePairing( getDvalue( j, otu2 ), _mappings[ otu2 ], mj ); + } + else { + _s.removePairing( getDvalue( j, otu2 ), mj, _mappings[ otu2 ] ); + } + double new_d; + if ( otu1 < mj ) { + new_d = ( ( _d_values[ otu1 ][ mj ] + getDvalue( j, otu2 ) ) - d ) / 2; + _s.addPairing( new_d, otu1, mj ); + _d_values[ otu1 ][ mj ] = new_d; + } + else { + new_d = ( ( _d_values[ mj ][ otu1 ] + getDvalue( j, otu2 ) ) - d ) / 2; + _s.addPairing( new_d, mj, otu1 ); + _d_values[ mj ][ otu1 ] = new_d; + } + } + + private double getDvalue( final int i, final int j ) { + if ( i < j ) { + return _d_values[ _mappings[ i ] ][ _mappings[ j ] ]; + } + return _d_values[ _mappings[ j ] ][ _mappings[ i ] ]; + } + private final void calculateNetDivergences() { + _rmax = -Double.MAX_VALUE; for( int i = 0; i < _n; ++i ) { _r[ i ] = calculateNetDivergence( i ); + if ( _r[ i ] > _rmax ) { + _rmax = _r[ i ]; + } } } private double calculateNetDivergence( final int i ) { - double d = 0; - final int m_i = _mappings[ i ]; + float d = 0; for( int n = 0; n < _n; ++n ) { if ( i != n ) { - if ( i > n ) { - d += _d_values[ _mappings[ n ] ][ m_i ]; - } - else { - d += _d_values[ m_i ][ _mappings[ n ] ]; - } + d += getDvalue( n, i ); } } return d; @@ -197,14 +238,30 @@ 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. @@ -214,35 +271,42 @@ public final class NeighborJoiningR { _d = distances; _r = new double[ _n ]; _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 ); - } + _rev_mappings = new int[ _n ]; + _d_values = distances.getValues(); + _s = new Sarray(); + _s.initialize( distances ); initExternalNodes(); - printM(); + if ( _verbose ) { + 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() / Sarray.FACTOR ) + "=" ); boolean first = true; - for( final Integer v : value ) { + for( final int v : entry.getValue() ) { if ( !first ) { System.out.print( "," ); } @@ -257,28 +321,84 @@ public final class NeighborJoiningR { private final void 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; - for( int j = 1; j < _n; ++j ) { + if ( _verbose ) { + printM(); + } + // + X: 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 ) { - final double m = _d_values[ _mappings[ i ] ][ m_j ] - ( ( _r[ i ] + r_j ) / n_minus_2 ); - if ( m < min ) { - min = m; - _min_i = i; - _min_j = j; + for( final Entry entry : _s.getSentrySet( m_j ) ) { + for( final int sorted_i : entry.getValue() ) { + final double m = _d_values[ sorted_i ][ m_j ] + - ( ( _r[ _rev_mappings[ sorted_i ] ] + r_j ) / n_minus_2 ); + if ( ( m < min_m ) ) { + min_m = m; + _min_i = sorted_i; + _min_j = j; + } } + continue X; } } + // + J: for( int j = 1; j < _n; ++j ) { + //System.out.println( "~~~~~~~~~~~~~ min_m=" + min_m ); + final double r_j = _r[ j ]; + final int m_j = _mappings[ j ]; + boolean first = true; + for( final Entry entry : _s.getSentrySet( m_j ) ) { + if ( first ) { + first = false; + continue; + } + for( final int sorted_i : entry.getValue() ) { + final double d = _d_values[ sorted_i ][ m_j ]; + if ( ( d - ( ( _umax + r_j ) / n_minus_2 ) ) > min_m ) { + continue J; + } + final double m = d - ( ( _r[ _rev_mappings[ sorted_i ] ] + r_j ) / n_minus_2 ); + if ( ( m < min_m ) ) { + min_m = m; + _min_i = sorted_i; + _min_j = j; + } + } + } + if ( _verbose ) { + 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(); + } + } + if ( _verbose ) { + System.out.println(); + } } // 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; } }