3 // FORESTER -- software libraries and applications
4 // for evolutionary biology research and applications.
6 // Copyright (C) 2008-2009 Christian M. Zmasek
7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
10 // This library is free software; you can redistribute it and/or
11 // modify it under the terms of the GNU Lesser General Public
12 // License as published by the Free Software Foundation; either
13 // version 2.1 of the License, or (at your option) any later version.
15 // This library is distributed in the hope that it will be useful,
16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 // Lesser General Public License for more details.
20 // You should have received a copy of the GNU Lesser General Public
21 // License along with this library; if not, write to the Free Software
22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 // Contact: phylosoft @ gmail . com
25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
27 package org.forester.surfacing;
29 import java.awt.Color;
30 import java.io.BufferedWriter;
32 import java.io.FileWriter;
33 import java.io.IOException;
34 import java.io.Writer;
35 import java.text.DecimalFormat;
36 import java.text.NumberFormat;
37 import java.util.ArrayList;
38 import java.util.Arrays;
39 import java.util.Collections;
40 import java.util.Comparator;
41 import java.util.HashMap;
42 import java.util.HashSet;
43 import java.util.Iterator;
44 import java.util.List;
46 import java.util.Map.Entry;
47 import java.util.PriorityQueue;
49 import java.util.SortedMap;
50 import java.util.SortedSet;
51 import java.util.TreeMap;
52 import java.util.TreeSet;
53 import java.util.regex.Matcher;
54 import java.util.regex.Pattern;
56 import org.forester.application.surfacing;
57 import org.forester.evoinference.distance.NeighborJoining;
58 import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
59 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
60 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
61 import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
62 import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
63 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
64 import org.forester.evoinference.matrix.distance.DistanceMatrix;
65 import org.forester.go.GoId;
66 import org.forester.go.GoNameSpace;
67 import org.forester.go.GoTerm;
68 import org.forester.go.PfamToGoMapping;
69 import org.forester.io.parsers.nexus.NexusConstants;
70 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
71 import org.forester.io.parsers.util.ParserUtils;
72 import org.forester.io.writers.PhylogenyWriter;
73 import org.forester.phylogeny.Phylogeny;
74 import org.forester.phylogeny.PhylogenyMethods;
75 import org.forester.phylogeny.PhylogenyNode;
76 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
77 import org.forester.phylogeny.data.BinaryCharacters;
78 import org.forester.phylogeny.data.Confidence;
79 import org.forester.phylogeny.data.Taxonomy;
80 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
81 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
82 import org.forester.protein.BasicDomain;
83 import org.forester.protein.BasicProtein;
84 import org.forester.protein.BinaryDomainCombination;
85 import org.forester.protein.Domain;
86 import org.forester.protein.Protein;
87 import org.forester.species.Species;
88 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
89 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
90 import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
91 import org.forester.util.AsciiHistogram;
92 import org.forester.util.BasicDescriptiveStatistics;
93 import org.forester.util.BasicTable;
94 import org.forester.util.BasicTableParser;
95 import org.forester.util.CommandLineArguments;
96 import org.forester.util.DescriptiveStatistics;
97 import org.forester.util.ForesterUtil;
98 import org.forester.util.TaxonomyColors;
100 public final class SurfacingUtil {
102 public final static Pattern PATTERN_SP_STYLE_TAXONOMY = Pattern.compile( "^[A-Z0-9]{3,5}$" );
103 private final static Map<String, String> _TAXCODE_HEXCOLORSTRING_MAP = new HashMap<String, String>();
104 private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
107 public int compare( final Domain d1,
109 if ( d1.getPerSequenceEvalue() < d2
110 .getPerSequenceEvalue() ) {
114 .getPerSequenceEvalue() > d2
115 .getPerSequenceEvalue() ) {
119 return d1.compareTo( d2 );
123 private final static NumberFormat FORMATTER_3 = new DecimalFormat( "0.000" );
124 private SurfacingUtil() {
125 // Hidden constructor.
128 public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
129 final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
130 final SortedMap<String, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
131 for( final String domain_id : all_cd.keySet() ) {
132 binary_domain_combinations.addAll( all_cd.get( domain_id ).toBinaryDomainCombinations() );
136 public static void addAllDomainIdsToSet( final GenomeWideCombinableDomains genome,
137 final SortedSet<String> domain_ids ) {
138 final SortedSet<String> domains = genome.getAllDomainIds();
139 for( final String domain : domains ) {
140 domain_ids.add( domain );
144 public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
145 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
146 for( final DomainSimilarity similarity : similarities ) {
147 stats.addValue( similarity.getMeanSimilarityScore() );
152 public static void checkForOutputFileWriteability( final File outfile ) {
153 final String error = ForesterUtil.isWritableFile( outfile );
154 if ( !ForesterUtil.isEmpty( error ) ) {
155 ForesterUtil.fatalError( surfacing.PRG_NAME, error );
159 public static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
160 final String[][] input_file_properties,
161 final String automated_pairwise_comparison_suffix,
162 final File outdir ) {
163 for( int i = 0; i < input_file_properties.length; ++i ) {
164 for( int j = 0; j < i; ++j ) {
165 final String species_i = input_file_properties[ i ][ 1 ];
166 final String species_j = input_file_properties[ j ][ 1 ];
167 String pairwise_similarities_output_file_str = surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i
168 + "_" + species_j + automated_pairwise_comparison_suffix;
169 switch ( domain_similarity_print_option ) {
171 if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
172 pairwise_similarities_output_file_str += ".html";
176 final String error = ForesterUtil
177 .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir
178 + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
179 if ( !ForesterUtil.isEmpty( error ) ) {
180 ForesterUtil.fatalError( surfacing.PRG_NAME, error );
186 public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
187 final BinaryDomainCombination.DomainCombinationType dc_type,
188 final List<BinaryDomainCombination> all_binary_domains_combination_gained,
189 final boolean get_gains ) {
190 final SortedSet<String> sorted_ids = new TreeSet<String>();
191 for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
192 sorted_ids.add( matrix.getIdentifier( i ) );
194 for( final String id : sorted_ids ) {
195 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
196 if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
197 || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
