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=52b6fba15d77c986127aa9146316e2b5a4f98546;hpb=52a93ce55f3ff62e74a54cf8a2a51c95c0997953;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 52b6fba..209b93f 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java @@ -29,7 +29,6 @@ import java.text.DecimalFormat; import java.util.ArrayList; import java.util.List; import java.util.Map.Entry; -import java.util.SortedSet; import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix; import org.forester.phylogeny.Phylogeny; @@ -49,9 +48,11 @@ public final class NeighborJoiningR { private final boolean _verbose; private int _min_i; private int _min_j; - private S _s; + private Sarray _s; private double _d_min; //TODO remove me private int[] _rev_mappings; + private double _umax; + private double _rmax; private NeighborJoiningR() { _verbose = false; @@ -73,17 +74,21 @@ public final class NeighborJoiningR { reset( distance ); final Phylogeny phylogeny = new Phylogeny(); while ( _n > 2 ) { - System.out.println( "N=" + _n ); - System.out.println(); + 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 - final double m = updateM(); + 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 ) + ")" ); + //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 ] ); + // System.out.println( "mapped otu 2 " + _mappings[ otu2 ] ); + // } final PhylogenyNode node = new PhylogenyNode(); //final double d = getDvalueUnmapped( otu1, _mappings[ otu2 ] ); final double d = _d_values[ otu1 ][ _mappings[ otu2 ] ]; @@ -103,16 +108,21 @@ public final class NeighborJoiningR { if ( _verbose ) { printProgress( otu1, otu2, node ); } - System.out.println( "otu1=" + otu1 ); - System.out.println( "otu2=" + otu2 ); + if ( _verbose ) { + System.out.println( "otu1=" + otu1 ); + System.out.println( "otu2=" + otu2 ); + } calculateDistancesFromNewNode( otu1, otu2, d ); // _external_nodes[ _mappings[ otu1 ] ] = node; _external_nodes[ otu1 ] = node; updateMappings( otu2 ); --_n; - System.out.println( "" ); - System.out.println( "----------------------------------------------------------------------------------" ); - System.out.println( "" ); + if ( _verbose ) { + System.out.println( "" ); + System.out + .println( "----------------------------------------------------------------------------------" ); + System.out.println( "" ); + } } final double d = getDvalue( 0, 1 ) / 2; if ( _df == null ) { @@ -144,49 +154,44 @@ public final class NeighborJoiningR { } private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) { - System.out.print( "new D values: " ); for( int j = 0; j < _n; ++j ) { - if ( j == otu2 ) { + if ( ( j == otu2 ) || ( j == _rev_mappings[ otu1 ] ) ) { continue; } - if ( otu1 < _mappings[ j ] ) { - updateDvalue( otu1, otu2, j, d ); - } - // else if ( otu1 > _mappings[ j ] ) { - // updateDvalue( otu2, otu1, j, d ); - // } + updateDvalue( otu1, otu2, j, d ); + } + if ( _verbose ) { + System.out.println(); } - System.out.println(); } 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 ] ); + 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( getDvalueUnmapped( otu1, _mappings[ j ] ), _mappings[ j ], otu1 ); + _s.removePairing( _d_values[ mj ][ otu1 ], mj, 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 ] ); + if ( _mappings[ otu2 ] < mj ) { + _s.removePairing( getDvalue( j, otu2 ), _mappings[ otu2 ], mj ); } else { - _s.removePairing( getDvalue( j, otu2 ), _mappings[ j ], _mappings[ otu2 ] ); + _s.removePairing( getDvalue( j, otu2 ), mj, _mappings[ otu2 ] ); } - _s.addPairing( new_d, otu1, _mappings[ j ] ); - setDvalueU( otu1, j, new_d ); - } - - private void setDvalueU( final int i, final int j, final double d ) { - if ( i < _mappings[ j ] ) { - _d_values[ i ][ _mappings[ j ] ] = d; + 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; } - _d_values[ _mappings[ j ] ][ i ] = d; } private double getDvalue( final int i, final int j ) { @@ -196,21 +201,18 @@ 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() { + _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; + float d = 0; for( int n = 0; n < _n; ++n ) { if ( i != n ) { d += getDvalue( n, i ); @@ -257,9 +259,9 @@ public final class NeighborJoiningR { + " (" + ( ForesterUtil.isEmpty( n.getChildNode1().getName() ) ? n.getChildNode1().getId() : n.getChildNode1() .getName() ) - + "+" - + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2() - .getName() ) + ")"; + + "+" + + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2() + .getName() ) + ")"; } // only the values in the lower triangle are used. @@ -270,15 +272,17 @@ public final class NeighborJoiningR { _r = new double[ _n ]; _mappings = new int[ _n ]; _rev_mappings = new int[ _n ]; - _d_values = _d.getValues(); - _s = new S(); + _d_values = distances.getValues(); + _s = new Sarray(); _s.initialize( distances ); initExternalNodes(); - System.out.println(); - printM(); - System.out.println( "----------------------------------------------------------------------------------" ); - System.out.println(); - System.out.println(); + if ( _verbose ) { + System.out.println(); + printM(); + System.out.println( "----------------------------------------------------------------------------------" ); + System.out.println(); + System.out.println(); + } } final private void printM() { @@ -299,8 +303,8 @@ public final class NeighborJoiningR { System.out.print( " " ); } System.out.print( "\t\t" ); - for( final Entry> entry : _s.getSentrySet( _mappings[ j ] ) ) { - System.out.print( DF.format( ( double ) entry.getKey() / S.FACTOR ) + "=" ); + for( final Entry entry : _s.getSentrySet( _mappings[ j ] ) ) { + System.out.print( DF.format( ( double ) entry.getKey() / Sarray.FACTOR ) + "=" ); boolean first = true; for( final int v : entry.getValue() ) { if ( !first ) { @@ -315,66 +319,84 @@ public final class NeighborJoiningR { } } - private final double updateM() { + private final void updateM() { calculateNetDivergences(); 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 ) { + if ( _verbose ) { + printM(); + } + // + X: for( int j = 1; j < _n; ++j ) { final double r_j = _r[ j ]; final int m_j = _mappings[ j ]; - System.out.print( "j=" + j + " mj=" + m_j + ": " ); - for( final Entry> entry : _s.getSentrySet( m_j ) ) { + for( final Entry entry : _s.getSentrySet( m_j ) ) { for( final int sorted_i : entry.getValue() ) { - System.out.print( sorted_i + " " ); - System.out.print( "(" + DF.format( getDvalueUnmapped( sorted_i, m_j ) ) + ") " ); - final double m = getDvalueUnmapped( sorted_i, m_j ) + final double m = _d_values[ 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; } } + continue X; } - System.out.println(); - for( final Entry> entry : _s.getSentrySet( m_j ) ) { + } + // + 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() ) { - System.out.print( sorted_i ); - System.out.print( "->" ); - System.out.print( DF.format( _r[ sorted_i ] ) ); - System.out.print( " " ); + 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; + } } } - 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; + 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(); } - 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 ] ); + //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 ] ); + //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; }