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.sdi;
31 import java.io.FileNotFoundException;
32 import java.io.IOException;
33 import java.util.ArrayList;
34 import java.util.Arrays;
35 import java.util.HashMap;
36 import java.util.HashSet;
37 import java.util.List;
40 import org.forester.datastructures.IntMatrix;
41 import org.forester.io.parsers.PhylogenyParser;
42 import org.forester.io.parsers.nhx.NHXParser;
43 import org.forester.io.parsers.util.ParserUtils;
44 import org.forester.phylogeny.Phylogeny;
45 import org.forester.phylogeny.PhylogenyMethods;
46 import org.forester.phylogeny.PhylogenyNode;
47 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
48 import org.forester.phylogeny.factories.PhylogenyFactory;
49 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
50 import org.forester.util.ForesterUtil;
52 public final class RIO {
54 private final static boolean ROOT_BY_MINIMIZING_SUM_OF_DUPS = true;
55 private final static boolean ROOT_BY_MINIMIZING_TREE_HEIGHT = true;
56 private Phylogeny[] _analyzed_gene_trees;
57 private HashMap<String, HashMap<String, Integer>> _o_maps;
58 private HashMap<String, HashMap<String, Integer>> _so_maps;
59 private HashMap<String, HashMap<String, Integer>> _up_maps;
60 private List<String> _seq_names;
61 private List<PhylogenyNode> _removed_gene_tree_nodes;
63 private int _ext_nodes;
66 * Default constructor.
67 * @throws SDIException
69 * @throws RIOException
71 public RIO( final File gene_trees_file, final Phylogeny species_tree, final String query ) throws IOException,
72 SDIException, RIOException {
73 if ( ForesterUtil.isEmpty( query ) ) {
74 throw new IllegalArgumentException( "query is empty" );
77 inferOrthologs( gene_trees_file, species_tree, query );
80 public RIO( final File gene_trees_file, final Phylogeny species_tree ) throws IOException, SDIException,
83 inferOrthologs( gene_trees_file, species_tree, null );
86 public final Phylogeny[] getAnalyzedGeneTrees() {
87 return _analyzed_gene_trees;
91 * Returns the numbers of number of ext nodes in gene trees analyzed (after
94 * @return number of ext nodes in gene trees analyzed (after stripping)
96 public final int getExtNodesOfAnalyzedGeneTrees() {
101 * Returns a HashMap containing the inferred "ultra paralogs" of the
102 * external gene tree node with the sequence name seq_name. Sequence names
103 * are the keys (String), numbers of observations are the values (Int).
104 * "ultra paralogs" are to be inferred by method "inferOrthologs". Throws an
105 * exception if seq_name is not found.
108 * sequence name of a external node of the gene trees
109 * @return HashMap containing the inferred ultra paralogs
110 * (name(String)->value(Int))
112 public final HashMap<String, Integer> getInferredUltraParalogs( final String seq_name ) {
113 if ( _up_maps == null ) {
116 return _up_maps.get( seq_name );
119 public final int getNumberOfSamples() {
124 * Returns a String containg the names of orthologs of the PhylogenyNode
125 * with seq name query_name. The String also contains how many times a
126 * particular ortholog has been observed.
129 * The output order is (per line): Name, Ortholog, Subtree neighbor, Super
133 * The sort priority of this is determined by sort in the following manner:
136 * <li>1 : Ortholog, Super ortholog
137 * <li>2 : Super ortholog, Ortholog
140 * Returns "-" if no putative orthologs have been found (given
141 * threshold_orthologs).
143 * Orthologs are to be inferred by method "inferOrthologs".
