2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2014 Christian M. Zmasek
8 // This library is free software; you can redistribute it and/or
9 // modify it under the terms of the GNU Lesser General Public
10 // License as published by the Free Software Foundation; either
11 // version 2.1 of the License, or (at your option) any later version.
13 // This library is distributed in the hope that it will be useful,
14 // but WITHOUT ANY WARRANTY; without even the implied warranty of
15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
16 // Lesser General Public License for more details.
18 // You should have received a copy of the GNU Lesser General Public
19 // License along with this library; if not, write to the Free Software
20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
22 // Contact: phylosoft @ gmail . com
23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
25 package org.forester.evoinference.distance;
27 import java.math.RoundingMode;
28 import java.text.DecimalFormat;
29 import java.util.ArrayList;
30 import java.util.List;
31 import java.util.Map.Entry;
32 import java.util.SortedMap;
33 import java.util.SortedSet;
34 import java.util.TreeMap;
35 import java.util.TreeSet;
37 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
38 import org.forester.phylogeny.Phylogeny;
39 import org.forester.phylogeny.PhylogenyNode;
40 import org.forester.util.ForesterUtil;
42 public final class NeighborJoiningR {
44 private BasicSymmetricalDistanceMatrix _d;
45 private double[][] _d_values;
46 private final DecimalFormat _df;
47 private PhylogenyNode[] _external_nodes;
48 private int[] _mappings;
51 private final boolean _verbose;
54 private List<SortedMap<Double, SortedSet<Integer>>> _s;
56 private NeighborJoiningR() {
61 private NeighborJoiningR( final boolean verbose, final int maximum_fraction_digits_for_distances ) {
62 if ( ( maximum_fraction_digits_for_distances < 1 ) || ( maximum_fraction_digits_for_distances > 9 ) ) {
63 throw new IllegalArgumentException( "maximum fraction digits for distances is out of range: "
64 + maximum_fraction_digits_for_distances );
67 _df = new DecimalFormat();
68 _df.setMaximumFractionDigits( maximum_fraction_digits_for_distances );
69 _df.setRoundingMode( RoundingMode.HALF_UP );
72 public final Phylogeny execute( final BasicSymmetricalDistanceMatrix distance ) {
74 final Phylogeny phylogeny = new Phylogeny();
76 // Calculates the minimal distance.
77 // If more than one minimal distances, always the first found is used
79 final int otu1 = _min_i;
80 final int otu2 = _min_j;
81 // It is a condition that otu1 < otu2.
82 final PhylogenyNode node = new PhylogenyNode();
83 final double d = _d_values[ _mappings[ otu1 ] ][ _mappings[ otu2 ] ];
84 final double d1 = ( d / 2 ) + ( ( _r[ otu1 ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) );
85 final double d2 = d - d1;
87 getExternalPhylogenyNode( otu1 ).setDistanceToParent( d1 );
88 getExternalPhylogenyNode( otu2 ).setDistanceToParent( d2 );
91 // yes, yes, slow but only grows with n (and not n^2 or worse)...
92 getExternalPhylogenyNode( otu1 ).setDistanceToParent( Double.parseDouble( _df.format( d1 ) ) );
93 getExternalPhylogenyNode( otu2 ).setDistanceToParent( Double.parseDouble( _df.format( d2 ) ) );
95 node.addAsChild( getExternalPhylogenyNode( otu1 ) );
96 node.addAsChild( getExternalPhylogenyNode( otu2 ) );
98 printProgress( otu1, otu2 );
100 calculateDistancesFromNewNode( otu1, otu2, d );
101 _external_nodes[ _mappings[ otu1 ] ] = node;
102 updateMappings( otu2 );
105 final double d = _d_values[ _mappings[ 0 ] ][ _mappings[ 1 ] ] / 2;
107 getExternalPhylogenyNode( 0 ).setDistanceToParent( d );
108 getExternalPhylogenyNode( 1 ).setDistanceToParent( d );
111 final double dd = Double.parseDouble( _df.format( d ) );
112 getExternalPhylogenyNode( 0 ).setDistanceToParent( dd );
113 getExternalPhylogenyNode( 1 ).setDistanceToParent( dd );
115 final PhylogenyNode root = new PhylogenyNode();
116 root.addAsChild( getExternalPhylogenyNode( 0 ) );
117 root.addAsChild( getExternalPhylogenyNode( 1 ) );
119 printProgress( 0, 1 );
121 phylogeny.setRoot( root );
122 phylogeny.setRooted( false );
126 public final List<Phylogeny> execute( final List<BasicSymmetricalDistanceMatrix> distances_list ) {
