import org.forester.evoinference.distance.NeighborJoining;
import org.forester.evoinference.distance.NeighborJoiningF;
+import org.forester.evoinference.distance.NeighborJoiningR;
import org.forester.evoinference.distance.PairwiseDistanceCalculator;
import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
import org.forester.evoinference.matrix.character.CharacterStateMatrix;
}
public static void main( final String[] args ) {
+ System.out.println( "NJ" );
if ( testNeighborJoining() ) {
- System.out.println( "OK." );
+ System.out.println( " OK." );
}
else {
- System.out.println( "failed." );
+ System.out.println( " failed." );
+ }
+ System.out.println( "NJR" );
+ if ( testNeighborJoiningR() ) {
+ System.out.println( " OK." );
}
- timeNeighborJoining();
+ else {
+ System.out.println( " failed." );
+ }
+ //timeNeighborJoining();
}
public static boolean test( final File test_dir ) {
return true;
}
+ private static boolean testNeighborJoiningR() {
+ try {
+ NeighborJoiningR nj = NeighborJoiningR.createInstance();
+ final BasicSymmetricalDistanceMatrix m0 = new BasicSymmetricalDistanceMatrix( 4 );
+ m0.setIdentifier( 0, "A" );
+ m0.setIdentifier( 1, "B" );
+ m0.setIdentifier( 2, "C" );
+ m0.setIdentifier( 3, "D" );
+ m0.setRow( "5 ", 1 );
+ m0.setRow( "3 6 ", 2 );
+ m0.setRow( "7.5 10.5 5.5", 3 );
+ final Phylogeny p0 = nj.execute( m0 );
+ BasicSymmetricalDistanceMatrix m = new BasicSymmetricalDistanceMatrix( 6 );
+ m.setRow( "5", 1 );
+ m.setRow( "4 7", 2 );
+ m.setRow( "7 10 7", 3 );
+ m.setRow( "6 9 6 5", 4 );
+ m.setRow( "8 11 8 9 8", 5 );
+ m.setIdentifier( 0, "A" );
+ m.setIdentifier( 1, "B" );
+ m.setIdentifier( 2, "C" );
+ m.setIdentifier( 3, "D" );
+ m.setIdentifier( 4, "E" );
+ m.setIdentifier( 5, "F" );
+ nj = NeighborJoiningR.createInstance();
+ final Phylogeny p1 = nj.execute( m );
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
private static boolean testSymmetricalDistanceMatrixParser() {
try {
final String l = ForesterUtil.getLineSeparator();
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// 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
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// 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: 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 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;
+import org.forester.phylogeny.PhylogenyNode;
+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<SortedMap<Double, SortedSet<Integer>>> _s;
+
+ private NeighborJoiningR() {
+ _verbose = false;
+ _df = null;
+ }
+
+ private NeighborJoiningR( 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 ) {
+ 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 otu1 = _min_i;
+ final int otu2 = _min_j;
+ // It is a condition that 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;
+ 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 ) {
+ printProgress( otu1, otu2 );
+ }
+ calculateDistancesFromNewNode( otu1, otu2, d );
+ _external_nodes[ _mappings[ otu1 ] ] = node;
+ updateMappings( otu2 );
+ --_n;
+ }
+ 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 ( _verbose ) {
+ printProgress( 0, 1 );
+ }
+ phylogeny.setRoot( root );
+ phylogeny.setRooted( false );
+ return phylogeny;
+ }
+
+ public final List<Phylogeny> execute( final List<BasicSymmetricalDistanceMatrix> distances_list ) {
+ final List<Phylogeny> pl = new ArrayList<Phylogeny>();
+ for( final BasicSymmetricalDistanceMatrix distances : distances_list ) {
+ pl.add( execute( distances ) );
+ }
+ return pl;
+ }
+
+ 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 void calculateNetDivergences() {
+ for( int i = 0; i < _n; ++i ) {
+ _r[ i ] = calculateNetDivergence( i );
+ }
+ }
+
+ private double calculateNetDivergence( final int i ) {
+ double 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 ] ];
+ }
+ }
+ }
+ return d;
+ }
+
+ private final PhylogenyNode getExternalPhylogenyNode( final int i ) {
+ return _external_nodes[ _mappings[ i ] ];
+ }
+
+ private final void initExternalNodes() {
+ _external_nodes = new PhylogenyNode[ _n ];
+ String id;
+ for( int i = 0; i < _n; ++i ) {
+ _external_nodes[ i ] = new PhylogenyNode();
+ id = _d.getIdentifier( i );
+ if ( id != null ) {
+ _external_nodes[ i ].setName( id );
+ }
+ else {
+ _external_nodes[ i ].setName( Integer.toString( i ) );
+ }
+ _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() ) );
+ }
+
+ // only the values in the lower triangle are used.
+ // !matrix values will be changed!
+ private final void reset( final BasicSymmetricalDistanceMatrix distances ) {
+ _n = distances.getSize();
+ _d = distances;
+ _r = new double[ _n ];
+ _mappings = new int[ _n ];
+ _d_values = _d.getValues();
+ _s = new ArrayList<SortedMap<Double, SortedSet<Integer>>>();
+ for( int j = 0; j < _n; ++j ) {
+ final TreeMap<Double, SortedSet<Integer>> map = new TreeMap<Double, SortedSet<Integer>>();
+ for( int i = 0; i < j; ++i ) {
+ if ( !map.containsKey( _d_values[ i ][ j ] ) ) {
+ map.put( _d_values[ i ][ j ], new TreeSet<Integer>() );
+ }
+ map.get( _d_values[ i ][ j ] ).add( i );
+ }
+ _s.add( map );
+ }
+ initExternalNodes();
+ printM();
+ }
+
+ final private void printM() {
+ for( int j = 1; j < _n; ++j ) {
+ for( int i = 0; i < _n; ++i ) {
+ System.out.print( _d_values[ i ][ j ] );
+ System.out.print( " " );
+ }
+ System.out.print( " " );
+ for( final Entry<Double, SortedSet<Integer>> entry : _s.get( j ).entrySet() ) {
+ final double key = entry.getKey();
+ final SortedSet<Integer> value = entry.getValue();
+ System.out.print( key + "=" );
+ boolean first = true;
+ for( final Integer v : value ) {
+ if ( !first ) {
+ System.out.print( "," );
+ }
+ first = false;
+ System.out.print( v );
+ }
+ System.out.print( " " );
+ }
+ System.out.println();
+ }
+ }
+
+ 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 ) {
+ 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;
+ }
+ }
+ }
+ }
+
+ // 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 ) {
+ _mappings[ i ] = _mappings[ i + 1 ];
+ }
+ }
+
+ public final static NeighborJoiningR createInstance() {
+ return new NeighborJoiningR();
+ }
+
+ public final static NeighborJoiningR createInstance( final boolean verbose,
+ final int maximum_fraction_digits_for_distances ) {
+ return new NeighborJoiningR( verbose, maximum_fraction_digits_for_distances );
+ }
+}
git://source.jalview.org / jalview.git / commitdiff