198 if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
199 all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
200 .createInstance( matrix.getCharacter( c ) ) );
202 else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
203 all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
204 .createInstance( matrix.getCharacter( c ) ) );
207 all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
208 .getCharacter( c ) ) );
215 public static Map<String, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
216 final Map<String, List<GoId>> domain_id_to_go_ids_map = new HashMap<String, List<GoId>>( pfam_to_go_mappings.size() );
217 for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
218 if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
219 domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
221 domain_id_to_go_ids_map.get( pfam_to_go.getKey() ).add( pfam_to_go.getValue() );
223 return domain_id_to_go_ids_map;
226 public static Map<String, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
228 final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, '\t' );
229 final Map<String, Set<String>> map = new TreeMap<String, Set<String>>();
230 for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
231 final String domain_id = primary_table.getValue( 0, r );
232 if ( !map.containsKey( domain_id ) ) {
233 map.put( domain_id, new HashSet<String>() );
235 map.get( domain_id ).add( primary_table.getValue( 1, r ) );
240 public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
241 checkForOutputFileWriteability( nj_tree_outfile );
242 final NeighborJoining nj = NeighborJoining.createInstance();
243 final Phylogeny phylogeny = nj.execute( ( BasicSymmetricalDistanceMatrix ) distance );
244 phylogeny.setName( nj_tree_outfile.getName() );
245 writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
249 public static StringBuilder createParametersAsString( final boolean ignore_dufs,
250 final double e_value_max,
251 final int max_allowed_overlap,
252 final boolean no_engulfing_overlaps,
253 final File cutoff_scores_file,
254 final BinaryDomainCombination.DomainCombinationType dc_type ) {
255 final StringBuilder parameters_sb = new StringBuilder();
256 parameters_sb.append( "E-value: " + e_value_max );
257 if ( cutoff_scores_file != null ) {
258 parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
261 parameters_sb.append( ", Cutoff-scores-file: not-set" );
263 if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
264 parameters_sb.append( ", Max-overlap: " + max_allowed_overlap );
267 parameters_sb.append( ", Max-overlap: not-set" );
269 if ( no_engulfing_overlaps ) {
270 parameters_sb.append( ", Engulfing-overlaps: not-allowed" );
273 parameters_sb.append( ", Engulfing-overlaps: allowed" );
276 parameters_sb.append( ", Ignore-dufs: true" );
279 parameters_sb.append( ", Ignore-dufs: false" );
281 parameters_sb.append( ", DC type (if applicable): " + dc_type );
282 return parameters_sb;
285 public static void createSplitWriters( final File out_dir,
286 final String my_outfile,
287 final Map<Character, Writer> split_writers ) throws IOException {
288 split_writers.put( 'a', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
289 + "_domains_A.html" ) ) );
290 split_writers.put( 'b', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
291 + "_domains_B.html" ) ) );
292 split_writers.put( 'c', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
293 + "_domains_C.html" ) ) );
294 split_writers.put( 'd', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
295 + "_domains_D.html" ) ) );
296 split_writers.put( 'e', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
297 + "_domains_E.html" ) ) );
298 split_writers.put( 'f', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
299 + "_domains_F.html" ) ) );
300 split_writers.put( 'g', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
301 + "_domains_G.html" ) ) );
302 split_writers.put( 'h', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
303 + "_domains_H.html" ) ) );
304 split_writers.put( 'i', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
305 + "_domains_I.html" ) ) );
306 split_writers.put( 'j', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
307 + "_domains_J.html" ) ) );
308 split_writers.put( 'k', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
309 + "_domains_K.html" ) ) );
310 split_writers.put( 'l', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
311 + "_domains_L.html" ) ) );
312 split_writers.put( 'm', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
313 + "_domains_M.html" ) ) );
314 split_writers.put( 'n', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
315 + "_domains_N.html" ) ) );
316 split_writers.put( 'o', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
317 + "_domains_O.html" ) ) );
318 split_writers.put( 'p', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
319 + "_domains_P.html" ) ) );
320 split_writers.put( 'q', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
321 + "_domains_Q.html" ) ) );
322 split_writers.put( 'r', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
323 + "_domains_R.html" ) ) );
324 split_writers.put( 's', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
325 + "_domains_S.html" ) ) );
326 split_writers.put( 't', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
327 + "_domains_T.html" ) ) );
328 split_writers.put( 'u', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
329 + "_domains_U.html" ) ) );
330 split_writers.put( 'v', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
331 + "_domains_V.html" ) ) );
332 split_writers.put( 'w', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
333 + "_domains_W.html" ) ) );
334 split_writers.put( 'x', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
335 + "_domains_X.html" ) ) );
336 split_writers.put( 'y', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
337 + "_domains_Y.html" ) ) );
338 split_writers.put( 'z', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
339 + "_domains_Z.html" ) ) );
340 split_writers.put( '0', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
341 + "_domains_0.html" ) ) );
344 public static Map<String, Integer> createTaxCodeToIdMap( final Phylogeny phy ) {
345 final Map<String, Integer> m = new HashMap<String, Integer>();
346 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
347 final PhylogenyNode n = iter.next();
348 if ( n.getNodeData().isHasTaxonomy() ) {
349 final Taxonomy t = n.getNodeData().getTaxonomy();
350 final String c = t.getTaxonomyCode();
351 if ( !ForesterUtil.isEmpty( c ) ) {
352 if ( n.getNodeData().getTaxonomy() == null ) {
353 ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy id for node " + n );
355 final String id = n.getNodeData().getTaxonomy().getIdentifier().getValue();
356 if ( ForesterUtil.isEmpty( id ) ) {
357 ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy id for node " + n );
359 if ( m.containsKey( c ) ) {
360 ForesterUtil.fatalError( surfacing.PRG_NAME, "taxonomy code " + c + " is not unique" );
362 final int iid = Integer.valueOf( id );
363 if ( m.containsValue( iid ) ) {
364 ForesterUtil.fatalError( surfacing.PRG_NAME, "taxonomy id " + iid + " is not unique" );
370 ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy for node " + n );
