// 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
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.evoinference.distance;
+import java.math.RoundingMode;
+import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.List;
import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
-import org.forester.evoinference.matrix.distance.DistanceMatrix;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.PhylogenyNodeI;
import org.forester.util.ForesterUtil;
-public class NeighborJoining {
+public final class NeighborJoining {
- private final static boolean VERBOSE_DEFAULT = false;
- private DistanceMatrix _d;
- private DistanceMatrix _m;
- private double[] _r;
- private int _n;
- private PhylogenyNodeI[] _external_nodes;
- private int[] _mappings;
- private boolean _verbose;
+ 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;
- public NeighborJoining() {
- init();
+ private NeighborJoining() {
+ _verbose = false;
+ _df = null;
}
- private void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) {
- for( int i = 0; i < _n; ++i ) {
- if ( ( i == otu1 ) || ( i == otu2 ) ) {
- continue;
- }
- final double nd = ( getValueFromD( otu1, i ) + getValueFromD( i, otu2 ) - d ) / 2;
- setValueInD( nd, otu1, i );
- }
- }
-
- private double calculateM( final int i, final int j ) {
- return getValueFromD( i, j ) - ( _r[ i ] + _r[ j ] ) / ( _n - 2 );
- }
-
- private void calculateNetDivergences() {
- for( int i = 0; i < _n; ++i ) {
- double d = 0.0;
- for( int n = 0; n < _n; ++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 Phylogeny execute( final DistanceMatrix distance ) {
+ public final Phylogeny execute( final BasicSymmetricalDistanceMatrix distance ) {
reset( distance );
final Phylogeny phylogeny = new Phylogeny();
while ( _n > 2 ) {
+ // Calculates the minimal distance.
+ // If more than one minimal distances, always the first found is used
updateM();
- final int[] s = findMinimalDistance();
- final int otu1 = s[ 0 ];
- final int otu2 = s[ 1 ];
+ final int otu1 = _min_i;
+ final int otu2 = _min_j;
+ System.out.println( _min_i + " " + _min_j );
// It is a condition that otu1 < otu2.
- if ( otu1 > otu2 ) {
- throw new AssertionError( "NJ code is faulty: otu1 > otu2" );
- }
- final PhylogenyNodeI node = new PhylogenyNode();
- final double d = getValueFromD( otu1, 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 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 ( isVerbose() ) {
+ if ( _verbose ) {
printProgress( otu1, otu2 );
}
calculateDistancesFromNewNode( otu1, otu2, d );
- setExternalPhylogenyNode( node, otu1 );
+ _external_nodes[ _mappings[ otu1 ] ] = node;
updateMappings( otu2 );
--_n;
}
- final double d = getValueFromD( 0, 1 ) / 2;
- getExternalPhylogenyNode( 0 ).setDistanceToParent( d );
- getExternalPhylogenyNode( 1 ).setDistanceToParent( d );
- final PhylogenyNodeI root = new PhylogenyNode();
+ 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 ) );
- if ( isVerbose() ) {
+ if ( _verbose ) {
printProgress( 0, 1 );
}
- phylogeny.setRoot( ( PhylogenyNode ) root );
+ phylogeny.setRoot( root );
phylogeny.setRooted( false );
return phylogeny;
}
- public List<Phylogeny> execute( final List<DistanceMatrix> distances_list ) {
+ public final List<Phylogeny> execute( final List<BasicSymmetricalDistanceMatrix> distances_list ) {
final List<Phylogeny> pl = new ArrayList<Phylogeny>();
- for( final DistanceMatrix distances : distances_list ) {
+ for( final BasicSymmetricalDistanceMatrix distances : distances_list ) {
pl.add( execute( distances ) );
}
return pl;
}
- private int[] findMinimalDistance() {
- // if more than one minimal distances, always the first found is
- // returned
- // i could randomize this, so that any would be returned in a randomized
- // fashion...
- double minimum = Double.MAX_VALUE;
- int otu_1 = -1;
- int otu_2 = -1;
- for( int j = 1; j < _n; ++j ) {
- for( int i = 0; i < j; ++i ) {
- if ( _m.getValue( i, j ) < minimum ) {
- minimum = _m.getValue( i, j );
- otu_1 = i;
- otu_2 = j;
+ 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;
}
}
}
- return new int[] { otu_1, otu_2 };
- }
-
- private PhylogenyNodeI getExternalPhylogenyNode( final int i ) {
- return _external_nodes[ _mappings[ i ] ];
}
- private double getValueFromD( final int otu1, final int otu2 ) {
- return _d.getValue( _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 void init() {
- setVerbose( VERBOSE_DEFAULT );
+ private final PhylogenyNode getExternalPhylogenyNode( final int i ) {
+ return _external_nodes[ _mappings[ i ] ];
}
- private void initExternalNodes() {
- _external_nodes = new PhylogenyNodeI[ _n ];
+ private final void initExternalNodes() {
+ _external_nodes = new PhylogenyNode[ _n ];
+ String id;
for( int i = 0; i < _n; ++i ) {
_external_nodes[ i ] = new PhylogenyNode();
- final String id = _d.getIdentifier( i );
+ id = _d.getIdentifier( i );
if ( id != null ) {
_external_nodes[ i ].setName( id );
}
else {
- _external_nodes[ i ].setName( "" + i );
+ _external_nodes[ i ].setName( Integer.toString( i ) );
}
_mappings[ i ] = i;
}
}
- private boolean isVerbose() {
- return _verbose;
+ private final void printProgress( final int otu1, final int otu2 ) {
+ System.out.println( "Node " + printProgressNodeToString( getExternalPhylogenyNode( otu1 ) ) + " joins "
+ + ( printProgressNodeToString( getExternalPhylogenyNode( otu2 ) ) ) );
}
- private void printProgress( final int otu1, final int otu2 ) {
- final PhylogenyNodeI n1 = getExternalPhylogenyNode( otu1 );
- final PhylogenyNodeI 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 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.
// !matrix values will be changed!
- private void reset( final DistanceMatrix distances ) {
+ private final void reset( final BasicSymmetricalDistanceMatrix distances ) {
_n = distances.getSize();
_d = distances;
- _m = new BasicSymmetricalDistanceMatrix( _n );
_r = new double[ _n ];
_mappings = new int[ _n ];
+ _d_values = _d.getValues();
initExternalNodes();
}
- private void setExternalPhylogenyNode( final PhylogenyNodeI node, final int i ) {
- _external_nodes[ _mappings[ i ] ] = node;
- }
-
- private void setValueInD( final double d, final int otu1, final int otu2 ) {
- _d.setValue( _mappings[ otu1 ], _mappings[ otu2 ], d );
- }
-
- public void setVerbose( final boolean verbose ) {
- _verbose = verbose;
- }
-
- private void updateM() {
+ private final void updateM() {
calculateNetDivergences();
+ Double min = Double.MAX_VALUE;
+ _min_i = -1;
+ _min_j = -1;
+ final int n_minus_2 = _n - 2;
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 ) {
- _m.setValue( i, j, calculateM( i, j ) );
+ 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( 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 ) {
+ System.out.print( i );
+ System.out.print( "->" );
+ System.out.print( DF.format( _r[ i ] ) );
+ System.out.print( " " );
+ }
+ System.out.println();
+ }
}
// otu2 will, in effect, be "deleted" from the matrix.
- private void updateMappings( final int otu2 ) {
- for( int i = otu2; i < _mappings.length - 1; ++i ) {
+ 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 ] );
}
}
- public static NeighborJoining createInstance() {
+ public final static NeighborJoining createInstance() {
return new NeighborJoining();
}
+
+ 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