145 * (Last modified: 05/08/01)
148 * sequence name of a external node of the gene trees
150 * order and sort priority
151 * @param threshold_orthologs
152 * the minimal number of observations for a a sequence to be
153 * reported as orthologous, in percents (0.0-100.0%)
154 * @param threshold_subtreeneighborings
155 * the minimal number of observations for a a sequence to be
156 * reported as orthologous, in percents (0.0-100.0%)
157 * @return String containing the inferred orthologs, String containing "-"
158 * if no orthologs have been found null in case of error
160 public final StringBuffer inferredOrthologsToString( final String query_name, int sort, double threshold_orthologs ) {
161 HashMap<String, Integer> o_hashmap = null;
162 HashMap<String, Integer> s_hashmap = null;
164 double o = 0.0; // Orthologs.
165 double s = 0.0; // Super orthologs.
168 final ArrayList<ResultLine> nv = new ArrayList<ResultLine>();
169 if ( ( _o_maps == null ) || ( _so_maps == null ) ) {
170 throw new RuntimeException( "orthologs have not been calculated (successfully)" );
172 if ( ( sort < 0 ) || ( sort > 2 ) ) {
175 if ( threshold_orthologs < 0.0 ) {
176 threshold_orthologs = 0.0;
178 else if ( threshold_orthologs > 100.0 ) {
179 threshold_orthologs = 100.0;
181 o_hashmap = getInferredOrthologs( query_name );
182 s_hashmap = getInferredSuperOrthologs( query_name );
183 if ( ( o_hashmap == null ) || ( s_hashmap == null ) ) {
184 throw new RuntimeException( "Orthologs for " + query_name + " were not established" );
186 final StringBuffer orthologs = new StringBuffer();
187 if ( _seq_names.size() > 0 ) {
188 I: for( int i = 0; i < _seq_names.size(); ++i ) {
189 name = _seq_names.get( i );
190 if ( name.equals( query_name ) ) {
193 o = getBootstrapValueFromHash( o_hashmap, name );
194 if ( o < threshold_orthologs ) {
197 s = getBootstrapValueFromHash( s_hashmap, name );
200 nv.add( new ResultLine( name, o, 5 ) );
203 nv.add( new ResultLine( name, o, s, 5 ) );
206 nv.add( new ResultLine( name, s, o, 5 ) );
209 nv.add( new ResultLine( name, o, 5 ) );
211 } // End of I for loop.
212 if ( ( nv != null ) && ( nv.size() > 0 ) ) {
213 orthologs.append( "seq name\t\tortho\ts-ortho" + ForesterUtil.LINE_SEPARATOR );
214 final ResultLine[] nv_array = new ResultLine[ nv.size() ];
215 for( int j = 0; j < nv.size(); ++j ) {
216 nv_array[ j ] = nv.get( j );
218 Arrays.sort( nv_array );
219 for( final ResultLine element : nv_array ) {
220 name = element.getKey();
221 value1 = element.getValue1();
222 value2 = element.getValue2();
223 orthologs.append( addNameAndValues( name, value1, value2, sort ) );
227 // No orthologs found.
228 if ( ( orthologs == null ) || ( orthologs.length() < 1 ) ) {
229 orthologs.append( "-" );
235 * Returns a String containg the names of orthologs of the PhylogenyNode
236 * with seq name query_name. The String also contains how many times a
237 * particular ortholog has been observed. Returns "-" if no putative
238 * orthologs have been found (given threshold_orthologs).
240 * Orthologs are to be inferred by method "inferOrthologs".