376 public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
377 final Detailedness detailedness ) {
378 for( final DomainSimilarity domain_similarity : domain_similarities ) {
379 if ( domain_similarity instanceof PrintableDomainSimilarity ) {
380 final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
381 printable_domain_similarity.setDetailedness( detailedness );
386 public static void doit( final List<Protein> proteins,
387 final List<String> query_domain_ids_nc_order,
389 final String separator,
390 final String limit_to_species,
391 final Map<String, List<Integer>> average_protein_lengths_by_dc ) throws IOException {
392 for( final Protein protein : proteins ) {
393 if ( ForesterUtil.isEmpty( limit_to_species )
394 || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
395 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
396 out.write( protein.getSpecies().getSpeciesId() );
397 out.write( separator );
398 out.write( protein.getProteinId().getId() );
399 out.write( separator );
401 final Set<String> visited_domain_ids = new HashSet<String>();
402 boolean first = true;
403 for( final Domain domain : protein.getProteinDomains() ) {
404 if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
405 visited_domain_ids.add( domain.getDomainId() );
412 out.write( domain.getDomainId() );
414 out.write( "" + domain.getTotalCount() );
419 out.write( separator );
420 if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
421 .equals( SurfacingConstants.NONE ) ) ) {
422 out.write( protein.getDescription() );
424 out.write( separator );
425 if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
426 .equals( SurfacingConstants.NONE ) ) ) {
427 out.write( protein.getAccession() );
429 out.write( SurfacingConstants.NL );
436 public static void domainsPerProteinsStatistics( final String genome,
437 final List<Protein> protein_list,
438 final DescriptiveStatistics all_genomes_domains_per_potein_stats,
439 final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
440 final SortedSet<String> domains_which_are_always_single,
441 final SortedSet<String> domains_which_are_sometimes_single_sometimes_not,
442 final SortedSet<String> domains_which_never_single,
443 final Writer writer ) {
444 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
445 for( final Protein protein : protein_list ) {
446 final int domains = protein.getNumberOfProteinDomains();
447 //System.out.println( domains );
448 stats.addValue( domains );
449 all_genomes_domains_per_potein_stats.addValue( domains );
450 if ( !all_genomes_domains_per_potein_histo.containsKey( domains ) ) {
451 all_genomes_domains_per_potein_histo.put( domains, 1 );
454 all_genomes_domains_per_potein_histo.put( domains,
455 1 + all_genomes_domains_per_potein_histo.get( domains ) );
457 if ( domains == 1 ) {
458 final String domain = protein.getProteinDomain( 0 ).getDomainId();
459 if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
460 if ( domains_which_never_single.contains( domain ) ) {
461 domains_which_never_single.remove( domain );
462 domains_which_are_sometimes_single_sometimes_not.add( domain );
465 domains_which_are_always_single.add( domain );
469 else if ( domains > 1 ) {
470 for( final Domain d : protein.getProteinDomains() ) {
471 final String domain = d.getDomainId();
472 // System.out.println( domain );
473 if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
474 if ( domains_which_are_always_single.contains( domain ) ) {
475 domains_which_are_always_single.remove( domain );
476 domains_which_are_sometimes_single_sometimes_not.add( domain );
479 domains_which_never_single.add( domain );
486 writer.write( genome );
487 writer.write( "\t" );
488 if ( stats.getN() >= 1 ) {
489 writer.write( stats.arithmeticMean() + "" );
490 writer.write( "\t" );
491 if ( stats.getN() >= 2 ) {
492 writer.write( stats.sampleStandardDeviation() + "" );
497 writer.write( "\t" );
498 writer.write( stats.median() + "" );
499 writer.write( "\t" );
500 writer.write( stats.getN() + "" );
501 writer.write( "\t" );
502 writer.write( stats.getMin() + "" );
503 writer.write( "\t" );
504 writer.write( stats.getMax() + "" );
507 writer.write( "\t" );
508 writer.write( "\t" );
509 writer.write( "\t" );
511 writer.write( "\t" );
512 writer.write( "\t" );
514 writer.write( "\n" );
516 catch ( final IOException e ) {
521 public static void executeDomainLengthAnalysis( final String[][] input_file_properties,
522 final int number_of_genomes,
523 final DomainLengthsTable domain_lengths_table,
524 final File outfile ) throws IOException {
525 final DecimalFormat df = new DecimalFormat( "#.00" );
526 checkForOutputFileWriteability( outfile );
527 final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
528 out.write( "MEAN BASED STATISTICS PER SPECIES" );
529 out.write( ForesterUtil.LINE_SEPARATOR );
530 out.write( domain_lengths_table.createMeanBasedStatisticsPerSpeciesTable().toString() );
531 out.write( ForesterUtil.LINE_SEPARATOR );
532 out.write( ForesterUtil.LINE_SEPARATOR );
533 final List<DomainLengths> domain_lengths_list = domain_lengths_table.getDomainLengthsList();
534 out.write( "OUTLIER SPECIES PER DOMAIN (Z>=1.5)" );
535 out.write( ForesterUtil.LINE_SEPARATOR );
536 for( final DomainLengths domain_lengths : domain_lengths_list ) {
537 final List<Species> species_list = domain_lengths.getMeanBasedOutlierSpecies( 1.5 );
538 if ( species_list.size() > 0 ) {
539 out.write( domain_lengths.getDomainId() + "\t" );
540 for( final Species species : species_list ) {
541 out.write( species + "\t" );
543 out.write( ForesterUtil.LINE_SEPARATOR );
546 out.write( ForesterUtil.LINE_SEPARATOR );
547 out.write( ForesterUtil.LINE_SEPARATOR );
548 out.write( "OUTLIER SPECIES (Z 1.0)" );
549 out.write( ForesterUtil.LINE_SEPARATOR );
550 final DescriptiveStatistics stats_for_all_species = domain_lengths_table
551 .calculateMeanBasedStatisticsForAllSpecies();
552 out.write( stats_for_all_species.asSummary() );
553 out.write( ForesterUtil.LINE_SEPARATOR );
554 final AsciiHistogram histo = new AsciiHistogram( stats_for_all_species );
555 out.write( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
556 out.write( ForesterUtil.LINE_SEPARATOR );
557 final double population_sd = stats_for_all_species.sampleStandardDeviation();
558 final double population_mean = stats_for_all_species.arithmeticMean();
559 for( final Species species : domain_lengths_table.getSpecies() ) {
560 final double x = domain_lengths_table.calculateMeanBasedStatisticsForSpecies( species ).arithmeticMean();
561 final double z = ( x - population_mean ) / population_sd;
562 out.write( species + "\t" + z );
563 out.write( ForesterUtil.LINE_SEPARATOR );
565 out.write( ForesterUtil.LINE_SEPARATOR );
566 for( final Species species : domain_lengths_table.getSpecies() ) {
567 final DescriptiveStatistics stats_for_species = domain_lengths_table
568 .calculateMeanBasedStatisticsForSpecies( species );
569 final double x = stats_for_species.arithmeticMean();
570 final double z = ( x - population_mean ) / population_sd;
571 if ( ( z <= -1.0 ) || ( z >= 1.0 ) ) {
572 out.write( species + "\t" + df.format( z ) + "\t" + stats_for_species.asSummary() );
573 out.write( ForesterUtil.LINE_SEPARATOR );
581 * Warning: This side-effects 'all_bin_domain_combinations_encountered'!
