2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
7 // Copyright (C) 2000-2001 Washington University School of Medicine
8 // and Howard Hughes Medical Institute
11 // This library is free software; you can redistribute it and/or
12 // modify it under the terms of the GNU Lesser General Public
13 // License as published by the Free Software Foundation; either
14 // version 2.1 of the License, or (at your option) any later version.
16 // This library is distributed in the hope that it will be useful,
17 // but WITHOUT ANY WARRANTY; without even the implied warranty of
18 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 // Lesser General Public License for more details.
21 // You should have received a copy of the GNU Lesser General Public
22 // License along with this library; if not, write to the Free Software
23 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
25 // Contact: phylosoft @ gmail . com
26 // WWW: www.phylosoft.org/forester
28 package org.forester.rio;
31 import java.io.FileNotFoundException;
32 import java.io.IOException;
33 import java.util.ArrayList;
34 import java.util.Arrays;
35 import java.util.Collections;
36 import java.util.HashMap;
37 import java.util.HashSet;
38 import java.util.List;
41 import org.forester.datastructures.IntMatrix;
42 import org.forester.io.parsers.PhylogenyParser;
43 import org.forester.io.parsers.nhx.NHXParser;
44 import org.forester.io.parsers.util.ParserUtils;
45 import org.forester.phylogeny.Phylogeny;
46 import org.forester.phylogeny.PhylogenyMethods;
47 import org.forester.phylogeny.PhylogenyNode;
48 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
49 import org.forester.phylogeny.factories.PhylogenyFactory;
50 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
51 import org.forester.sdi.GSDIR;
52 import org.forester.sdi.SDI;
53 import org.forester.sdi.SDIException;
54 import org.forester.sdi.SDIR;
55 import org.forester.util.ForesterUtil;
57 public final class RIO {
59 private final static boolean ROOT_BY_MINIMIZING_SUM_OF_DUPS = true;
60 private final static boolean ROOT_BY_MINIMIZING_TREE_HEIGHT = true;
61 private Phylogeny[] _analyzed_gene_trees;
62 private HashMap<String, HashMap<String, Integer>> _o_maps;
63 private HashMap<String, HashMap<String, Integer>> _so_maps;
64 private HashMap<String, HashMap<String, Integer>> _up_maps;
65 private List<String> _seq_names;
66 private List<PhylogenyNode> _removed_gene_tree_nodes;
68 private int _ext_nodes;
71 * Default constructor.
72 * @throws SDIException
74 * @throws RIOException
76 public RIO( final File gene_trees_file,
77 final Phylogeny species_tree,
79 final SDI.ALGORITHM algorithm ) throws IOException, SDIException, RIOException {
80 if ( ForesterUtil.isEmpty( query ) ) {
81 throw new IllegalArgumentException( "query is empty" );
84 inferOrthologs( gene_trees_file, species_tree, query, algorithm );
87 public RIO( final File gene_trees_file, final Phylogeny species_tree, final SDI.ALGORITHM algorithm )
88 throws IOException, SDIException, RIOException {
90 inferOrthologs( gene_trees_file, species_tree, null, algorithm );
93 public final Phylogeny[] getAnalyzedGeneTrees() {
94 return _analyzed_gene_trees;
98 * Returns the numbers of number of ext nodes in gene trees analyzed (after
101 * @return number of ext nodes in gene trees analyzed (after stripping)
103 public final int getExtNodesOfAnalyzedGeneTrees() {
108 * Returns a HashMap containing the inferred "ultra paralogs" of the
109 * external gene tree node with the sequence name seq_name. Sequence names
110 * are the keys (String), numbers of observations are the values (Int).
111 * "ultra paralogs" are to be inferred by method "inferOrthologs". Throws an
112 * exception if seq_name is not found.
115 * sequence name of a external node of the gene trees
116 * @return HashMap containing the inferred ultra paralogs
117 * (name(String)->value(Int))
119 public final HashMap<String, Integer> getInferredUltraParalogs( final String seq_name ) {
120 if ( _up_maps == null ) {
123 return _up_maps.get( seq_name );
126 public final int getNumberOfSamples() {
131 * Returns a String containg the names of orthologs of the PhylogenyNode
132 * with seq name query_name. The String also contains how many times a
133 * particular ortholog has been observed.
