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
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.application;
29 import java.io.IOException;
30 import java.text.SimpleDateFormat;
31 import java.util.ArrayList;
32 import java.util.Date;
33 import java.util.List;
34 import java.util.SortedMap;
35 import java.util.SortedSet;
36 import java.util.TreeMap;
37 import java.util.TreeSet;
39 import org.forester.io.parsers.PhylogenyParser;
40 import org.forester.io.parsers.nhx.NHXParser;
41 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
42 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
43 import org.forester.io.parsers.util.ParserUtils;
44 import org.forester.io.writers.PhylogenyWriter;
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.sdi.GSDI;
51 import org.forester.sdi.GSDIR;
52 import org.forester.sdi.SDI;
53 import org.forester.sdi.SDI.TaxonomyComparisonBase;
54 import org.forester.sdi.SDIException;
55 import org.forester.sdi.SDIse;
56 import org.forester.util.CommandLineArguments;
57 import org.forester.util.EasyWriter;
58 import org.forester.util.ForesterConstants;
59 import org.forester.util.ForesterUtil;
61 public final class gsdi {
63 private enum BASE_ALGORITHM {
66 final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true;
67 final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION = "g";
68 final static private String SDISE_OPTION = "b";
69 final static private String GSDIR_OPTION = "r";
70 final static private String MOST_PARSIMONIOUS_OPTION = "m";
71 final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q";
72 final static private String HELP_OPTION_1 = "help";
73 final static private String HELP_OPTION_2 = "h";
74 final static private String SUFFIX_FOR_SPECIES_TREE_USED = "_species_tree_used.xml";
75 final static private String LOGFILE_SUFFIX = "_gsdi_log.txt";
76 final static private String REMAPPED_SUFFIX = "_gsdi_remapped.txt";
77 final static private String PRG_NAME = "gsdi";
78 final static private String PRG_VERSION = "1.000";
79 final static private String PRG_DATE = "120629";
80 final static private String PRG_DESC = "general speciation duplication inference";
81 final static private String E_MAIL = "phylosoft@gmail.com";
82 final static private String WWW = "www.phylosoft.org/forester";
84 public static void main( final String args[] ) {
86 ForesterUtil.printProgramInformation( PRG_NAME,
92 ForesterUtil.getForesterLibraryInformation() );
93 CommandLineArguments cla = null;
95 cla = new CommandLineArguments( args );
97 catch ( final Exception e ) {
98 ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
100 if ( cla.isOptionSet( gsdi.HELP_OPTION_1 ) || cla.isOptionSet( gsdi.HELP_OPTION_2 ) ) {
101 System.out.println();
105 else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() != 3 ) ) {
106 System.out.println();
107 System.out.println( "Wrong number of arguments." );
108 System.out.println();
112 final List<String> allowed_options = new ArrayList<String>();
113 allowed_options.add( gsdi.SDISE_OPTION );
114 allowed_options.add( gsdi.GSDIR_OPTION );
115 allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE );
116 allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION );
117 allowed_options.add( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION );
118 final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
119 if ( dissallowed_options.length() > 0 ) {
120 ForesterUtil.fatalError( gsdi.PRG_NAME, "unknown option(s): " + dissallowed_options );
124 catch ( final IOException e ) {
125 ForesterUtil.fatalError( gsdi.PRG_NAME, e.getMessage() );
129 private static void execute( final CommandLineArguments cla ) throws IOException {
130 BASE_ALGORITHM base_algorithm = BASE_ALGORITHM.GSDI;
131 boolean most_parsimonous_duplication_model = false;
132 boolean allow_stripping_of_gene_tree = false;
133 if ( cla.isOptionSet( gsdi.GSDIR_OPTION ) ) {
134 base_algorithm = BASE_ALGORITHM.GSDIR;
136 else if ( cla.isOptionSet( gsdi.SDISE_OPTION ) ) {
137 base_algorithm = BASE_ALGORITHM.SDI;
139 if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) {
140 if ( base_algorithm == BASE_ALGORITHM.SDI ) {
141 ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" );
143 most_parsimonous_duplication_model = true;
145 if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
146 if ( base_algorithm == BASE_ALGORITHM.SDI ) {
147 ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot allow stripping of gene tree with SDI" );
149 allow_stripping_of_gene_tree = true;
151 Phylogeny species_tree = null;
152 Phylogeny gene_tree = null;
153 File gene_tree_file = null;
154 File species_tree_file = null;
155 File out_file = null;
156 File log_file = null;
157 EasyWriter log_writer = null;
159 gene_tree_file = cla.getFile( 0 );
160 species_tree_file = cla.getFile( 1 );
161 out_file = cla.getFile( 2 );
162 log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX );
164 catch ( final IllegalArgumentException e ) {