585 * @param all_bin_domain_combinations_changed
586 * @param sum_of_all_domains_encountered
587 * @param all_bin_domain_combinations_encountered
588 * @param is_gains_analysis
589 * @param protein_length_stats_by_dc
590 * @throws IOException
592 public static void executeFitchGainsAnalysis( final File output_file,
593 final List<BinaryDomainCombination> all_bin_domain_combinations_changed,
594 final int sum_of_all_domains_encountered,
595 final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered,
596 final boolean is_gains_analysis ) throws IOException {
597 checkForOutputFileWriteability( output_file );
598 final Writer out = ForesterUtil.createBufferedWriter( output_file );
599 final SortedMap<Object, Integer> bdc_to_counts = ForesterUtil
600 .listToSortedCountsMap( all_bin_domain_combinations_changed );
601 final SortedSet<String> all_domains_in_combination_changed_more_than_once = new TreeSet<String>();
602 final SortedSet<String> all_domains_in_combination_changed_only_once = new TreeSet<String>();
605 for( final Object bdc_object : bdc_to_counts.keySet() ) {
606 final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object;
607 final int count = bdc_to_counts.get( bdc_object );
609 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "count < 1 " );
611 out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR );
613 all_domains_in_combination_changed_more_than_once.add( bdc.getId0() );
614 all_domains_in_combination_changed_more_than_once.add( bdc.getId1() );
617 else if ( count == 1 ) {
618 all_domains_in_combination_changed_only_once.add( bdc.getId0() );
619 all_domains_in_combination_changed_only_once.add( bdc.getId1() );
623 final int all = all_bin_domain_combinations_encountered.size();
625 if ( !is_gains_analysis ) {
626 all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed );
627 never_lost = all_bin_domain_combinations_encountered.size();
628 for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) {
629 out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR );
632 if ( is_gains_analysis ) {
633 out.write( "Sum of all distinct domain combinations appearing once : " + one
634 + ForesterUtil.LINE_SEPARATOR );
635 out.write( "Sum of all distinct domain combinations appearing more than once : " + above_one
636 + ForesterUtil.LINE_SEPARATOR );
637 out.write( "Sum of all distinct domains in combinations apppearing only once : "
638 + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
639 out.write( "Sum of all distinct domains in combinations apppearing more than once: "
640 + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
643 out.write( "Sum of all distinct domain combinations never lost : " + never_lost
644 + ForesterUtil.LINE_SEPARATOR );
645 out.write( "Sum of all distinct domain combinations lost once : " + one
646 + ForesterUtil.LINE_SEPARATOR );
647 out.write( "Sum of all distinct domain combinations lost more than once : " + above_one
648 + ForesterUtil.LINE_SEPARATOR );
649 out.write( "Sum of all distinct domains in combinations lost only once : "
650 + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
651 out.write( "Sum of all distinct domains in combinations lost more than once: "
652 + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
654 out.write( "All binary combinations : " + all
655 + ForesterUtil.LINE_SEPARATOR );
656 out.write( "All domains : "
657 + sum_of_all_domains_encountered );
659 ForesterUtil.programMessage( surfacing.PRG_NAME,
660 "Wrote fitch domain combination dynamics counts analysis to \"" + output_file
666 * @param all_binary_domains_combination_lost_fitch
667 * @param use_last_in_fitch_parsimony
668 * @param consider_directedness_and_adjacency_for_bin_combinations
669 * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
670 * which were gained under unweighted (Fitch) parsimony.
672 public static void executeParsimonyAnalysis( final long random_number_seed_for_fitch_parsimony,
673 final boolean radomize_fitch_parsimony,
674 final String outfile_name,
675 final DomainParsimonyCalculator domain_parsimony,
676 final Phylogeny phylogeny,
677 final Map<String, List<GoId>> domain_id_to_go_ids_map,
678 final Map<GoId, GoTerm> go_id_to_term_map,
679 final GoNameSpace go_namespace_limit,
680 final String parameters_str,
681 final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
682 final SortedSet<String> positive_filter,
683 final boolean output_binary_domain_combinations_for_graphs,
684 final List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch,
685 final List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch,
686 final BinaryDomainCombination.DomainCombinationType dc_type,
687 final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
688 final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
689 final Map<String, DescriptiveStatistics> domain_length_stats_by_domain,
690 final Map<String, Integer> tax_code_to_id_map,
691 final boolean write_to_nexus,
692 final boolean use_last_in_fitch_parsimony ) {
693 final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
694 final String date_time = ForesterUtil.getCurrentDateTime();
695 final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
696 final SortedSet<String> all_pfams_gained_as_domains = new TreeSet<String>();
697 final SortedSet<String> all_pfams_lost_as_domains = new TreeSet<String>();
698 final SortedSet<String> all_pfams_gained_as_dom_combinations = new TreeSet<String>();
699 final SortedSet<String> all_pfams_lost_as_dom_combinations = new TreeSet<String>();
700 if ( write_to_nexus ) {
701 writeToNexus( outfile_name, domain_parsimony, phylogeny );
705 Phylogeny local_phylogeny_l = phylogeny.copy();
706 if ( ( positive_filter != null ) && ( positive_filter.size() > 0 ) ) {
707 domain_parsimony.executeDolloParsimonyOnDomainPresence( positive_filter );
710 domain_parsimony.executeDolloParsimonyOnDomainPresence();
712 SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
713 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
714 SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
715 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
716 SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
717 CharacterStateMatrix.GainLossStates.GAIN,
718 outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
720 ForesterUtil.LINE_SEPARATOR,
722 SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
723 CharacterStateMatrix.GainLossStates.LOSS,
724 outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
726 ForesterUtil.LINE_SEPARATOR,
728 SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
729 + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
731 writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
735 domain_parsimony.getGainLossMatrix(),
736 CharacterStateMatrix.GainLossStates.GAIN,
737 outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
739 ForesterUtil.LINE_SEPARATOR,
740 "Dollo Parsimony | Gains | Domains",
742 domain_id_to_secondary_features_maps,
743 all_pfams_encountered,
744 all_pfams_gained_as_domains,
746 tax_code_to_id_map );
747 writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