136 * The output order is (per line): Name, Ortholog, Subtree neighbor, Super
140 * The sort priority of this is determined by sort in the following manner:
143 * <li>1 : Ortholog, Super ortholog
144 * <li>2 : Super ortholog, Ortholog
147 * Returns "-" if no putative orthologs have been found (given
148 * threshold_orthologs).
150 * Orthologs are to be inferred by method "inferOrthologs".
152 * (Last modified: 05/08/01)
155 * sequence name of a external node of the gene trees
157 * order and sort priority
158 * @param threshold_orthologs
159 * the minimal number of observations for a a sequence to be
160 * reported as orthologous, in percents (0.0-100.0%)
161 * @param threshold_subtreeneighborings
162 * the minimal number of observations for a a sequence to be
163 * reported as orthologous, in percents (0.0-100.0%)
164 * @return String containing the inferred orthologs, String containing "-"
165 * if no orthologs have been found null in case of error
167 public final StringBuffer inferredOrthologsToString( final String query_name, int sort, double threshold_orthologs ) {
168 HashMap<String, Integer> o_hashmap = null;
169 HashMap<String, Integer> s_hashmap = null;
171 double o = 0.0; // Orthologs.
172 double s = 0.0; // Super orthologs.
175 final ArrayList<ResultLine> nv = new ArrayList<ResultLine>();
176 if ( ( _o_maps == null ) || ( _so_maps == null ) ) {
177 throw new RuntimeException( "orthologs have not been calculated (successfully)" );
179 if ( ( sort < 0 ) || ( sort > 2 ) ) {
182 if ( threshold_orthologs < 0.0 ) {
183 threshold_orthologs = 0.0;
185 else if ( threshold_orthologs > 100.0 ) {
186 threshold_orthologs = 100.0;
188 o_hashmap = getInferredOrthologs( query_name );
189 s_hashmap = getInferredSuperOrthologs( query_name );
190 if ( ( o_hashmap == null ) || ( s_hashmap == null ) ) {
191 throw new RuntimeException( "Orthologs for " + query_name + " were not established" );
193 final StringBuffer orthologs = new StringBuffer();
194 if ( _seq_names.size() > 0 ) {
195 I: for( int i = 0; i < _seq_names.size(); ++i ) {
196 name = _seq_names.get( i );
197 if ( name.equals( query_name ) ) {
200 o = getBootstrapValueFromHash( o_hashmap, name );
201 if ( o < threshold_orthologs ) {
204 s = getBootstrapValueFromHash( s_hashmap, name );
207 nv.add( new ResultLine( name, o, 5 ) );
210 nv.add( new ResultLine( name, o, s, 5 ) );
213 nv.add( new ResultLine( name, s, o, 5 ) );
216 nv.add( new ResultLine( name, o, 5 ) );
218 } // End of I for loop.
219 if ( ( nv != null ) && ( nv.size() > 0 ) ) {
220 orthologs.append( "seq name\t\tortho\ts-ortho" + ForesterUtil.LINE_SEPARATOR );
221 final ResultLine[] nv_array = new ResultLine[ nv.size() ];
222 for( int j = 0; j < nv.size(); ++j ) {
223 nv_array[ j ] = nv.get( j );
225 Arrays.sort( nv_array );
226 for( final ResultLine element : nv_array ) {
227 name = element.getKey();
228 value1 = element.getValue1();
229 value2 = element.getValue2();
230 orthologs.append( addNameAndValues( name, value1, value2, sort ) );
234 // No orthologs found.
235 if ( ( orthologs == null ) || ( orthologs.length() < 1 ) ) {
236 orthologs.append( "-" );
242 * Returns a String containg the names of orthologs of the PhylogenyNode
243 * with seq name query_name. The String also contains how many times a
244 * particular ortholog has been observed. Returns "-" if no putative
245 * orthologs have been found (given threshold_orthologs).
247 * Orthologs are to be inferred by method "inferOrthologs".
