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
55 private NeighborJoiningR() {
60 private NeighborJoiningR( final boolean verbose, final int maximum_fraction_digits_for_distances ) {
61 if ( ( maximum_fraction_digits_for_distances < 1 ) || ( maximum_fraction_digits_for_distances > 9 ) ) {
62 throw new IllegalArgumentException( "maximum fraction digits for distances is out of range: "
63 + maximum_fraction_digits_for_distances );
66 _df = new DecimalFormat();
67 _df.setMaximumFractionDigits( maximum_fraction_digits_for_distances );
68 _df.setRoundingMode( RoundingMode.HALF_UP );
71 public final Phylogeny execute( final BasicSymmetricalDistanceMatrix distance ) {
73 final Phylogeny phylogeny = new Phylogeny();
75 System.out.println( "N=" + _n );
77 // Calculates the minimal distance.
78 // If more than one minimal distances, always the first found is used
79 final double m = updateM();
80 final int otu1 = _min_i;
81 final int otu2 = _min_j;
82 System.out.println( _min_i + " " + _min_j + " => " + DF.format( m ) + " (" + DF.format( _d_min ) + ")" );
83 // It is a condition that otu1 < otu2.
84 //System.out.println( "mapped 1 " + _mappings[ otu1 ] );
85 System.out.println( "mapped otu 2 " + _mappings[ otu2 ] );
86 final PhylogenyNode node = new PhylogenyNode();
87 //final double d = getDvalueUnmapped( otu1, _mappings[ otu2 ] );
88 final double d = _d_values[ otu1 ][ _mappings[ otu2 ] ];
89 final double d1 = ( d / 2 ) + ( ( _r[ otu1 ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) );
90 final double d2 = d - d1;
92 _external_nodes[ otu1 ].setDistanceToParent( d1 );
93 getExternalPhylogenyNode( otu2 ).setDistanceToParent( d2 );
96 // yes, yes, slow but only grows with n (and not n^2 or worse)...
97 _external_nodes[ otu1 ].setDistanceToParent( Double.parseDouble( _df.format( d1 ) ) );
98 getExternalPhylogenyNode( otu2 ).setDistanceToParent( Double.parseDouble( _df.format( d2 ) ) );
100 node.addAsChild( _external_nodes[ otu1 ] );
101 node.addAsChild( getExternalPhylogenyNode( otu2 ) );
103 printProgress( otu1, otu2, node );
105 System.out.println( "otu1=" + otu1 );
106 System.out.println( "otu2=" + otu2 );
107 calculateDistancesFromNewNode( otu1, otu2, d );
108 // _external_nodes[ _mappings[ otu1 ] ] = node;
109 _external_nodes[ otu1 ] = node;
110 updateMappings( otu2 );
112 System.out.println( "" );
113 System.out.println( "----------------------------------------------------------------------------------" );
114 System.out.println( "" );
116 final double d = getDvalue( 0, 1 ) / 2;
118 getExternalPhylogenyNode( 0 ).setDistanceToParent( d );
119 getExternalPhylogenyNode( 1 ).setDistanceToParent( d );
122 final double dd = Double.parseDouble( _df.format( d ) );
123 getExternalPhylogenyNode( 0 ).setDistanceToParent( dd );
124 getExternalPhylogenyNode( 1 ).setDistanceToParent( dd );
126 final PhylogenyNode root = new PhylogenyNode();
127 root.addAsChild( getExternalPhylogenyNode( 0 ) );
128 root.addAsChild( getExternalPhylogenyNode( 1 ) );
130 printProgress( 0, 1, root );
132 phylogeny.setRoot( root );
133 phylogeny.setRooted( false );
137 public final List<Phylogeny> execute( final List<BasicSymmetricalDistanceMatrix> distances_list ) {
138 final List<Phylogeny> pl = new ArrayList<Phylogeny>();
139 for( final BasicSymmetricalDistanceMatrix distances : distances_list ) {
140 pl.add( execute( distances ) );
145 private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) {
146 System.out.print( "new D values: " );
147 for( int j = 0; j < _n; ++j ) {
151 if ( _mappings[ j ] > _mappings[ otu1 ] ) {
152 updateDvalue( otu1, otu2, j, d );
155 System.out.println();
158 private final void updateDvalue( final int otu1, final int otu2, final int j, final double d ) {
159 final double new_d = ( getDvalueUnmapped( otu1, _mappings[ j ] ) + getDvalue( j, otu2 ) - d ) / 2;
160 System.out.print( DF.format( new_d ) + " " );
161 System.out.println( "going to remove: " + getDvalueUnmapped( otu1, _mappings[ j ] ) + ", " + otu1 + ", "
163 _s.removePairing( getDvalueUnmapped( otu1, _mappings[ j ] ), otu1, _mappings[ j ] );
164 System.out.println( "going to remove: " + getDvalue( j, otu2 ) + ", " + _mappings[ otu2 ] + ", "
166 _s.removePairing( getDvalue( j, otu2 ), _mappings[ otu2 ], _mappings[ j ] );
167 _s.addPairing( new_d, otu1, _mappings[ j ] );
168 setDvalueU( otu1, j, new_d );
171 private void setDvalueU( final int i, final int j, final double d ) {
172 if ( i < _mappings[ j ] ) {
173 _d_values[ i ][ _mappings[ j ] ] = d;
175 _d_values[ j ][ _mappings[ i ] ] = d;
178 private double getDvalue( final int i, final int j ) {
180 return _d_values[ _mappings[ i ] ][ _mappings[ j ] ];
182 return _d_values[ _mappings[ j ] ][ _mappings[ i ] ];
185 private double getDvalueUnmapped( final int i, final int j ) {
187 return _d_values[ i ][ j ];
189 return _d_values[ j ][ i ];
192 private final void calculateNetDivergences() {
193 for( int i = 0; i < _n; ++i ) {
194 _r[ i ] = calculateNetDivergence( i );
198 private double calculateNetDivergence( final int i ) {
200 for( int n = 0; n < _n; ++n ) {
202 d += getDvalue( n, i );
208 private final PhylogenyNode getExternalPhylogenyNode( final int i ) {
209 return _external_nodes[ _mappings[ i ] ];
212 private final void initExternalNodes() {
213 _external_nodes = new PhylogenyNode[ _n ];
215 for( int i = 0; i < _n; ++i ) {
216 _external_nodes[ i ] = new PhylogenyNode();
217 id = _d.getIdentifier( i );
219 _external_nodes[ i ].setName( id );
222 _external_nodes[ i ].setName( Integer.toString( i ) );
228 private final void printProgress( final int otu1, final int otu2, final PhylogenyNode node ) {
229 System.out.println( "Node " + printProgressNodeToString( _external_nodes[ otu1 ] ) + " joins "
230 + ( printProgressNodeToString( getExternalPhylogenyNode( otu2 ) ) ) + " [resulting in node "
231 + ( printProgressNodeToString( node ) ) + "]" );
234 private final String printProgressNodeToString( final PhylogenyNode n ) {
235 if ( n.isExternal() ) {
236 if ( ForesterUtil.isEmpty( n.getName() ) ) {
237 return Long.toString( n.getId() );
243 + ( ForesterUtil.isEmpty( n.getChildNode1().getName() ) ? n.getChildNode1().getId() : n.getChildNode1()
246 + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2()
250 // only the values in the lower triangle are used.