751 domain_parsimony.getGainLossMatrix(),
752 CharacterStateMatrix.GainLossStates.LOSS,
753 outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
755 ForesterUtil.LINE_SEPARATOR,
756 "Dollo Parsimony | Losses | Domains",
758 domain_id_to_secondary_features_maps,
759 all_pfams_encountered,
760 all_pfams_lost_as_domains,
762 tax_code_to_id_map );
763 // writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
764 // go_id_to_term_map,
765 // go_namespace_limit,
767 // domain_parsimony.getGainLossMatrix(),
769 // outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
771 // ForesterUtil.LINE_SEPARATOR,
772 // "Dollo Parsimony | Present | Domains",
774 // domain_id_to_secondary_features_maps,
775 // all_pfams_encountered,
777 // "_dollo_present_d",
778 // tax_code_to_id_map );
779 preparePhylogeny( local_phylogeny_l,
782 "Dollo parsimony on domain presence/absence",
783 "dollo_on_domains_" + outfile_name,
785 SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
786 + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
788 writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
789 writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
791 catch ( final IOException e ) {
793 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
795 if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
796 // FITCH DOMAIN COMBINATIONS
797 // -------------------------
798 local_phylogeny_l = phylogeny.copy();
799 String randomization = "no";
800 if ( radomize_fitch_parsimony ) {
801 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( random_number_seed_for_fitch_parsimony );
802 randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
805 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( use_last_in_fitch_parsimony );
807 SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
808 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
809 SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
810 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
812 .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
813 CharacterStateMatrix.GainLossStates.GAIN,
814 outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
816 ForesterUtil.LINE_SEPARATOR,
818 SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
819 CharacterStateMatrix.GainLossStates.LOSS,
821 + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
823 ForesterUtil.LINE_SEPARATOR,
825 SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
826 + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
827 if ( all_binary_domains_combination_gained_fitch != null ) {
828 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
830 all_binary_domains_combination_gained_fitch,
833 if ( all_binary_domains_combination_lost_fitch != null ) {
834 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
836 all_binary_domains_combination_lost_fitch,
839 if ( output_binary_domain_combinations_for_graphs ) {
841 .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
842 .getGainLossMatrix(),
845 + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
847 ForesterUtil.LINE_SEPARATOR,
848 BinaryDomainCombination.OutputFormat.DOT );
851 writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
855 domain_parsimony.getGainLossMatrix(),
856 CharacterStateMatrix.GainLossStates.GAIN,
857 outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
859 ForesterUtil.LINE_SEPARATOR,
860 "Fitch Parsimony | Gains | Domain Combinations",
863 all_pfams_encountered,
864 all_pfams_gained_as_dom_combinations,
866 tax_code_to_id_map );
867 writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
871 domain_parsimony.getGainLossMatrix(),
872 CharacterStateMatrix.GainLossStates.LOSS,
873 outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
875 ForesterUtil.LINE_SEPARATOR,
876 "Fitch Parsimony | Losses | Domain Combinations",
879 all_pfams_encountered,
880 all_pfams_lost_as_dom_combinations,
882 tax_code_to_id_map );
883 // writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
884 // go_id_to_term_map,
885 // go_namespace_limit,
887 // domain_parsimony.getGainLossMatrix(),
889 // outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
891 // ForesterUtil.LINE_SEPARATOR,
892 // "Fitch Parsimony | Present | Domain Combinations",
895 // all_pfams_encountered,
897 // "_fitch_present_dc",
898 // tax_code_to_id_map );
899 writeAllEncounteredPfamsToFile( domain_id_to_go_ids_map,
902 all_pfams_encountered );
903 writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX, all_pfams_gained_as_domains );
904 writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
905 writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
906 all_pfams_gained_as_dom_combinations );
907 writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DC_SUFFIX, all_pfams_lost_as_dom_combinations );
908 preparePhylogeny( local_phylogeny_l,
911 "Fitch parsimony on binary domain combination presence/absence randomization: "
913 "fitch_on_binary_domain_combinations_" + outfile_name,
915 SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
916 + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
917 calculateIndependentDomainCombinationGains( local_phylogeny_l,
919 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX,
921 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX,
923 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX,
925 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX,
926 outfile_name + "_indep_dc_gains_fitch_lca_ranks.txt",
927 outfile_name + "_indep_dc_gains_fitch_lca_taxonomies.txt",
928 outfile_name + "_indep_dc_gains_fitch_protein_statistics.txt",
929 protein_length_stats_by_dc,
930 domain_number_stats_by_dc,
931 domain_length_stats_by_domain );
935 public static void executeParsimonyAnalysisForSecondaryFeatures( final String outfile_name,
936 final DomainParsimonyCalculator secondary_features_parsimony,
937 final Phylogeny phylogeny,
938 final String parameters_str,
939 final Map<Species, MappingResults> mapping_results_map,
940 final boolean use_last_in_fitch_parsimony ) {
941 final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
942 final String date_time = ForesterUtil.getCurrentDateTime();
943 System.out.println();
944 writeToNexus( outfile_name + surfacing.NEXUS_SECONDARY_FEATURES,
945 secondary_features_parsimony.createMatrixOfSecondaryFeaturePresenceOrAbsence( null ),
947 Phylogeny local_phylogeny_copy = phylogeny.copy();
948 secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
949 SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
950 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
951 SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
952 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
954 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
955 CharacterStateMatrix.GainLossStates.GAIN,
957 + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
959 ForesterUtil.LINE_SEPARATOR,
962 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
963 CharacterStateMatrix.GainLossStates.LOSS,
965 + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
967 ForesterUtil.LINE_SEPARATOR,