250 * sequence name of a external node of the gene trees
251 * @param return_dists
252 * @param threshold_ultra_paralogs
254 * @return String containing the inferred orthologs, String containing "-"
255 * if no orthologs have been found null in case of error
257 public final String inferredUltraParalogsToString( final String query_name, double threshold_ultra_paralogs ) {
258 HashMap<String, Integer> sp_hashmap = null;
259 String name = "", ultra_paralogs = "";
264 final List<ResultLine> nv = new ArrayList<ResultLine>();
265 if ( threshold_ultra_paralogs < 1.0 ) {
266 threshold_ultra_paralogs = 1.0;
268 else if ( threshold_ultra_paralogs > 100.0 ) {
269 threshold_ultra_paralogs = 100.0;
271 if ( _up_maps == null ) {
272 throw new RuntimeException( "Ultra paralogs have not been calculated (successfully)." );
274 sp_hashmap = getInferredUltraParalogs( query_name );
275 if ( sp_hashmap == null ) {
276 throw new RuntimeException( "Ultra paralogs for " + query_name + " were not established" );
278 if ( _seq_names.size() > 0 ) {
279 I: for( int i = 0; i < _seq_names.size(); ++i ) {
280 name = _seq_names.get( i );
281 if ( name.equals( query_name ) ) {
284 sp = getBootstrapValueFromHash( sp_hashmap, name );
285 if ( sp < threshold_ultra_paralogs ) {
288 nv.add( new ResultLine( name, sp, 5 ) );
289 } // End of I for loop.
290 if ( ( nv != null ) && ( nv.size() > 0 ) ) {
291 final ResultLine[] nv_array = new ResultLine[ nv.size() ];
292 for( int j = 0; j < nv.size(); ++j ) {
293 nv_array[ j ] = nv.get( j );
295 Arrays.sort( nv_array );
297 for( final ResultLine element : nv_array ) {
298 name = element.getKey();
299 value1 = element.getValue1();
300 value2 = element.getValue2();
301 ultra_paralogs += addNameAndValues( name, value1, value2, sort );
305 // No ultra paralogs found.
306 if ( ( ultra_paralogs == null ) || ( ultra_paralogs.length() < 1 ) ) {
307 ultra_paralogs = "-";
309 return ultra_paralogs;
312 // Helper method for inferredOrthologsToString.
313 // inferredOrthologsToArrayList,
314 // and inferredUltraParalogsToString.
315 private final double getBootstrapValueFromHash( final HashMap<String, Integer> h, final String name ) {
316 if ( !h.containsKey( name ) ) {
319 final int i = h.get( name );
320 return ( ( i * 100.0 ) / getNumberOfSamples() );
324 * Returns a HashMap containing the inferred orthologs of the external gene
325 * tree node with the sequence name seq_name. Sequence names are the keys
326 * (String), numbers of observations are the values (Int). Orthologs are to
327 * be inferred by method "inferOrthologs". Throws an exception if seq_name
331 * sequence name of a external node of the gene trees
332 * @return HashMap containing the inferred orthologs
333 * (name(String)->value(Int))
335 private final HashMap<String, Integer> getInferredOrthologs( final String seq_name ) {
336 if ( _o_maps == null ) {
339 return _o_maps.get( seq_name );
343 * Returns a HashMap containing the inferred "super orthologs" of the
344 * external gene tree node with the sequence name seq_name. Sequence names
345 * are the keys (String), numbers of observations are the values (Int).
346 * Super orthologs are to be inferred by method "inferOrthologs". Throws an
347 * exception if seq_name is not found.
350 * sequence name of a external node of the gene trees
351 * @return HashMap containing the inferred super orthologs
352 * (name(String)->value(Int))
354 private final HashMap<String, Integer> getInferredSuperOrthologs( final String seq_name ) {
355 if ( _so_maps == null ) {
358 return _so_maps.get( seq_name );
362 * Infers the orthologs (as well the "super orthologs", the "subtree
363 * neighbors", and the "ultra paralogs") for each external node of the gene
364 * Trees in multiple tree File gene_trees_file (=output of PHYLIP NEIGHBOR,
365 * for example). Tallies how many times each sequence is (super-)
366 * orthologous towards the query. Tallies how many times each sequence is
367 * ultra paralogous towards the query. Tallies how many times each sequence
368 * is a subtree neighbor of the query. Gene duplications are inferred using
369 * SDI. Modifies its argument species_tree. Is a little faster than
370 * "inferOrthologs(File,Phylogeny)" since orthologs are only inferred for
373 * To obtain the results use the methods listed below.