165 ForesterUtil.fatalError( gsdi.PRG_NAME, "error in command line: " + e.getMessage() );
167 if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
168 ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
170 if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
171 ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
173 if ( ForesterUtil.isWritableFile( out_file ) != null ) {
174 ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
176 if ( ForesterUtil.isWritableFile( log_file ) != null ) {
177 ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
180 log_writer = ForesterUtil.createEasyWriter( log_file );
182 catch ( final IOException e ) {
183 ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
186 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
187 gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
189 catch ( final IOException e ) {
191 "Failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(),
195 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
196 final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
197 if ( p instanceof PhyloXmlParser ) {
198 species_tree = factory.create( species_tree_file, p )[ 0 ];
201 if ( REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE && ( p instanceof NHXParser ) ) {
202 ( ( NHXParser ) p ).setReplaceUnderscores( true );
204 species_tree = factory.create( species_tree_file, p )[ 0 ];
205 final TaxonomyComparisonBase comp_base = GSDI.determineTaxonomyComparisonBase( gene_tree );
206 switch ( comp_base ) {
207 case SCIENTIFIC_NAME:
210 .transferNodeNameToField( species_tree,
211 PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
214 catch ( final PhyloXmlDataFormatException e ) {
215 fatalError( "USER ERROR", "Failed to transfer general node name to scientific name, in ["
216 + species_tree_file + "]: " + e.getMessage(), log_writer );
222 .transferNodeNameToField( species_tree,
223 PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE,
226 catch ( final PhyloXmlDataFormatException e ) {
227 fatalError( "USER ERROR", "Failed to transfer general node name to taxonomy code, in ["
228 + species_tree_file + "]: " + e.getMessage(), log_writer );
233 PhylogenyMethods.transferNodeNameToField( species_tree,
234 PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID,
237 catch ( final PhyloXmlDataFormatException e ) {
238 fatalError( "USER ERROR", "Failed to transfer general node name to taxonomy id, in ["
239 + species_tree_file + "]: " + e.getMessage(), log_writer );
243 fatalError( "UNEXPECTED ERROR", "unable to determine comparison base", log_writer );
247 catch ( final IOException e ) {
249 "Failed to read species tree from [" + species_tree_file + "]: " + e.getMessage(),
252 gene_tree.setRooted( true );
253 species_tree.setRooted( true );
254 if ( !gene_tree.isCompletelyBinary() ) {
255 fatalError( "user error", "gene tree is not completely binary", log_writer );
257 if ( base_algorithm == BASE_ALGORITHM.SDI ) {
258 if ( !species_tree.isCompletelyBinary() ) {
259 fatalError( "user error",
260 "species tree is not completely binary, use GSDI or GSDIR instead",
264 log_writer.println( PRG_NAME + " - " + PRG_DESC );
265 log_writer.println( " version : " + PRG_VERSION );
266 log_writer.println( " date : " + PRG_DATE );
267 log_writer.println( " forester version: " + ForesterConstants.FORESTER_VERSION );
268 log_writer.println();
269 log_writer.println( "Start time : "
270 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
271 System.out.println( "Start time : "
272 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
273 log_writer.println( "Gene tree file : " + gene_tree_file.getCanonicalPath() );
274 System.out.println( "Gene tree file : " + gene_tree_file.getCanonicalPath() );
275 log_writer.println( "Gene tree name : "
276 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
277 System.out.println( "Gene tree name : "
278 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
279 log_writer.println( "Species tree file : " + species_tree_file.getCanonicalPath() );
280 System.out.println( "Species tree file : " + species_tree_file.getCanonicalPath() );
281 log_writer.println( "Species tree name : "
282 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
283 System.out.println( "Species tree name : "
284 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
286 final long start_time = new Date().getTime();
288 if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) || ( base_algorithm == BASE_ALGORITHM.GSDIR ) ) {
289 if ( base_algorithm == BASE_ALGORITHM.GSDI ) {
290 System.out.println( "Algorithm : GSDI" );
291 log_writer.println( "Algorithm : GSDI" );
293 else if ( base_algorithm == BASE_ALGORITHM.GSDIR ) {
294 System.out.println( "Algorithm : GSDIR" );
295 log_writer.println( "Algorithm : GSDIR" );
297 System.out.println( "Use most parsimonous duplication model : " + most_parsimonous_duplication_model );
298 System.out.println( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree );
299 log_writer.println( "Use most parsimonous duplication model : " + most_parsimonous_duplication_model );
300 log_writer.println( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree );
302 if ( base_algorithm == BASE_ALGORITHM.GSDI ) {
303 sdi = new GSDI( gene_tree,
305 most_parsimonous_duplication_model,
306 allow_stripping_of_gene_tree,
309 else if ( base_algorithm == BASE_ALGORITHM.GSDIR ) {
310 sdi = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, 1 );
314 System.out.println();
315 System.out.println( "Algorithm : SDI" );
316 log_writer.println( "Algorithm : SDI" );
318 sdi = new SDIse( gene_tree, species_tree );
321 catch ( final SDIException e ) {
322 fatalError( "user error", e.getLocalizedMessage(), log_writer );
324 catch ( final IOException e ) {
325 fatalError( "error", e.toString(), log_writer );
327 catch ( final Exception e ) {
329 fatalError( "unexpected error", e.toString(), log_writer );
331 System.out.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time )
333 log_writer.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time )
335 if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
336 final GSDI gsdi = ( GSDI ) sdi;
337 System.out.println( "Mapping based on : " + gsdi.getTaxCompBase() );
338 log_writer.println( "Mapping based on : " + gsdi.getTaxCompBase() );
340 if ( ( base_algorithm == BASE_ALGORITHM.GSDIR ) ) {
341 final GSDIR gsdir = ( GSDIR ) sdi;
342 System.out.println( "Mapping based on : " + gsdir.getTaxCompBase() );
343 log_writer.println( "Mapping based on : " + gsdir.getTaxCompBase() );
344 System.out.println( "Minimal duplications sum : " + gsdir.getMinDuplicationsSum() );
345 log_writer.println( "Minimal duplications sum : " + gsdir.getMinDuplicationsSum() );
346 System.out.println( "Duplications sum statistics : " + gsdir.getMinDuplicationsSum() );
347 log_writer.println( "Duplications sum statistics : " + gsdir.getMinDuplicationsSum() );
350 final PhylogenyWriter writer = new PhylogenyWriter();
351 if ( base_algorithm == BASE_ALGORITHM.GSDIR ) {
352 writer.toPhyloXML( out_file,
353 ( ( GSDIR ) sdi ).getMinDuplicationsSumGeneTrees(),
355 ForesterUtil.LINE_SEPARATOR );
358 writer.toPhyloXML( out_file, gene_tree, 0 );
361 catch ( final IOException e ) {
362 ForesterUtil.fatalError( PRG_NAME,
363 "Failed to write to [" + out_file.getCanonicalPath() + "]: " + e.getMessage() );
365 System.out.println( "Wrote resulting gene tree to : " + out_file.getCanonicalPath() );
366 log_writer.println( "Wrote resulting gene tree to : " + out_file.getCanonicalPath() );
367 if ( base_algorithm == BASE_ALGORITHM.SDI ) {
368 sdi.computeMappingCostL();
369 System.out.println( "Mapping cost : " + sdi.computeMappingCostL() );
370 log_writer.println( "Mapping cost : " + sdi.computeMappingCostL() );
372 else if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) || ( base_algorithm == BASE_ALGORITHM.GSDIR ) ) {
373 final GSDI gsdi = ( GSDI ) sdi;
374 final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() )
375 + SUFFIX_FOR_SPECIES_TREE_USED );
377 final PhylogenyWriter writer = new PhylogenyWriter();
378 writer.toPhyloXML( species_tree_used_file, gsdi.getSpeciesTree(), 0 );
380 catch ( final IOException e ) {
381 ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + species_tree_used_file.getCanonicalPath()
382 + "]: " + e.getMessage() );
384 System.out.println( "Wrote (stripped) species tree to : "
385 + species_tree_used_file.getCanonicalPath() );
386 log_writer.println( "Wrote (stripped) species tree to : "
387 + species_tree_used_file.getCanonicalPath() );
388 if ( ( gsdi.getReMappedScientificNamesFromGeneTree() != null )
389 && !gsdi.getReMappedScientificNamesFromGeneTree().isEmpty() ) {
390 System.out.println( "Number of gene tree species remapped : "
391 + gsdi.getReMappedScientificNamesFromGeneTree().size() );
392 log_writer.println( "Number of gene tree species remapped : "
393 + gsdi.getReMappedScientificNamesFromGeneTree().size() );
394 writeToRemappedFile( out_file, gsdi.getReMappedScientificNamesFromGeneTree(), log_writer );
397 System.out.println( "Number of external nodes in gene tree : " + gene_tree.getNumberOfExternalNodes() );
398 log_writer.println( "Number of external nodes in gene tree : " + gene_tree.getNumberOfExternalNodes() );
399 System.out.println( "Number of external nodes in species tree : "
400 + sdi.getSpeciesTree().getNumberOfExternalNodes() );
401 log_writer.println( "Number of external nodes in species tree : "
402 + sdi.getSpeciesTree().getNumberOfExternalNodes() );
403 if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
404 final GSDI gsdi = ( GSDI ) sdi;
405 final int poly = PhylogenyMethods.countNumberOfPolytomies( gsdi.getSpeciesTree() );
406 System.out.println( "Number of polytomies in species tree : " + poly );
407 log_writer.println( "Number of polytomies in species tree : " + poly );
408 System.out.println( "External nodes stripped from gene tree : "