970 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
973 + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
975 ForesterUtil.LINE_SEPARATOR,
977 preparePhylogeny( local_phylogeny_copy,
978 secondary_features_parsimony,
980 "Dollo parsimony on secondary feature presence/absence",
981 "dollo_on_secondary_features_" + outfile_name,
983 SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
984 + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
985 // FITCH DOMAIN COMBINATIONS
986 // -------------------------
987 local_phylogeny_copy = phylogeny.copy();
988 final String randomization = "no";
989 secondary_features_parsimony
990 .executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( use_last_in_fitch_parsimony );
991 preparePhylogeny( local_phylogeny_copy,
992 secondary_features_parsimony,
994 "Fitch parsimony on secondary binary domain combination presence/absence randomization: "
996 "fitch_on_binary_domain_combinations_" + outfile_name,
998 SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
999 + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED );
1000 calculateIndependentDomainCombinationGains( local_phylogeny_copy, outfile_name
1001 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name
1002 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
1003 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
1004 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
1005 + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name
1006 + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null );
1009 public static void executePlusMinusAnalysis( final File output_file,
1010 final List<String> plus_minus_analysis_high_copy_base,
1011 final List<String> plus_minus_analysis_high_copy_target,
1012 final List<String> plus_minus_analysis_low_copy,
1013 final List<GenomeWideCombinableDomains> gwcd_list,
1014 final SortedMap<Species, List<Protein>> protein_lists_per_species,
1015 final Map<String, List<GoId>> domain_id_to_go_ids_map,
1016 final Map<GoId, GoTerm> go_id_to_term_map,
1017 final List<Object> plus_minus_analysis_numbers ) {
1018 final Set<String> all_spec = new HashSet<String>();
1019 for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
1020 all_spec.add( gwcd.getSpecies().getSpeciesId() );
1022 final File html_out_dom = new File( output_file + surfacing.PLUS_MINUS_DOM_SUFFIX_HTML );
1023 final File plain_out_dom = new File( output_file + surfacing.PLUS_MINUS_DOM_SUFFIX );
1024 final File html_out_dc = new File( output_file + surfacing.PLUS_MINUS_DC_SUFFIX_HTML );
1025 final File all_domains_go_ids_out_dom = new File( output_file + surfacing.PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX );
1026 final File passing_domains_go_ids_out_dom = new File( output_file
1027 + surfacing.PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX );
1028 final File proteins_file_base = new File( output_file + "" );
1029 final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue();
1030 final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue();
1032 DomainCountsDifferenceUtil.calculateCopyNumberDifferences( gwcd_list,
1033 protein_lists_per_species,
1034 plus_minus_analysis_high_copy_base,
1035 plus_minus_analysis_high_copy_target,
1036 plus_minus_analysis_low_copy,
1042 domain_id_to_go_ids_map,
1044 all_domains_go_ids_out_dom,
1045 passing_domains_go_ids_out_dom,
1046 proteins_file_base );
1048 catch ( final IOException e ) {
1049 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
1051 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
1052 + html_out_dom + "\"" );
1053 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
1054 + plain_out_dom + "\"" );
1055 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \"" + html_out_dc
1057 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based passing GO ids to \""
1058 + passing_domains_go_ids_out_dom + "\"" );
1059 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based all GO ids to \""
1060 + all_domains_go_ids_out_dom + "\"" );
1063 public static void extractProteinNames( final List<Protein> proteins,
1064 final List<String> query_domain_ids_nc_order,
1066 final String separator,
1067 final String limit_to_species ) throws IOException {
1068 for( final Protein protein : proteins ) {
1069 if ( ForesterUtil.isEmpty( limit_to_species )
1070 || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
1071 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
1072 out.write( protein.getSpecies().getSpeciesId() );
1073 out.write( separator );
1074 out.write( protein.getProteinId().getId() );
1075 out.write( separator );
1077 final Set<String> visited_domain_ids = new HashSet<String>();
1078 boolean first = true;
1079 for( final Domain domain : protein.getProteinDomains() ) {
1080 if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
1081 visited_domain_ids.add( domain.getDomainId() );
1088 out.write( domain.getDomainId() );
1090 out.write( "" + domain.getTotalCount() );
1095 out.write( separator );
1096 if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
1097 .equals( SurfacingConstants.NONE ) ) ) {
1098 out.write( protein.getDescription() );
1100 out.write( separator );
1101 if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
1102 .equals( SurfacingConstants.NONE ) ) ) {
1103 out.write( protein.getAccession() );
1105 out.write( SurfacingConstants.NL );
1112 public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
1113 final String domain_id,
1115 final String separator,
1116 final String limit_to_species,
1117 final double domain_e_cutoff ) throws IOException {
1118 //System.out.println( "Per domain E-value: " + domain_e_cutoff );
1119 for( final Species species : protein_lists_per_species.keySet() ) {
1120 //System.out.println( species + ":" );
1121 for( final Protein protein : protein_lists_per_species.get( species ) ) {
1122 if ( ForesterUtil.isEmpty( limit_to_species )
1123 || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
1124 final List<Domain> domains = protein.getProteinDomains( domain_id );
1125 if ( domains.size() > 0 ) {
1126 out.write( protein.getSpecies().getSpeciesId() );
1127 out.write( separator );
1128 out.write( protein.getProteinId().getId() );
1129 out.write( separator );
1130 out.write( domain_id.toString() );
1131 out.write( separator );
1133 for( final Domain domain : domains ) {
1134 if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
1136 out.write( domain.getFrom() + "-" + domain.getTo() );
1137 if ( prev_to >= 0 ) {
1138 final int l = domain.getFrom() - prev_to;
1139 // System.out.println( l );
1141 prev_to = domain.getTo();
1145 out.write( separator );
1146 final List<Domain> domain_list = new ArrayList<Domain>();
1147 for( final Domain domain : protein.getProteinDomains() ) {
1148 if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
1149 domain_list.add( domain );
1152 final Domain domain_ary[] = new Domain[ domain_list.size() ];
1153 for( int i = 0; i < domain_list.size(); ++i ) {
1154 domain_ary[ i ] = domain_list.get( i );
1156 Arrays.sort( domain_ary, new DomainComparator( true ) );
1158 boolean first = true;
