// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// Copyright (C) 2014 Christian M. Zmasek
// All rights reserved
//
// This library is free software; you can redistribute it and/or
package org.forester.evoinference.distance;
+import java.math.RoundingMode;
+import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.List;
public final class NeighborJoining {
private BasicSymmetricalDistanceMatrix _d;
- // private BasicSymmetricalDistanceMatrix _m;
private double[][] _d_values;
- private double[][] _m_values;
- private double[] _r;
- private int _n;
+ private final DecimalFormat _df;
private PhylogenyNode[] _external_nodes;
+ private double[][] _m_values;
private int[] _mappings;
+ private int _n;
+ private double[] _r;
private final boolean _verbose;
- private final static boolean DEBUG = false;
- private NeighborJoining( final boolean verbose ) {
- _verbose = verbose;
- }
-
- private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) {
- final int otu1_m = _mappings[ otu1 ];
- final int otu2_m = _mappings[ otu2 ];
- int i_m;
- for( int i = 0; i < _n; ++i ) {
- if ( ( i == otu1 ) || ( i == otu2 ) ) {
- continue;
- }
- // _d_values[ _mappings[ otu1 ] ][ _mappings[ i ] ] = ( getValueFromD( otu1, i ) + getValueFromD( i, otu2 ) - d ) / 2;
- i_m = _mappings[ i ];
- _d_values[ otu1_m ][ i_m ] = ( ( _d_values[ otu1_m ][ i_m ] + _d_values[ i_m ][ otu2_m ] ) - 2 ) / 2;
- }
+ private NeighborJoining() {
+ _verbose = false;
+ _df = null;
}
- private final void calculateNetDivergences() {
- double d;
- int i_m;
- for( int i = 0; i < _n; ++i ) {
- d = 0;
- i_m = _mappings[ i ];
- for( int n = 0; n < _n; ++n ) {
- d += _d_values[ i_m ][ _mappings[ n ] ];
- //d += getValueFromD( i, n );
- }
- _r[ i ] = d;
+ private NeighborJoining( final boolean verbose, final int maximum_fraction_digits_for_distances ) {
+ if ( ( maximum_fraction_digits_for_distances < 1 ) || ( maximum_fraction_digits_for_distances > 9 ) ) {
+ throw new IllegalArgumentException( "maximum fraction digits for distances is out of range: "
+ + maximum_fraction_digits_for_distances );
}
+ _verbose = verbose;
+ _df = new DecimalFormat();
+ _df.setMaximumFractionDigits( maximum_fraction_digits_for_distances );
+ _df.setRoundingMode( RoundingMode.HALF_UP );
}
public final Phylogeny execute( final BasicSymmetricalDistanceMatrix distance ) {
// Calculates the minimal distance.
// If more than one minimal distances, always the first found is used
// could randomize this, so that any would be returned in a randomized fashion...
- double minimum = Double.MAX_VALUE;
- int otu1 = -1;
- int otu2 = -1;
+ double minimum = _m_values[ 0 ][ 1 ];
+ int otu1 = 0;
+ int otu2 = 1;
for( int j = 1; j < _n; ++j ) {
for( int i = 0; i < j; ++i ) {
if ( _m_values[ i ][ j ] < minimum ) {
}
}
// It is a condition that otu1 < otu2.