409 + gsdi.getStrippedExternalGeneTreeNodes().size() );
410 log_writer.println( "External nodes stripped from gene tree : "
411 + gsdi.getStrippedExternalGeneTreeNodes().size() );
412 System.out.println( "External nodes stripped from species tree: "
413 + gsdi.getStrippedSpeciesTreeNodes().size() );
414 log_writer.println( "External nodes stripped from species tree: "
415 + gsdi.getStrippedSpeciesTreeNodes().size() );
417 System.out.println();
418 System.out.println( "Number of duplications : " + sdi.getDuplicationsSum() );
419 log_writer.println( "Number of duplications : " + sdi.getDuplicationsSum() );
420 if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
421 final GSDI gsdi = ( GSDI ) sdi;
422 if ( !most_parsimonous_duplication_model ) {
423 final int u = gsdi.getSpeciationOrDuplicationEventsSum();
424 System.out.println( "Number of potential duplications : " + u );
425 log_writer.println( "Number of potential duplications : " + u );
427 System.out.println( "Number of speciations : " + gsdi.getSpeciationsSum() );
428 log_writer.println( "Number of speciations : " + gsdi.getSpeciationsSum() );
429 log_writer.println();
430 printMappedNodesToLog( log_writer, gsdi );
431 log_writer.println();
432 printStrippedGeneTreeNodesToLog( log_writer, gsdi );
434 System.out.println();
435 System.out.println( "Wrote log to : " + log_file.getCanonicalPath() );
436 System.out.println();
440 private static void writeToRemappedFile( final File out_file,
441 final SortedSet<String> remapped,
442 final EasyWriter log_writer ) throws IOException {
443 final File file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + REMAPPED_SUFFIX );
444 final EasyWriter remapped_writer = ForesterUtil.createEasyWriter( file );
445 for( final String s : remapped ) {
446 remapped_writer.println( s );
448 remapped_writer.close();
449 System.out.println( "Wrote remapped gene tree species to : " + file.getCanonicalPath() );
450 log_writer.println( "Wrote remapped gene tree species to : " + file.getCanonicalPath() );
453 private static void printMappedNodesToLog( final EasyWriter log_writer, final GSDI gsdi ) throws IOException {
454 final SortedSet<String> ss = new TreeSet<String>();
455 for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
456 ss.add( n.toString() );
458 log_writer.println( "The following " + ss.size() + " species were used: " );
459 for( final String s : ss ) {
460 log_writer.println( " " + s );
464 private static void fatalError( final String type, final String msg, final EasyWriter log_writer ) {
467 log_writer.println();
468 log_writer.print( type.toUpperCase() + ": " );
469 log_writer.println( msg );
472 catch ( final IOException e ) {
475 ForesterUtil.fatalError( gsdi.PRG_NAME, msg );
478 private static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDI gsdi )
480 final SortedMap<String, Integer> sm = new TreeMap<String, Integer>();
481 for( final PhylogenyNode n : gsdi.getStrippedExternalGeneTreeNodes() ) {
482 final String s = n.toString();
483 if ( sm.containsKey( s ) ) {
484 sm.put( s, sm.get( s ) + 1 );
490 log_writer.println( "The following " + sm.size() + " nodes were stripped from the gene tree: " );
491 for( final String s : sm.keySet() ) {
492 final int count = sm.get( s );
494 log_writer.println( " " + s );
497 log_writer.println( " " + s + " [" + count + "]" );
502 private static void print_help() {
503 System.out.println( "Usage: " + gsdi.PRG_NAME
504 + " [-options] <gene tree in phyloXML format> <species tree> <outfile>" );
505 System.out.println();
506 System.out.println( "Options:" );
507 System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION
508 + ": to allow stripping of gene tree nodes without a matching species" );
509 System.out.println( " -" + gsdi.MOST_PARSIMONIOUS_OPTION
510 + ": use most parimonious duplication model for GSDI: " );
511 System.out.println( " assign nodes as speciations which would otherwise be assiged" );
512 System.out.println( " as potential duplications due to polytomies in the species tree" );
513 System.out.println( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE
514 + ": to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" );
515 System.out.println( " -" + gsdi.SDISE_OPTION
516 + ": to use SDIse algorithm instead of GSDI algorithm (for binary species trees)" );
517 System.out.println( " -" + gsdi.GSDIR_OPTION
518 + ": to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" );
519 System.out.println();
520 System.out.println( "Gene tree:" );
521 System.out.println( " in phyloXM format, with taxonomy and sequence data in appropriate fields" );
522 System.out.println();
523 System.out.println( "Species tree:" );
524 System.out.println( " in phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + " is used)" );
525 System.out.println();
526 System.out.println( "Example: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
527 + " gene_tree.xml tree_of_life.xml out.xml" );
528 System.out.println();