1159 for( final Domain domain : domain_ary ) {
1166 out.write( domain.getDomainId().toString() );
1167 out.write( ":" + domain.getFrom() + "-" + domain.getTo() );
1168 out.write( ":" + domain.getPerDomainEvalue() );
1171 if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
1172 .equals( SurfacingConstants.NONE ) ) ) {
1173 out.write( protein.getDescription() );
1175 out.write( separator );
1176 if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
1177 .equals( SurfacingConstants.NONE ) ) ) {
1178 out.write( protein.getAccession() );
1180 out.write( SurfacingConstants.NL );
1188 public static SortedSet<String> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
1189 final SortedSet<String> all_domains_ids = new TreeSet<String>();
1190 for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
1191 final Set<String> all_domains = gwcd.getAllDomainIds();
1192 // for( final Domain domain : all_domains ) {
1193 all_domains_ids.addAll( all_domains );
1196 return all_domains_ids;
1199 public static SortedMap<String, Integer> getDomainCounts( final List<Protein> protein_domain_collections ) {
1200 final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
1201 for( final Protein protein_domain_collection : protein_domain_collections ) {
1202 for( final Object name : protein_domain_collection.getProteinDomains() ) {
1203 final BasicDomain protein_domain = ( BasicDomain ) name;
1204 final String id = protein_domain.getDomainId();
1205 if ( map.containsKey( id ) ) {
1206 map.put( id, map.get( id ) + 1 );
1216 public static int getNumberOfNodesLackingName( final Phylogeny p, final StringBuilder names ) {
1217 final PhylogenyNodeIterator it = p.iteratorPostorder();
1219 while ( it.hasNext() ) {
1220 final PhylogenyNode n = it.next();
1221 if ( ForesterUtil.isEmpty( n.getName() )
1222 && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1223 .getScientificName() ) )
1224 && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1225 .getCommonName() ) ) ) {
1226 if ( n.getParent() != null ) {
1227 names.append( " " );
1228 names.append( n.getParent().getName() );
1230 final List l = n.getAllExternalDescendants();
1231 for( final Object object : l ) {
1232 System.out.println( l.toString() );
1240 public static void log( final String msg, final Writer w ) {
1243 w.write( ForesterUtil.LINE_SEPARATOR );
1245 catch ( final IOException e ) {
1246 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
1250 public static Phylogeny[] obtainAndPreProcessIntrees( final File[] intree_files,
1251 final int number_of_genomes,
1252 final String[][] input_file_properties ) {
1253 final Phylogeny[] intrees = new Phylogeny[ intree_files.length ];
1255 for( final File intree_file : intree_files ) {
1256 Phylogeny intree = null;
1257 final String error = ForesterUtil.isReadableFile( intree_file );
1258 if ( !ForesterUtil.isEmpty( error ) ) {
1259 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read input tree file [" + intree_file + "]: "
1263 final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
1264 .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) );
1265 if ( p_array.length < 1 ) {
1266 ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
1267 + "] does not contain any phylogeny in phyloXML format" );
1269 else if ( p_array.length > 1 ) {
1270 ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
1271 + "] contains more than one phylogeny in phyloXML format" );
1273 intree = p_array[ 0 ];
1275 catch ( final Exception e ) {
1276 ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read input tree from file [" + intree_file
1279 if ( ( intree == null ) || intree.isEmpty() ) {
1280 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
1282 if ( !intree.isRooted() ) {
1283 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
1285 if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
1286 ForesterUtil.fatalError( surfacing.PRG_NAME,
1287 "number of external nodes [" + intree.getNumberOfExternalNodes()
1288 + "] of input tree [" + intree_file
1289 + "] is smaller than the number of genomes the be analyzed ["
1290 + number_of_genomes + "]" );
1292 final StringBuilder parent_names = new StringBuilder();
1293 final int nodes_lacking_name = getNumberOfNodesLackingName( intree, parent_names );
1294 if ( nodes_lacking_name > 0 ) {
1295 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] has "
1296 + nodes_lacking_name + " node(s) lacking a name [parent names:" + parent_names + "]" );
1298 preparePhylogenyForParsimonyAnalyses( intree, input_file_properties );
1299 if ( !intree.isCompletelyBinary() ) {
1300 ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "input tree [" + intree_file
1301 + "] is not completely binary" );
1303 intrees[ i++ ] = intree;
1308 public static Phylogeny obtainFirstIntree( final File intree_file ) {
1309 Phylogeny intree = null;
1310 final String error = ForesterUtil.isReadableFile( intree_file );
1311 if ( !ForesterUtil.isEmpty( error ) ) {
1312 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read input tree file [" + intree_file + "]: " + error );
1315 final Phylogeny[] phys = ParserBasedPhylogenyFactory.getInstance()
1316 .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) );
1317 if ( phys.length < 1 ) {
1318 ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
1319 + "] does not contain any phylogeny in phyloXML format" );
1321 else if ( phys.length > 1 ) {
1322 ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
1323 + "] contains more than one phylogeny in phyloXML format" );
1327 catch ( final Exception e ) {
1328 ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read input tree from file [" + intree_file + "]: "
1331 if ( ( intree == null ) || intree.isEmpty() ) {
1332 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
1334 if ( !intree.isRooted() ) {
1335 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
1340 public static String obtainHexColorStringDependingOnTaxonomyGroup( final String tax_code, final Phylogeny phy )
1341 throws IllegalArgumentException {
1342 if ( !_TAXCODE_HEXCOLORSTRING_MAP.containsKey( tax_code ) ) {
1343 if ( ( phy != null ) && !phy.isEmpty() ) {
1344 final List<PhylogenyNode> nodes = phy.getNodesViaTaxonomyCode( tax_code );
1346 if ( ( nodes == null ) || nodes.isEmpty() ) {
1347 throw new IllegalArgumentException( "code " + tax_code + " is not found" );
1349 if ( nodes.size() != 1 ) {
1350 throw new IllegalArgumentException( "code " + tax_code + " is not unique" );
1352 PhylogenyNode n = nodes.get( 0 );
1353 while ( n != null ) {
1354 if ( n.getNodeData().isHasTaxonomy()
1355 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
1356 c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( n.getNodeData().getTaxonomy()
1357 .getScientificName(), tax_code );
1359 if ( ( c == null ) && !ForesterUtil.isEmpty( n.getName() ) ) {
1360 c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( n.getName(), tax_code );
1368 throw new IllegalArgumentException( "no color found for taxonomy code \"" + tax_code + "\"" );
1370 final String hex = String.format( "#%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue() );