- if ( DEBUG ) {
- if ( otu1 > otu2 ) {
- throw new RuntimeException( "NJ code is faulty: otu1 > otu2" );
- }
- }
final PhylogenyNode node = new PhylogenyNode();
- final double d = getValueFromD( otu1, otu2 );
+ final double d = _d_values[ _mappings[ otu1 ] ][ _mappings[ otu2 ] ];
final double d1 = ( d / 2 ) + ( ( _r[ otu1 ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) );
final double d2 = d - d1;
- getExternalPhylogenyNode( otu1 ).setDistanceToParent( d1 );
- getExternalPhylogenyNode( otu2 ).setDistanceToParent( d2 );
+ if ( _df == null ) {
+ getExternalPhylogenyNode( 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 ) ) );
+ getExternalPhylogenyNode( otu2 ).setDistanceToParent( Double.parseDouble( _df.format( d2 ) ) );
+ }
node.addAsChild( getExternalPhylogenyNode( otu1 ) );
node.addAsChild( getExternalPhylogenyNode( otu2 ) );
if ( _verbose ) {
updateMappings( otu2 );
--_n;
}
- final double d = getValueFromD( 0, 1 ) / 2;
- getExternalPhylogenyNode( 0 ).setDistanceToParent( d );
- getExternalPhylogenyNode( 1 ).setDistanceToParent( d );
+ final double d = _d_values[ _mappings[ 0 ] ][ _mappings[ 1 ] ] / 2;
+ if ( _df == null ) {
+ getExternalPhylogenyNode( 0 ).setDistanceToParent( d );
+ getExternalPhylogenyNode( 1 ).setDistanceToParent( d );
+ }
+ else {
+ final double dd = Double.parseDouble( _df.format( d ) );
+ getExternalPhylogenyNode( 0 ).setDistanceToParent( dd );
+ getExternalPhylogenyNode( 1 ).setDistanceToParent( dd );
+ }
final PhylogenyNode root = new PhylogenyNode();
root.addAsChild( getExternalPhylogenyNode( 0 ) );
root.addAsChild( getExternalPhylogenyNode( 1 ) );
return pl;
}
- private final PhylogenyNode getExternalPhylogenyNode( final int i ) {
- return _external_nodes[ _mappings[ i ] ];
+ 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 ) ) {
+ 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;
+ }
+ }
+ }
}
- private final double getValueFromD( final int otu1, final int otu2 ) {
- return _d_values[ _mappings[ otu1 ] ][ _mappings[ otu2 ] ];
+ private final void calculateNetDivergences() {
+ double d;
+ for( int i = 0; i < _n; ++i ) {
+ d = 0;
+ final int m_i = _mappings[ i ];
+ 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 ] ];
+ }
+ }
+ }
+ _r[ i ] = d;
+ }
+ }
+
+ private final PhylogenyNode getExternalPhylogenyNode( final int i ) {
+ return _external_nodes[ _mappings[ i ] ];
}
private final void initExternalNodes() {
_external_nodes[ i ].setName( id );
}
else {
- _external_nodes[ i ].setName( "" + i );
+ _external_nodes[ i ].setName( Integer.toString( i ) );
}
_mappings[ i ] = i;
}
private final void updateM() {
calculateNetDivergences();
- double r_j;
- int j_m;
- final int _n_2 = _n - 2;
+ final int n_minus_2 = _n - 2;
for( int j = 1; j < _n; ++j ) {
- r_j = _r[ j ];
- j_m = _mappings[ j ];
+ final double r_j = _r[ j ];
+ final int m_j = _mappings[ j ];
for( int i = 0; i < j; ++i ) {
- // _m_values[ i ][ j ] = getValueFromD( i, j ) - ( _r[ i ] + r_j ) / ( _n - 2 );
- _m_values[ i ][ j ] = _d_values[ _mappings[ i ] ][ j_m ] - ( ( _r[ i ] + r_j ) / ( _n_2 ) );
+ _m_values[ i ][ j ] = _d_values[ _mappings[ i ] ][ m_j ] - ( ( _r[ i ] + r_j ) / n_minus_2 );
}
}
}
}
public final static NeighborJoining createInstance() {
- return new NeighborJoining( false );
+ return new NeighborJoining();
}
- public final static NeighborJoining createInstance( final boolean verbose ) {
- return new NeighborJoining( verbose );
+ public final static NeighborJoining createInstance( final boolean verbose,
+ final int maximum_fraction_digits_for_distances ) {
+ return new NeighborJoining( verbose, maximum_fraction_digits_for_distances );
}
}
git://source.jalview.org / jalview.git / blobdiff