243 * sequence name of a external node of the gene trees
244 * @param return_dists
245 * @param threshold_ultra_paralogs
247 * @return String containing the inferred orthologs, String containing "-"
248 * if no orthologs have been found null in case of error
250 public final String inferredUltraParalogsToString( final String query_name, double threshold_ultra_paralogs ) {
251 HashMap<String, Integer> sp_hashmap = null;
252 String name = "", ultra_paralogs = "";
257 final List<ResultLine> nv = new ArrayList<ResultLine>();
258 if ( threshold_ultra_paralogs < 1.0 ) {
259 threshold_ultra_paralogs = 1.0;
261 else if ( threshold_ultra_paralogs > 100.0 ) {
262 threshold_ultra_paralogs = 100.0;
264 if ( _up_maps == null ) {
265 throw new RuntimeException( "Ultra paralogs have not been calculated (successfully)." );
267 sp_hashmap = getInferredUltraParalogs( query_name );
268 if ( sp_hashmap == null ) {
269 throw new RuntimeException( "Ultra paralogs for " + query_name + " were not established" );
271 if ( _seq_names.size() > 0 ) {
272 I: for( int i = 0; i < _seq_names.size(); ++i ) {
273 name = _seq_names.get( i );
274 if ( name.equals( query_name ) ) {
277 sp = getBootstrapValueFromHash( sp_hashmap, name );
278 if ( sp < threshold_ultra_paralogs ) {
281 nv.add( new ResultLine( name, sp, 5 ) );
282 } // End of I for loop.
283 if ( ( nv != null ) && ( nv.size() > 0 ) ) {
284 final ResultLine[] nv_array = new ResultLine[ nv.size() ];
285 for( int j = 0; j < nv.size(); ++j ) {
286 nv_array[ j ] = nv.get( j );
288 Arrays.sort( nv_array );
290 for( final ResultLine element : nv_array ) {
291 name = element.getKey();
292 value1 = element.getValue1();
293 value2 = element.getValue2();
294 ultra_paralogs += addNameAndValues( name, value1, value2, sort );
298 // No ultra paralogs found.
299 if ( ( ultra_paralogs == null ) || ( ultra_paralogs.length() < 1 ) ) {
300 ultra_paralogs = "-";
302 return ultra_paralogs;
305 // Helper method for inferredOrthologsToString.
306 // inferredOrthologsToArrayList,
307 // and inferredUltraParalogsToString.
308 private final double getBootstrapValueFromHash( final HashMap<String, Integer> h, final String name ) {
309 if ( !h.containsKey( name ) ) {
312 final int i = h.get( name );
313 return ( ( i * 100.0 ) / getNumberOfSamples() );
317 * Returns a HashMap containing the inferred orthologs of the external gene
318 * tree node with the sequence name seq_name. Sequence names are the keys
319 * (String), numbers of observations are the values (Int). Orthologs are to
320 * be inferred by method "inferOrthologs". Throws an exception if seq_name
324 * sequence name of a external node of the gene trees
325 * @return HashMap containing the inferred orthologs
326 * (name(String)->value(Int))
328 private final HashMap<String, Integer> getInferredOrthologs( final String seq_name ) {
329 if ( _o_maps == null ) {
332 return _o_maps.get( seq_name );
336 * Returns a HashMap containing the inferred "super orthologs" of the
337 * external gene tree node with the sequence name seq_name. Sequence names
338 * are the keys (String), numbers of observations are the values (Int).
339 * Super orthologs are to be inferred by method "inferOrthologs". Throws an
340 * exception if seq_name is not found.
343 * sequence name of a external node of the gene trees
344 * @return HashMap containing the inferred super orthologs
345 * (name(String)->value(Int))
347 private final HashMap<String, Integer> getInferredSuperOrthologs( final String seq_name ) {
348 if ( _so_maps == null ) {
351 return _so_maps.get( seq_name );
355 * Infers the orthologs (as well the "super orthologs", the "subtree
356 * neighbors", and the "ultra paralogs") for each external node of the gene
357 * Trees in multiple tree File gene_trees_file (=output of PHYLIP NEIGHBOR,
358 * for example). Tallies how many times each sequence is (super-)
359 * orthologous towards the query. Tallies how many times each sequence is
360 * ultra paralogous towards the query. Tallies how many times each sequence
361 * is a subtree neighbor of the query. Gene duplications are inferred using
362 * SDI. Modifies its argument species_tree. Is a little faster than
363 * "inferOrthologs(File,Phylogeny)" since orthologs are only inferred for
366 * To obtain the results use the methods listed below.
