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.SortedSet;
34 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
35 import org.forester.phylogeny.Phylogeny;
36 import org.forester.phylogeny.PhylogenyNode;
37 import org.forester.util.ForesterUtil;
39 public final class NeighborJoiningR {
41 private final static DecimalFormat DF = new DecimalFormat( "0.00000" );
42 private BasicSymmetricalDistanceMatrix _d;
43 private double[][] _d_values;
44 private final DecimalFormat _df;
45 private PhylogenyNode[] _external_nodes;
46 private int[] _mappings;
49 private final boolean _verbose;
53 private double _d_min; //TODO remove me
54 private int[] _rev_mappings;
57 private NeighborJoiningR() {
62 private NeighborJoiningR( final boolean verbose, final int maximum_fraction_digits_for_distances ) {
63 if ( ( maximum_fraction_digits_for_distances < 1 ) || ( maximum_fraction_digits_for_distances > 9 ) ) {
64 throw new IllegalArgumentException( "maximum fraction digits for distances is out of range: "
65 + maximum_fraction_digits_for_distances );
68 _df = new DecimalFormat();
69 _df.setMaximumFractionDigits( maximum_fraction_digits_for_distances );
70 _df.setRoundingMode( RoundingMode.HALF_UP );
73 public final Phylogeny execute( final BasicSymmetricalDistanceMatrix distance ) {
75 final Phylogeny phylogeny = new Phylogeny();
78 System.out.println( "N=" + _n );
81 // Calculates the minimal distance.
82 // If more than one minimal distances, always the first found is used
83 final double m = updateM();
84 final int otu1 = _min_i;
85 final int otu2 = _min_j;
87 System.out.println( _min_i + " " + _min_j + " => " + DF.format( m ) + " (" + DF.format( _d_min ) + ")" );
88 // It is a condition that otu1 < otu2.
89 //System.out.println( "mapped 1 " + _mappings[ otu1 ] );
90 System.out.println( "mapped otu 2 " + _mappings[ otu2 ] );
92 final PhylogenyNode node = new PhylogenyNode();
93 //final double d = getDvalueUnmapped( otu1, _mappings[ otu2 ] );
94 final double d = _d_values[ otu1 ][ _mappings[ otu2 ] ];
95 final double d1 = ( d / 2 ) + ( ( _r[ _rev_mappings[ otu1 ] ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) );
96 final double d2 = d - d1;
98 _external_nodes[ otu1 ].setDistanceToParent( d1 );
99 getExternalPhylogenyNode( otu2 ).setDistanceToParent( d2 );
102 // yes, yes, slow but only grows with n (and not n^2 or worse)...
103 _external_nodes[ otu1 ].setDistanceToParent( Double.parseDouble( _df.format( d1 ) ) );
104 getExternalPhylogenyNode( otu2 ).setDistanceToParent( Double.parseDouble( _df.format( d2 ) ) );
106 node.addAsChild( _external_nodes[ otu1 ] );
107 node.addAsChild( getExternalPhylogenyNode( otu2 ) );
109 printProgress( otu1, otu2, node );
112 System.out.println( "otu1=" + otu1 );
113 System.out.println( "otu2=" + otu2 );
115 calculateDistancesFromNewNode( otu1, otu2, d );
116 // _external_nodes[ _mappings[ otu1 ] ] = node;
117 _external_nodes[ otu1 ] = node;
118 updateMappings( otu2 );
121 System.out.println( "" );
123 .println( "----------------------------------------------------------------------------------" );
124 System.out.println( "" );
127 final double d = getDvalue( 0, 1 ) / 2;
129 getExternalPhylogenyNode( 0 ).setDistanceToParent( d );
130 getExternalPhylogenyNode( 1 ).setDistanceToParent( d );
133 final double dd = Double.parseDouble( _df.format( d ) );
134 getExternalPhylogenyNode( 0 ).setDistanceToParent( dd );
135 getExternalPhylogenyNode( 1 ).setDistanceToParent( dd );