375 * @param gene_trees_file
376 * a File containing gene Trees in NH format, which is the result
377 * of performing a bootstrap analysis in PHYLIP
378 * @param species_tree
379 * a species Phylogeny, which has species names in its species
382 * the sequence name of the squence whose orthologs are to be
384 * @throws SDIException
385 * @throws RIOException
386 * @throws IOException
387 * @throws FileNotFoundException
389 private final void inferOrthologs( final File gene_trees_file,
390 final Phylogeny species_tree,
392 final SDI.ALGORITHM algorithm ) throws SDIException, RIOException,
393 FileNotFoundException, IOException {
394 // Read in first tree to get its sequence names
395 // and strip species_tree.
396 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
397 final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( gene_trees_file, true );
398 if ( p instanceof NHXParser ) {
399 final NHXParser nhx = ( NHXParser ) p;
400 nhx.setReplaceUnderscores( false );
401 nhx.setIgnoreQuotes( true );
402 nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
404 final Phylogeny[] gene_trees = factory.create( gene_trees_file, p );
405 // Removes from species_tree all species not found in gene_tree.
406 final List<PhylogenyNode> _removed_gene_tree_nodes = PhylogenyMethods
407 .taxonomyBasedDeletionOfExternalNodes( gene_trees[ 0 ], species_tree );
408 if ( species_tree.isEmpty() ) {
409 throw new RIOException( "failed to establish species based mapping between gene and species trees" );
411 if ( !ForesterUtil.isEmpty( query ) ) {
412 PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gene_trees[ 0 ] );
413 if ( gene_trees[ 0 ].isEmpty() ) {
414 throw new RIOException( "failed to establish species based mapping between gene and species trees" );
416 _seq_names = getAllExternalSequenceNames( gene_trees[ 0 ] );
417 if ( ( _seq_names == null ) || ( _seq_names.size() < 1 ) ) {
418 throw new RIOException( "could not get sequence names" );
420 _o_maps = new HashMap<String, HashMap<String, Integer>>();
421 _so_maps = new HashMap<String, HashMap<String, Integer>>();
422 _up_maps = new HashMap<String, HashMap<String, Integer>>();
423 _o_maps.put( query, new HashMap<String, Integer>( _seq_names.size() ) );
424 _so_maps.put( query, new HashMap<String, Integer>( _seq_names.size() ) );
425 _up_maps.put( query, new HashMap<String, Integer>( _seq_names.size() ) );
427 _analyzed_gene_trees = new Phylogeny[ gene_trees.length ];
429 int gene_tree_ext_nodes = 0;
430 for( final Phylogeny gt : gene_trees ) {
431 // Removes from gene_tree all species not found in species_tree.
432 PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gt );
433 if ( gt.isEmpty() ) {
434 throw new RIOException( "failed to establish species based mapping between gene and species trees" );
437 gene_tree_ext_nodes = gt.getNumberOfExternalNodes();
439 else if ( gene_tree_ext_nodes != gt.getNumberOfExternalNodes() ) {
440 throw new RIOException( "(cleaned up) gene tree #" + ( c + 1 )
441 + " has a different number of external nodes (" + gt.getNumberOfExternalNodes()
442 + ") than those gene trees preceding it (" + gene_tree_ext_nodes + ")" );
444 _analyzed_gene_trees[ c++ ] = performOrthologInference( gt, species_tree, query, algorithm );
446 setNumberOfSamples( gene_trees.length );
449 private final Phylogeny performOrthologInference( final Phylogeny gene_tree,
450 final Phylogeny species_tree,
452 final SDI.ALGORITHM algorithm ) throws SDIException, RIOException {
453 final Phylogeny assigned_tree;
454 switch ( algorithm ) {
456 final SDIR sdir = new SDIR();
457 assigned_tree = sdir.infer( gene_tree,
460 RIO.ROOT_BY_MINIMIZING_SUM_OF_DUPS,
461 RIO.ROOT_BY_MINIMIZING_TREE_HEIGHT,
467 final GSDIR gsdir = new GSDIR( gene_tree, species_tree, true, 1 );
468 assigned_tree = gsdir.getMinDuplicationsSumGeneTrees().get( 1 );
472 throw new IllegalArgumentException( "illegal algorithm: " + algorithm );
475 setExtNodesOfAnalyzedGeneTrees( assigned_tree.getNumberOfExternalNodes() );
476 if ( !ForesterUtil.isEmpty( query ) ) {
477 final List<PhylogenyNode> nodes = getNodesViaSequenceName( assigned_tree, query );
478 if ( nodes.size() > 1 ) {
479 throw new RIOException( "node named [" + query + "] not unique" );
481 else if ( nodes.isEmpty() ) {