368 * @param gene_trees_file
369 * a File containing gene Trees in NH format, which is the result
370 * of performing a bootstrap analysis in PHYLIP
371 * @param species_tree
372 * a species Phylogeny, which has species names in its species
375 * the sequence name of the squence whose orthologs are to be
377 * @throws SDIException
378 * @throws RIOException
379 * @throws IOException
380 * @throws FileNotFoundException
382 private final void inferOrthologs( final File gene_trees_file, final Phylogeny species_tree, final String query )
383 throws SDIException, RIOException, FileNotFoundException, IOException {
384 // Read in first tree to get its sequence names
385 // and strip species_tree.
386 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
387 final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( gene_trees_file, true );
388 if ( p instanceof NHXParser ) {
389 final NHXParser nhx = ( NHXParser ) p;
390 nhx.setReplaceUnderscores( false );
391 nhx.setIgnoreQuotes( true );
392 nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
394 final Phylogeny[] gene_trees = factory.create( gene_trees_file, p );
395 // Removes from species_tree all species not found in gene_tree.
396 List<PhylogenyNode> _removed_gene_tree_nodes = PhylogenyMethods
397 .taxonomyBasedDeletionOfExternalNodes( gene_trees[ 0 ], species_tree );
398 if ( species_tree.isEmpty() ) {
399 throw new RIOException( "failed to establish species based mapping between gene and species trees" );
401 if ( !ForesterUtil.isEmpty( query ) ) {
402 PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gene_trees[ 0 ] );
403 if ( gene_trees[ 0 ].isEmpty() ) {
404 throw new RIOException( "failed to establish species based mapping between gene and species trees" );
406 _seq_names = getAllExternalSequenceNames( gene_trees[ 0 ] );
407 if ( ( _seq_names == null ) || ( _seq_names.size() < 1 ) ) {
408 throw new RIOException( "could not get sequence names" );
410 _o_maps = new HashMap<String, HashMap<String, Integer>>();
411 _so_maps = new HashMap<String, HashMap<String, Integer>>();
412 _up_maps = new HashMap<String, HashMap<String, Integer>>();
413 _o_maps.put( query, new HashMap<String, Integer>( _seq_names.size() ) );
414 _so_maps.put( query, new HashMap<String, Integer>( _seq_names.size() ) );
415 _up_maps.put( query, new HashMap<String, Integer>( _seq_names.size() ) );
417 _analyzed_gene_trees = new Phylogeny[ gene_trees.length ];
419 int gene_tree_ext_nodes = 0;
420 for( final Phylogeny gt : gene_trees ) {
421 // Removes from gene_tree all species not found in species_tree.
422 PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gt );
423 if ( gt.isEmpty() ) {
424 throw new RIOException( "failed to establish species based mapping between gene and species trees" );
427 gene_tree_ext_nodes = gt.getNumberOfExternalNodes();
429 else if ( gene_tree_ext_nodes != gt.getNumberOfExternalNodes() ) {
430 throw new RIOException( "(cleaned up) gene tree #" + ( c + 1 )
431 + " has a different number of external nodes (" + gt.getNumberOfExternalNodes()
432 + ") than those gene trees preceding it (" + gene_tree_ext_nodes + ")" );
434 _analyzed_gene_trees[ c++ ] = performOrthologInference( gt, species_tree, query );
436 setNumberOfSamples( gene_trees.length );
439 private final Phylogeny performOrthologInference( final Phylogeny gene_tree,
440 final Phylogeny species_tree,
441 final String query ) throws SDIException, RIOException {
442 final SDIR sdiunrooted = new SDIR();
443 final Phylogeny assigned_tree = sdiunrooted.infer( gene_tree,
446 RIO.ROOT_BY_MINIMIZING_SUM_OF_DUPS,
447 RIO.ROOT_BY_MINIMIZING_TREE_HEIGHT,
450 setExtNodesOfAnalyzedGeneTrees( assigned_tree.getNumberOfExternalNodes() );
451 if ( !ForesterUtil.isEmpty( query ) ) {
452 final List<PhylogenyNode> nodes = getNodesViaSequenceName( assigned_tree, query );
453 if ( nodes.size() > 1 ) {
454 throw new RIOException( "node named [" + query + "] not unique" );
456 else if ( nodes.isEmpty() ) {
457 throw new RIOException( "no node containing a sequence named [" + query + "] found" );
459 final PhylogenyNode query_node = nodes.get( 0 );
460 updateCounts( _o_maps, query, PhylogenyMethods.getOrthologousNodes( assigned_tree, query_node ) );
461 updateCounts( _so_maps, query, PhylogenyMethods.getSuperOrthologousNodes( query_node ) );
462 updateCounts( _up_maps, query, PhylogenyMethods.getUltraParalogousNodes( query_node ) );
464 return assigned_tree;
467 private final void init() {
476 private final void setExtNodesOfAnalyzedGeneTrees( final int i ) {
480 private final void setNumberOfSamples( int i ) {
487 // Helper for doInferOrthologs( Phylogeny, Phylogeny, String )
488 // and doInferOrthologs( Phylogeny, Phylogeny ).