137 final PhylogenyNode root = new PhylogenyNode();
138 root.addAsChild( getExternalPhylogenyNode( 0 ) );
139 root.addAsChild( getExternalPhylogenyNode( 1 ) );
141 printProgress( 0, 1, root );
143 phylogeny.setRoot( root );
144 phylogeny.setRooted( false );
148 public final List<Phylogeny> execute( final List<BasicSymmetricalDistanceMatrix> distances_list ) {
149 final List<Phylogeny> pl = new ArrayList<Phylogeny>();
150 for( final BasicSymmetricalDistanceMatrix distances : distances_list ) {
151 pl.add( execute( distances ) );
156 private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) {
157 for( int j = 0; j < _n; ++j ) {
158 if ( ( j == otu2 ) || ( j == _rev_mappings[ otu1 ] ) ) {
161 updateDvalue( otu1, otu2, j, d );
164 System.out.println();
168 private final void updateDvalue( final int otu1, final int otu2, final int j, final double d ) {
169 final int mj = _mappings[ j ];
170 // final double new_d = ( getDvalueUnmapped( otu1, _mappings[ j ] ) + getDvalue( j, otu2 ) - d ) / 2;
171 // System.out.println( "\nnew d value: " + DF.format( new_d ) );
173 _s.removePairing( _d_values[ otu1][ mj ] , otu1, mj );
176 _s.removePairing( _d_values[ mj ][ otu1 ], mj, otu1 );
178 if ( _mappings[ otu2 ] < mj ) {
179 _s.removePairing( getDvalue( j, otu2 ), _mappings[ otu2 ], mj );
182 _s.removePairing( getDvalue( j, otu2 ), mj, _mappings[ otu2 ] );
186 new_d = ( _d_values[ otu1 ][ mj ] + getDvalue( j, otu2 ) - d ) / 2;
187 _s.addPairing( new_d, otu1, mj );
188 _d_values[ otu1 ][ mj ] = new_d;
191 new_d = ( _d_values[ mj ][ otu1 ] + getDvalue( j, otu2 ) - d ) / 2;
192 _s.addPairing( new_d, mj, otu1 );
193 _d_values[ mj ][ otu1 ] = new_d;
197 private double getDvalue( final int i, final int j ) {
199 return _d_values[ _mappings[ i ] ][ _mappings[ j ] ];
201 return _d_values[ _mappings[ j ] ][ _mappings[ i ] ];
204 private final void calculateNetDivergences() {
206 for( int i = 0; i < _n; ++i ) {
207 _r[ i ] = calculateNetDivergence( i );
208 if ( _r[i ] > _umax ) {
212 // System.out.println( "umax=" + _umax );
215 private double calculateNetDivergence( final int i ) {
217 for( int n = 0; n < _n; ++n ) {
219 d += getDvalue( n, i );
225 private final PhylogenyNode getExternalPhylogenyNode( final int i ) {
226 return _external_nodes[ _mappings[ i ] ];
229 private final void initExternalNodes() {
230 _external_nodes = new PhylogenyNode[ _n ];
232 for( int i = 0; i < _n; ++i ) {
233 _external_nodes[ i ] = new PhylogenyNode();
234 id = _d.getIdentifier( i );
236 _external_nodes[ i ].setName( id );
239 _external_nodes[ i ].setName( Integer.toString( i ) );
242 _rev_mappings[ i ] = i;
246 private final void printProgress( final int otu1, final int otu2, final PhylogenyNode node ) {
247 System.out.println( "Node " + printProgressNodeToString( _external_nodes[ otu1 ] ) + " joins "
248 + ( printProgressNodeToString( getExternalPhylogenyNode( otu2 ) ) ) + " [resulting in node "
249 + ( printProgressNodeToString( node ) ) + "]" );
252 private final String printProgressNodeToString( final PhylogenyNode n ) {
253 if ( n.isExternal() ) {
254 if ( ForesterUtil.isEmpty( n.getName() ) ) {
255 return Long.toString( n.getId() );
261 + ( ForesterUtil.isEmpty( n.getChildNode1().getName() ) ? n.getChildNode1().getId() : n.getChildNode1()
264 + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2()
268 // only the values in the lower triangle are used.
269 // !matrix values will be changed!