251 // !matrix values will be changed!
252 private final void reset( final BasicSymmetricalDistanceMatrix distances ) {
253 _n = distances.getSize();
255 _r = new double[ _n ];
256 _mappings = new int[ _n ];
257 _d_values = _d.getValues();
259 _s.initialize( distances );
261 System.out.println();
263 System.out.println( "----------------------------------------------------------------------------------" );
264 System.out.println();
265 System.out.println();
268 final private void printM() {
269 for( int j = 0; j < _d_values.length; ++j ) {
270 System.out.print( _external_nodes[ j ] );
271 System.out.print( "\t\t" );
272 for( int i = 0; i < _d_values[ j ].length; ++i ) {
273 System.out.print( DF.format( _d_values[ i ][ j ] ) );
274 System.out.print( " " );
276 System.out.println();
278 for( int j = 0; j < _n; ++j ) {
279 System.out.print( getExternalPhylogenyNode( j ) );
280 System.out.print( "\t\t" );
281 for( int i = 0; i < _n; ++i ) {
282 System.out.print( DF.format( _d_values[ _mappings[ i ] ][ _mappings[ j ] ] ) );
283 System.out.print( " " );
285 System.out.print( "\t\t" );
286 for( final Entry<Integer, SortedSet<Integer>> entry : _s.getSentrySet( _mappings[ j ] ) ) {
287 System.out.print( DF.format( ( double ) entry.getKey() / S.FACTOR ) + "=" );
288 boolean first = true;
289 for( final int v : entry.getValue() ) {
291 System.out.print( "," );
294 System.out.print( v );
296 System.out.print( " " );
298 System.out.println();
302 private final double updateM() {
303 calculateNetDivergences();
304 Double min_m = Double.MAX_VALUE;
307 final int n_minus_2 = _n - 2;
309 for( int j = 1; j < _n; ++j ) {
310 final double r_j = _r[ j ];
311 final int m_j = _mappings[ j ];
312 System.out.print( "j=" + j + " mj=" + m_j + ": " );
313 for( final Entry<Integer, SortedSet<Integer>> entry : _s.getSentrySet( m_j ) ) {
314 for( final int sorted_i : entry.getValue() ) {
315 System.out.print( sorted_i + " " );
316 System.out.print( "(" + DF.format( getDvalueUnmapped( sorted_i, m_j ) ) + ") " );
317 final double m = getDvalueUnmapped( sorted_i, m_j ) - ( ( _r[ sorted_i ] + r_j ) / n_minus_2 );
318 if ( ( m < min_m ) ) {
319 _d_min = getDvalueUnmapped( sorted_i, m_j );
326 System.out.println();
327 for( final Entry<Integer, SortedSet<Integer>> entry : _s.getSentrySet( m_j ) ) {
328 for( final int sorted_i : entry.getValue() ) {
329 System.out.print( sorted_i );
330 System.out.print( "->" );
331 System.out.print( DF.format( _r[ sorted_i ] ) );
332 System.out.print( " " );
335 System.out.println();
337 for( int i = 0; i < j; ++i ) {
338 final double m = getDvalue( i, j ) - ( ( _r[ i ] + r_j ) / n_minus_2 );
341 _d_min = getDvalue( i, j );
347 System.out.println();
351 // otu2 will, in effect, be "deleted" from the matrix.
352 private final void updateMappings( final int otu2 ) {
353 for( int i = otu2; i < ( _mappings.length - 1 ); ++i ) {
354 System.out.print( _mappings[ i ] );
355 _mappings[ i ] = _mappings[ i + 1 ];
356 System.out.println( "----->" + _mappings[ i ] );
358 for( int i = 0; i < _mappings.length; ++i ) {
359 System.out.println( i + "-->" + _mappings[ i ] );
363 public final static NeighborJoiningR createInstance() {
364 return new NeighborJoiningR();
367 public final static NeighborJoiningR createInstance( final boolean verbose,
368 final int maximum_fraction_digits_for_distances ) {
369 return new NeighborJoiningR( verbose, maximum_fraction_digits_for_distances );