X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fevoinference%2Fdistance%2FNeighborJoiningR.java;h=a0ffd60595e70508b14452bc89104e008b9b6b4d;hb=73979ccd545aa73fa45321f7590f6d234b979e5e;hp=bf2a59f89d036e4357481259268a70d345c6dee6;hpb=a7372ecbb1d6deb19c6be8a810a08fa7494562bd;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 bf2a59f..a0ffd60 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java @@ -40,17 +40,17 @@ public final class NeighborJoiningR { private final static DecimalFormat DF = new DecimalFormat( "0.00000" ); private BasicSymmetricalDistanceMatrix _d; - private float[][] _d_values; + private double[][] _d_values; private final DecimalFormat _df; private PhylogenyNode[] _external_nodes; private int[] _mappings; private int _n; - private float[] _r; + private double[] _r; private final boolean _verbose; private int _min_i; private int _min_j; private S _s; - private float _d_min; //TODO remove me + private double _d_min; //TODO remove me private int[] _rev_mappings; private NeighborJoiningR() { @@ -73,22 +73,26 @@ 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(); 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 ] ); + 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 = getDvalueUnmapped( otu1, _mappings[ otu2 ] ); - final float d = _d_values[ otu1 ][ _mappings[ otu2 ] ]; - final float d1 = ( d / 2 ) + ( ( _r[ _rev_mappings[ otu1 ] ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) ); - final float d2 = d - d1; + 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 ) { _external_nodes[ otu1 ].setDistanceToParent( d1 ); getExternalPhylogenyNode( otu2 ).setDistanceToParent( d2 ); @@ -103,24 +107,29 @@ 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 float d = getDvalue( 0, 1 ) / 2; + final double d = getDvalue( 0, 1 ) / 2; if ( _df == null ) { getExternalPhylogenyNode( 0 ).setDistanceToParent( d ); getExternalPhylogenyNode( 1 ).setDistanceToParent( d ); } else { - final float dd = Float.parseFloat( _df.format( d ) ); + final double dd = Double.parseDouble( _df.format( d ) ); getExternalPhylogenyNode( 0 ).setDistanceToParent( dd ); getExternalPhylogenyNode( 1 ).setDistanceToParent( dd ); } @@ -143,69 +152,55 @@ public final class NeighborJoiningR { return pl; } - private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final float d ) { + private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) { for( int j = 0; j < _n; ++j ) { if ( ( j == otu2 ) || ( j == _rev_mappings[ otu1 ] ) ) { continue; } updateDvalue( otu1, otu2, j, d ); } - System.out.println(); + if ( _verbose ) { + System.out.println(); + } } - private final void updateDvalue( final int otu1, final int otu2, final int j, final float d ) { - final float new_d = ( getDvalueUnmapped( otu1, _mappings[ j ] ) + getDvalue( j, otu2 ) - d ) / 2; - System.out.println( "\nnew d value: " + DF.format( new_d ) ); - if ( otu1 < _mappings[ j ] ) { - System.out.println( " otu1=" + otu1 ); - System.out.println( " otu2=" + otu2 ); - System.out.println( "motu1=" + _mappings[ otu1 ] ); - System.out.println( "motu2=" + _mappings[ otu2 ] ); - System.out.println( " j=" + j ); - System.out.println( "mj=" + _mappings[ j ] ); - System.out.println( "d=" + DF.format( getDvalueUnmapped( otu1, _mappings[ j ] ) ) ); - _s.removePairing( getDvalueUnmapped( otu1, _mappings[ j ] ), otu1, _mappings[ j ] ); + 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( getDvalueUnmapped( otu1, mj ), otu1, mj ); } else { - System.out.println( " otu1=" + otu1 ); - System.out.println( " otu2=" + otu2 ); - System.out.println( "motu1=" + _mappings[ otu1 ] ); - System.out.println( "motu2=" + _mappings[ otu2 ] ); - System.out.println( " j=" + j ); - System.out.println( "mj=" + _mappings[ j ] ); - System.out.println( "d=" + DF.format( getDvalueUnmapped( otu1, _mappings[ j ] ) ) ); - _s.removePairing( getDvalueUnmapped( otu1, _mappings[ j ] ), _mappings[ j ], otu1 ); + _s.removePairing( getDvalueUnmapped( otu1, mj ), mj, otu1 ); } - 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 ] ); } - if ( otu1 < _mappings[ j ] ) { - _s.addPairing( new_d, otu1, _mappings[ j ] ); + 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 { - _s.addPairing( new_d, _mappings[ j ], otu1 ); + new_d = ( _d_values[ mj ][ otu1 ] + getDvalue( j, otu2 ) - d ) / 2; + _s.addPairing( new_d, mj, otu1 ); + _d_values[ mj ][ otu1 ] = new_d; } - setDvalueU( otu1, j, new_d ); } - private void setDvalueU( final int i, final int j, final float d ) { - if ( i < _mappings[ j ] ) { - _d_values[ i ][ _mappings[ j ] ] = d; - } - _d_values[ _mappings[ j ] ][ i ] = d; - } - - private float getDvalue( final int i, final int j ) { + 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 float getDvalueUnmapped( final int i, final int j ) { + private double getDvalueUnmapped( final int i, final int j ) { if ( i < j ) { return _d_values[ i ][ j ]; } @@ -218,7 +213,7 @@ public final class NeighborJoiningR { } } - private float calculateNetDivergence( final int i ) { + private double calculateNetDivergence( final int i ) { float d = 0; for( int n = 0; n < _n; ++n ) { if ( i != n ) { @@ -276,23 +271,20 @@ public final class NeighborJoiningR { private final void reset( final BasicSymmetricalDistanceMatrix distances ) { _n = distances.getSize(); _d = distances; - _r = new float[ _n ]; + _r = new double[ _n ]; _mappings = new int[ _n ]; _rev_mappings = new int[ _n ]; - _d_values = new float[ distances.getSize() ][ distances.getSize() ]; - for( int i = 0; i < distances.getSize(); ++i ) { - for( int j = 0; j < distances.getSize(); ++j ) { - _d_values[ i ][ j ] = ( float ) distances.getValue( i, j ); - } - } + _d_values = distances.getValues(); _s = new S(); _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() { @@ -335,60 +327,58 @@ public final class NeighborJoiningR { _min_i = -1; _min_j = -1; final int n_minus_2 = _n - 2; - printM(); + if ( _verbose ) { + printM(); + } 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 + ": " ); + if ( _verbose ) { + 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 + " " ); - 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 ); + //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 ); + // _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( " " ); + 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(); - /* - 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 ] ); + //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; }