270 private final void reset( final BasicSymmetricalDistanceMatrix distances ) {
271 _n = distances.getSize();
273 _r = new double[ _n ];
274 _mappings = new int[ _n ];
275 _rev_mappings = new int[ _n ];
276 _d_values = distances.getValues();
278 _s.initialize( distances );
281 System.out.println();
283 System.out.println( "----------------------------------------------------------------------------------" );
284 System.out.println();
285 System.out.println();
289 final private void printM() {
290 for( int j = 0; j < _d_values.length; ++j ) {
291 System.out.print( _external_nodes[ j ] );
292 System.out.print( "\t\t" );
293 for( int i = 0; i < _d_values[ j ].length; ++i ) {
294 System.out.print( DF.format( _d_values[ i ][ j ] ) );
295 System.out.print( " " );
297 System.out.println();
299 for( int j = 0; j < _n; ++j ) {
300 System.out.print( getExternalPhylogenyNode( j ) );
301 System.out.print( "\t\t" );
302 for( int i = 0; i < _n; ++i ) {
303 System.out.print( DF.format( _d_values[ _mappings[ i ] ][ _mappings[ j ] ] ) );
304 System.out.print( " " );
306 System.out.print( "\t\t" );
307 for( final Entry<Integer, SortedSet<Integer>> entry : _s.getSentrySet( _mappings[ j ] ) ) {
308 System.out.print( DF.format( ( double ) entry.getKey() / S.FACTOR ) + "=" );
309 boolean first = true;
310 for( final int v : entry.getValue() ) {
312 System.out.print( "," );
315 System.out.print( v );
317 System.out.print( " " );
319 System.out.println();
323 private final double updateM() {
324 calculateNetDivergences();
325 Double min_m = Double.MAX_VALUE;
328 final int n_minus_2 = _n - 2;
332 for( int j = 1; j < _n; ++j ) {
333 final double r_j = _r[ j ];
334 final int m_j = _mappings[ j ];
336 System.out.print( "j=" + j + " mj=" + m_j + ": " );
338 X: for( final Entry<Integer, SortedSet<Integer>> entry : _s.getSentrySet( m_j ) ) {
339 for( final int sorted_i : entry.getValue() ) {
340 final double m = _d_values[ sorted_i ][ m_j ]
341 - ( ( _r[ _rev_mappings[ sorted_i ] ] + r_j ) / n_minus_2 );
342 //final double m = getDvalueUnmapped( sorted_i, m_j )
343 // - ( ( _r[ _rev_mappings[ sorted_i ] ] + r_j ) / n_minus_2 );
345 if ( m - r_j - _umax > min_m ) {
346 System.out.println( m );
351 if ( ( m < min_m ) ) {
352 // _d_min = getDvalueUnmapped( sorted_i, m_j );
360 System.out.println();
361 for( final Entry<Integer, SortedSet<Integer>> entry : _s.getSentrySet( m_j ) ) {
362 for( final int sorted_i : entry.getValue() ) {
363 System.out.print( sorted_i );
364 System.out.print( "->" );
365 System.out.print( DF.format( _r[ sorted_i ] ) );
366 System.out.print( " " );
369 System.out.println();
373 System.out.println();
378 // otu2 will, in effect, be "deleted" from the matrix.
379 private final void updateMappings( final int otu2 ) {
380 for( int i = otu2; i < ( _mappings.length - 1 ); ++i ) {
381 //System.out.print( _mappings[ i ] );
382 _mappings[ i ] = _mappings[ i + 1 ];
383 //System.out.println( "----->" + _mappings[ i ] );
385 // for( int i = 0; i < _mappings.length; ++i ) {
386 // System.out.println( i + "-->" + _mappings[ i ] );
388 for( int i = 0; i < _n; ++i ) {
389 _rev_mappings[ _mappings[ i ] ] = i;
393 public final static NeighborJoiningR createInstance() {
394 return new NeighborJoiningR();
397 public final static NeighborJoiningR createInstance( final boolean verbose,
398 final int maximum_fraction_digits_for_distances ) {
399 return new NeighborJoiningR( verbose, maximum_fraction_digits_for_distances );