482 throw new RIOException( "no node containing a sequence named [" + query + "] found" );
484 final PhylogenyNode query_node = nodes.get( 0 );
485 updateCounts( _o_maps, query, PhylogenyMethods.getOrthologousNodes( assigned_tree, query_node ) );
486 updateCounts( _so_maps, query, PhylogenyMethods.getSuperOrthologousNodes( query_node ) );
487 updateCounts( _up_maps, query, PhylogenyMethods.getUltraParalogousNodes( query_node ) );
489 return assigned_tree;
492 private final void init() {
501 private final void setExtNodesOfAnalyzedGeneTrees( final int i ) {
505 private final void setNumberOfSamples( int i ) {
512 // Helper for doInferOrthologs( Phylogeny, Phylogeny, String )
513 // and doInferOrthologs( Phylogeny, Phylogeny ).
514 private final void updateCounts( final HashMap<String, HashMap<String, Integer>> counter_map,
515 final String query_seq_name,
516 final List<PhylogenyNode> nodes ) {
517 final HashMap<String, Integer> hash_map = counter_map.get( query_seq_name );
518 if ( hash_map == null ) {
519 throw new RuntimeException( "unexpected error in updateCounts" );
521 for( int j = 0; j < nodes.size(); ++j ) {
523 if ( ( nodes.get( j ) ).getNodeData().isHasSequence()
524 && !ForesterUtil.isEmpty( ( nodes.get( j ) ).getNodeData().getSequence().getName() ) ) {
525 seq_name = ( nodes.get( j ) ).getNodeData().getSequence().getName();
528 seq_name = ( nodes.get( j ) ).getName();
530 if ( hash_map.containsKey( seq_name ) ) {
531 hash_map.put( seq_name, hash_map.get( seq_name ) + 1 );
534 hash_map.put( seq_name, 1 );
539 public final static IntMatrix calculateOrthologTable( final Phylogeny[] analyzed_gene_trees, final boolean sort )
540 throws RIOException {
541 final List<String> labels = new ArrayList<String>();
542 final Set<String> labels_set = new HashSet<String>();
544 for( final PhylogenyNode n : analyzed_gene_trees[ 0 ].getExternalNodes() ) {
545 if ( n.getNodeData().isHasSequence() && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
546 label = n.getNodeData().getSequence().getName();
548 else if ( n.getNodeData().isHasSequence()
549 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
550 label = n.getNodeData().getSequence().getSymbol();
552 else if ( !ForesterUtil.isEmpty( n.getName() ) ) {
556 throw new IllegalArgumentException( "node " + n + " has no appropriate label" );
558 if ( labels_set.contains( label ) ) {
559 throw new IllegalArgumentException( "label " + label + " is not unique" );
561 labels_set.add( label );
565 Collections.sort( labels );
567 final IntMatrix m = new IntMatrix( labels );
569 for( final Phylogeny gt : analyzed_gene_trees ) {
571 PhylogenyMethods.preOrderReId( gt );
572 final HashMap<String, PhylogenyNode> map = PhylogenyMethods.createNameToExtNodeMap( gt );
573 for( int x = 0; x < m.size(); ++x ) {
574 final String mx = m.getLabel( x );
575 final PhylogenyNode nx = map.get( mx );
577 throw new RIOException( "node \"" + mx + "\" not present in gene tree #" + counter );
581 for( int y = 0; y < m.size(); ++y ) {
582 my = m.getLabel( y );
585 throw new RIOException( "node \"" + my + "\" not present in gene tree #" + counter );
587 if ( !PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( nx, ny ).isDuplication() ) {
588 m.inreaseByOne( x, y );
597 * Returns the order in which ortholog (o), "super ortholog" (s) and
598 * distance (d) are returned and sorted (priority of sort always goes from
599 * left to right), given sort. For the meaning of sort
601 * @see #inferredOrthologsToString(String,int,double,double)
604 * determines order and sort priority
605 * @return String indicating the order
607 public final static String getOrder( final int sort ) {
611 order = "orthologies";
614 order = "orthologies > super orthologies";
617 order = "super orthologies > orthologies";
620 order = "orthologies";
626 public final static StringBuffer getOrderHelp() {
627 final StringBuffer sb = new StringBuffer();
628 sb.append( " 0: orthologies" + ForesterUtil.LINE_SEPARATOR );
629 sb.append( " 1: orthologies > super orthologies" + ForesterUtil.LINE_SEPARATOR );
630 sb.append( " 2: super orthologies > orthologies" + ForesterUtil.LINE_SEPARATOR );
634 // Helper method for inferredOrthologsToString
635 // and inferredUltraParalogsToString.