127 final List<Phylogeny> pl = new ArrayList<Phylogeny>();
128 for( final BasicSymmetricalDistanceMatrix distances : distances_list ) {
129 pl.add( execute( distances ) );
134 private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) {
135 final int m_otu1 = _mappings[ otu1 ];
136 final int m_otu2 = _mappings[ otu2 ];
137 for( int i = 0; i < _n; ++i ) {
138 if ( ( i == otu1 ) || ( i == otu2 ) ) {
141 final int m_i = _mappings[ i ];
144 _d_values[ m_otu1 ][ m_i ] = ( _d_values[ m_otu1 ][ m_i ] + _d_values[ m_i ][ m_otu2 ] - d ) / 2;
147 _d_values[ m_otu1 ][ m_i ] = ( _d_values[ m_otu1 ][ m_i ] + _d_values[ m_otu2 ][ m_i ] - d ) / 2;
152 _d_values[ m_i ][ m_otu1 ] = ( _d_values[ m_i ][ m_otu1 ] + _d_values[ m_i ][ m_otu2 ] - d ) / 2;
155 _d_values[ m_i ][ m_otu1 ] = ( _d_values[ m_i ][ m_otu1 ] + _d_values[ m_otu2 ][ m_i ] - d ) / 2;
161 private final void calculateNetDivergences() {
162 for( int i = 0; i < _n; ++i ) {
163 _r[ i ] = calculateNetDivergence( i );
167 private double calculateNetDivergence( final int i ) {
169 final int m_i = _mappings[ i ];
170 for( int n = 0; n < _n; ++n ) {
173 d += _d_values[ _mappings[ n ] ][ m_i ];
176 d += _d_values[ m_i ][ _mappings[ n ] ];
183 private final PhylogenyNode getExternalPhylogenyNode( final int i ) {
184 return _external_nodes[ _mappings[ i ] ];
187 private final void initExternalNodes() {
188 _external_nodes = new PhylogenyNode[ _n ];
190 for( int i = 0; i < _n; ++i ) {
191 _external_nodes[ i ] = new PhylogenyNode();
192 id = _d.getIdentifier( i );
194 _external_nodes[ i ].setName( id );
197 _external_nodes[ i ].setName( Integer.toString( i ) );
203 private final void printProgress( final int otu1, final int otu2 ) {
204 final PhylogenyNode n1 = getExternalPhylogenyNode( otu1 );
205 final PhylogenyNode n2 = getExternalPhylogenyNode( otu2 );
206 System.out.println( "Node " + ( ForesterUtil.isEmpty( n1.getName() ) ? n1.getId() : n1.getName() ) + " joins "
207 + ( ForesterUtil.isEmpty( n2.getName() ) ? n2.getId() : n2.getName() ) );
210 // only the values in the lower triangle are used.
211 // !matrix values will be changed!
212 private final void reset( final BasicSymmetricalDistanceMatrix distances ) {
213 _n = distances.getSize();
215 _r = new double[ _n ];
216 _mappings = new int[ _n ];
217 _d_values = _d.getValues();
218 _s = new ArrayList<SortedMap<Double, SortedSet<Integer>>>();
219 for( int j = 0; j < _n; ++j ) {
220 final TreeMap<Double, SortedSet<Integer>> map = new TreeMap<Double, SortedSet<Integer>>();
221 for( int i = 0; i < j; ++i ) {
222 if ( !map.containsKey( _d_values[ i ][ j ] ) ) {
223 map.put( _d_values[ i ][ j ], new TreeSet<Integer>() );
225 map.get( _d_values[ i ][ j ] ).add( i );
233 final private void printM() {
234 for( int j = 1; j < _n; ++j ) {
235 for( int i = 0; i < _n; ++i ) {
236 System.out.print( _d_values[ i ][ j ] );
237 System.out.print( " " );
239 System.out.print( " " );
240 for( final Entry<Double, SortedSet<Integer>> entry : _s.get( j ).entrySet() ) {
241 final double key = entry.getKey();
242 final SortedSet<Integer> value = entry.getValue();
243 System.out.print( key + "=" );
244 boolean first = true;
245 for( final Integer v : value ) {
247 System.out.print( "," );
250 System.out.print( v );
252 System.out.print( " " );
254 System.out.println();
258 private final void updateM() {
259 calculateNetDivergences();
260 Double min = Double.MAX_VALUE;
263 final int n_minus_2 = _n - 2;
264 for( int j = 1; j < _n; ++j ) {
265 final double r_j = _r[ j ];
266 final int m_j = _mappings[ j ];
267 for( int i = 0; i < j; ++i ) {
268 final double m = _d_values[ _mappings[ i ] ][ m_j ] - ( ( _r[ i ] + r_j ) / n_minus_2 );
278 // otu2 will, in effect, be "deleted" from the matrix.
279 private final void updateMappings( final int otu2 ) {
280 for( int i = otu2; i < ( _mappings.length - 1 ); ++i ) {
281 _mappings[ i ] = _mappings[ i + 1 ];
285 public final static NeighborJoiningR createInstance() {
286 return new NeighborJoiningR();
289 public final static NeighborJoiningR createInstance( final boolean verbose,
290 final int maximum_fraction_digits_for_distances ) {
291 return new NeighborJoiningR( verbose, maximum_fraction_digits_for_distances );