489 private final void updateCounts( final HashMap<String, HashMap<String, Integer>> counter_map,
490 final String query_seq_name,
491 final List<PhylogenyNode> nodes ) {
492 final HashMap<String, Integer> hash_map = counter_map.get( query_seq_name );
493 if ( hash_map == null ) {
494 throw new RuntimeException( "unexpected error in updateCounts" );
496 for( int j = 0; j < nodes.size(); ++j ) {
498 if ( ( nodes.get( j ) ).getNodeData().isHasSequence()
499 && !ForesterUtil.isEmpty( ( nodes.get( j ) ).getNodeData().getSequence().getName() ) ) {
500 seq_name = ( nodes.get( j ) ).getNodeData().getSequence().getName();
503 seq_name = ( nodes.get( j ) ).getName();
505 if ( hash_map.containsKey( seq_name ) ) {
506 hash_map.put( seq_name, hash_map.get( seq_name ) + 1 );
509 hash_map.put( seq_name, 1 );
514 public final static IntMatrix calculateOrthologTable( final Phylogeny[] analyzed_gene_trees ) throws RIOException {
515 final List<String> labels = new ArrayList<String>();
516 final Set<String> labels_set = new HashSet<String>();
518 for( final PhylogenyNode n : analyzed_gene_trees[ 0 ].getExternalNodes() ) {
519 if ( n.getNodeData().isHasSequence() && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
520 label = n.getNodeData().getSequence().getName();
522 else if ( n.getNodeData().isHasSequence()
523 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
524 label = n.getNodeData().getSequence().getSymbol();
526 else if ( !ForesterUtil.isEmpty( n.getName() ) ) {
530 throw new IllegalArgumentException( "node " + n + " has no appropriate label" );
532 if ( labels_set.contains( label ) ) {
533 throw new IllegalArgumentException( "label " + label + " is not unique" );
535 labels_set.add( label );
538 final IntMatrix m = new IntMatrix( labels );
540 for( final Phylogeny gt : analyzed_gene_trees ) {
542 PhylogenyMethods.preOrderReId( gt );
543 final HashMap<String, PhylogenyNode> map = PhylogenyMethods.createNameToExtNodeMap( gt );
544 for( int x = 0; x < m.size(); ++x ) {
545 final String mx = m.getLabel( x );
546 final PhylogenyNode nx = map.get( mx );
548 throw new RIOException( "node \"" + mx + "\" not present in gene tree #" + counter );
552 for( int y = 0; y < m.size(); ++y ) {
553 my = m.getLabel( y );
556 throw new RIOException( "node \"" + my + "\" not present in gene tree #" + counter );
558 if ( !PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( nx, ny ).isDuplication() ) {
559 m.inreaseByOne( x, y );
568 * Returns the order in which ortholog (o), "super ortholog" (s) and
569 * distance (d) are returned and sorted (priority of sort always goes from
570 * left to right), given sort. For the meaning of sort
572 * @see #inferredOrthologsToString(String,int,double,double)
575 * determines order and sort priority
576 * @return String indicating the order
578 public final static String getOrder( final int sort ) {
582 order = "orthologies";
585 order = "orthologies > super orthologies";
588 order = "super orthologies > orthologies";
591 order = "orthologies";
597 public final static StringBuffer getOrderHelp() {
598 final StringBuffer sb = new StringBuffer();
599 sb.append( " 0: orthologies" + ForesterUtil.LINE_SEPARATOR );
600 sb.append( " 1: orthologies > super orthologies" + ForesterUtil.LINE_SEPARATOR );
601 sb.append( " 2: super orthologies > orthologies" + ForesterUtil.LINE_SEPARATOR );
605 // Helper method for inferredOrthologsToString
606 // and inferredUltraParalogsToString.