636 private final static String addNameAndValues( final String name,
640 final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.#####" );
641 df.setDecimalSeparatorAlwaysShown( false );
643 if ( name.length() < 8 ) {
644 line += ( name + "\t\t\t" );
646 else if ( name.length() < 16 ) {
647 line += ( name + "\t\t" );
650 line += ( name + "\t" );
654 line += addToLine( value1, df );
658 line += addToLine( value1, df );
659 line += addToLine( value2, df );
662 line += addToLine( value2, df );
663 line += addToLine( value1, df );
666 line += addToLine( value1, df );
670 line += addToLine( value1, df );
671 line += addToLine( value2, df );
674 line += ForesterUtil.LINE_SEPARATOR;
678 // Helper for addNameAndValues.
679 private final static String addToLine( final double value, final java.text.DecimalFormat df ) {
681 if ( value != ResultLine.DEFAULT ) {
682 s = df.format( value ) + "\t";
690 private final static List<String> getAllExternalSequenceNames( final Phylogeny phy ) throws RIOException {
691 final List<String> names = new ArrayList<String>();
692 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
693 final PhylogenyNode n = iter.next();
694 if ( n.getNodeData().isHasSequence() && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
695 names.add( n.getNodeData().getSequence().getName() );
697 else if ( !ForesterUtil.isEmpty( n.getName() ) ) {
698 names.add( n.getName() );
701 throw new RIOException( "node has no (sequence) name: " + n );
707 private final static List<PhylogenyNode> getNodesViaSequenceName( final Phylogeny phy, final String seq_name ) {
708 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
709 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
710 final PhylogenyNode n = iter.next();
711 if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getName().equals( seq_name ) ) {
714 if ( !n.getNodeData().isHasSequence() && n.getName().equals( seq_name ) ) {
721 public final List<PhylogenyNode> getRemovedGeneTreeNodes() {
722 return _removed_gene_tree_nodes;
725 private final class ResultLine implements Comparable<ResultLine> {
727 public static final int DEFAULT = -999;
728 private final String _key;
729 private final double _value1;
730 private final double _value2;
733 ResultLine( final String name, final double value1, final double value2, final int c ) {
738 if ( ( c >= 0 ) && ( c <= 2 ) ) {
743 ResultLine( final String name, final double value1, final int c ) {
747 _value2 = ResultLine.DEFAULT;
754 public int compareTo( final ResultLine n ) {
755 if ( ( getValue1() != ResultLine.DEFAULT ) && ( n.getValue1() != ResultLine.DEFAULT ) ) {
756 if ( getValue1() < n.getValue1() ) {
759 if ( getValue1() > n.getValue1() ) {
763 if ( ( getValue2() != ResultLine.DEFAULT ) && ( n.getValue2() != ResultLine.DEFAULT ) ) {
764 if ( getValue2() < n.getValue2() ) {
767 if ( getValue2() > n.getValue2() ) {
771 return ( getKey().compareTo( n.getKey() ) );
786 private void setSigns() {
788 _p[ 0 ] = _p[ 1 ] = +1;