607 private final static String addNameAndValues( final String name,
611 final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.#####" );
612 df.setDecimalSeparatorAlwaysShown( false );
614 if ( name.length() < 8 ) {
615 line += ( name + "\t\t\t" );
617 else if ( name.length() < 16 ) {
618 line += ( name + "\t\t" );
621 line += ( name + "\t" );
625 line += addToLine( value1, df );
629 line += addToLine( value1, df );
630 line += addToLine( value2, df );
633 line += addToLine( value2, df );
634 line += addToLine( value1, df );
637 line += addToLine( value1, df );
641 line += addToLine( value1, df );
642 line += addToLine( value2, df );
645 line += ForesterUtil.LINE_SEPARATOR;
649 // Helper for addNameAndValues.
650 private final static String addToLine( final double value, final java.text.DecimalFormat df ) {
652 if ( value != ResultLine.DEFAULT ) {
653 s = df.format( value ) + "\t";
661 private final static List<String> getAllExternalSequenceNames( final Phylogeny phy ) throws RIOException {
662 final List<String> names = new ArrayList<String>();
663 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
664 final PhylogenyNode n = iter.next();
665 if ( n.getNodeData().isHasSequence() && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
666 names.add( n.getNodeData().getSequence().getName() );
668 else if ( !ForesterUtil.isEmpty( n.getName() ) ) {
669 names.add( n.getName() );
672 throw new RIOException( "node has no (sequence) name: " + n );
678 private final static List<PhylogenyNode> getNodesViaSequenceName( final Phylogeny phy, final String seq_name ) {
679 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
680 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
681 final PhylogenyNode n = iter.next();
682 if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getName().equals( seq_name ) ) {
685 if ( !n.getNodeData().isHasSequence() && n.getName().equals( seq_name ) ) {
692 public final List<PhylogenyNode> getRemovedGeneTreeNodes() {
693 return _removed_gene_tree_nodes;
696 private final class ResultLine implements Comparable<ResultLine> {
698 public static final int DEFAULT = -999;
699 private final String _key;
700 private final double _value1;
701 private final double _value2;
704 ResultLine( final String name, final double value1, final double value2, final int c ) {
709 if ( ( c >= 0 ) && ( c <= 2 ) ) {
714 ResultLine( final String name, final double value1, final int c ) {
718 _value2 = ResultLine.DEFAULT;
725 public int compareTo( final ResultLine n ) {
726 if ( ( getValue1() != ResultLine.DEFAULT ) && ( n.getValue1() != ResultLine.DEFAULT ) ) {
727 if ( getValue1() < n.getValue1() ) {
730 if ( getValue1() > n.getValue1() ) {
734 if ( ( getValue2() != ResultLine.DEFAULT ) && ( n.getValue2() != ResultLine.DEFAULT ) ) {
735 if ( getValue2() < n.getValue2() ) {
738 if ( getValue2() > n.getValue2() ) {
742 return ( getKey().compareTo( n.getKey() ) );
757 private void setSigns() {
759 _p[ 0 ] = _p[ 1 ] = +1;