1371 _TAXCODE_HEXCOLORSTRING_MAP.put( tax_code, hex );
1374 throw new IllegalArgumentException( "unable to obtain color for code " + tax_code
1375 + " (tree is null or empty and code is not in map)" );
1378 return _TAXCODE_HEXCOLORSTRING_MAP.get( tax_code );
1381 public static void performDomainArchitectureAnalysis( final SortedMap<String, Set<String>> domain_architecutures,
1382 final SortedMap<String, Integer> domain_architecuture_counts,
1383 final int min_count,
1384 final File da_counts_outfile,
1385 final File unique_da_outfile ) {
1386 checkForOutputFileWriteability( da_counts_outfile );
1387 checkForOutputFileWriteability( unique_da_outfile );
1389 final BufferedWriter da_counts_out = new BufferedWriter( new FileWriter( da_counts_outfile ) );
1390 final BufferedWriter unique_da_out = new BufferedWriter( new FileWriter( unique_da_outfile ) );
1391 final Iterator<Entry<String, Integer>> it = domain_architecuture_counts.entrySet().iterator();
1392 while ( it.hasNext() ) {
1393 final Map.Entry<String, Integer> e = it.next();
1394 final String da = e.getKey();
1395 final int count = e.getValue();
1396 if ( count >= min_count ) {
1397 da_counts_out.write( da );
1398 da_counts_out.write( "\t" );
1399 da_counts_out.write( String.valueOf( count ) );
1400 da_counts_out.write( ForesterUtil.LINE_SEPARATOR );
1403 final Iterator<Entry<String, Set<String>>> it2 = domain_architecutures.entrySet().iterator();
1404 while ( it2.hasNext() ) {
1405 final Map.Entry<String, Set<String>> e2 = it2.next();
1406 final String genome = e2.getKey();
1407 final Set<String> das = e2.getValue();
1408 if ( das.contains( da ) ) {
1409 unique_da_out.write( genome );
1410 unique_da_out.write( "\t" );
1411 unique_da_out.write( da );
1412 unique_da_out.write( ForesterUtil.LINE_SEPARATOR );
1417 unique_da_out.close();
1418 da_counts_out.close();
1420 catch ( final IOException e ) {
1421 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1423 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + da_counts_outfile + "\"" );
1424 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + unique_da_outfile + "\"" );
1428 public static void preparePhylogeny( final Phylogeny p,
1429 final DomainParsimonyCalculator domain_parsimony,
1430 final String date_time,
1431 final String method,
1433 final String parameters_str ) {
1434 domain_parsimony.decoratePhylogenyWithDomains( p );
1435 final StringBuilder desc = new StringBuilder();
1436 desc.append( "[Method: " + method + "] [Date: " + date_time + "] " );
1437 desc.append( "[Cost: " + domain_parsimony.getCost() + "] " );
1438 desc.append( "[Gains: " + domain_parsimony.getTotalGains() + "] " );
1439 desc.append( "[Losses: " + domain_parsimony.getTotalLosses() + "] " );
1440 desc.append( "[Unchanged: " + domain_parsimony.getTotalUnchanged() + "] " );
1441 desc.append( "[Parameters: " + parameters_str + "]" );
1443 p.setDescription( desc.toString() );
1444 p.setConfidence( new Confidence( domain_parsimony.getCost(), "parsimony" ) );
1445 p.setRerootable( false );
1446 p.setRooted( true );
1449 public static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree,
1450 final String[][] input_file_properties ) {
1451 final String[] genomes = new String[ input_file_properties.length ];
1452 for( int i = 0; i < input_file_properties.length; ++i ) {
1453 if ( intree.getNodes( input_file_properties[ i ][ 1 ] ).size() > 1 ) {
1454 ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
1455 + "] is not unique in input tree " + intree.getName() );
1457 genomes[ i ] = input_file_properties[ i ][ 1 ];
1460 final PhylogenyNodeIterator it = intree.iteratorPostorder();
1461 while ( it.hasNext() ) {
1462 final PhylogenyNode n = it.next();
1463 if ( ForesterUtil.isEmpty( n.getName() ) ) {
1464 if ( n.getNodeData().isHasTaxonomy()
1465 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
1466 n.setName( n.getNodeData().getTaxonomy().getTaxonomyCode() );
1468 else if ( n.getNodeData().isHasTaxonomy()
1469 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
1470 n.setName( n.getNodeData().getTaxonomy().getScientificName() );
1472 else if ( n.getNodeData().isHasTaxonomy()
1473 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
1474 n.setName( n.getNodeData().getTaxonomy().getCommonName() );
1478 .fatalError( surfacing.PRG_NAME,
1479 "node with no name, scientific name, common name, or taxonomy code present" );
1484 final List<String> igns = PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
1485 if ( igns.size() > 0 ) {
1486 System.out.println( "Not using the following " + igns.size() + " nodes:" );
1487 for( int i = 0; i < igns.size(); ++i ) {
1488 System.out.println( " " + i + ": " + igns.get( i ) );
1490 System.out.println( "--" );
1492 for( final String[] input_file_propertie : input_file_properties ) {
1494 intree.getNode( input_file_propertie[ 1 ] );
1496 catch ( final IllegalArgumentException e ) {
1497 ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_propertie[ 1 ]
1498 + "] not present/not unique in input tree" );
1503 public static void printOutPercentageOfMultidomainProteins( final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
1504 final Writer log_writer ) {
1506 for( final Entry<Integer, Integer> entry : all_genomes_domains_per_potein_histo.entrySet() ) {
1507 sum += entry.getValue();
1509 final double percentage = ( 100.0 * ( sum - all_genomes_domains_per_potein_histo.get( 1 ) ) ) / sum;
1510 ForesterUtil.programMessage( surfacing.PRG_NAME, "Percentage of multidomain proteins: " + percentage + "%" );
1511 log( "Percentage of multidomain proteins: : " + percentage + "%", log_writer );
1514 public static void processFilter( final File filter_file, final SortedSet<String> filter ) {
1515 SortedSet<String> filter_str = null;
1517 filter_str = ForesterUtil.file2set( filter_file );
1519 catch ( final IOException e ) {
1520 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1522 if ( filter_str != null ) {
1523 for( final String string : filter_str ) {
1524 filter.add( string );
1527 if ( surfacing.VERBOSE ) {
1528 System.out.println( "Filter:" );
1529 for( final String domainId : filter ) {
1530 System.out.println( domainId );
1535 public static String[][] processInputGenomesFile( final File input_genomes ) {
1536 String[][] input_file_properties = null;
1538 input_file_properties = ForesterUtil.file22dArray( input_genomes );
1540 catch ( final IOException e ) {
1541 ForesterUtil.fatalError( surfacing.PRG_NAME,
1542 "genomes files is to be in the following format \"<hmmpfam output file> <species>\": "
1543 + e.getLocalizedMessage() );
1545 final Set<String> specs = new HashSet<String>();
1546 final Set<String> paths = new HashSet<String>();
1547 for( int i = 0; i < input_file_properties.length; ++i ) {
1548 if ( !PhyloXmlUtil.TAXOMONY_CODE_PATTERN.matcher( input_file_properties[ i ][ 1 ] ).matches() ) {
1549 ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for species code: "
1550 + input_file_properties[ i ][ 1 ] );
1552 if ( specs.contains( input_file_properties[ i ][ 1 ] ) ) {
1553 ForesterUtil.fatalError( surfacing.PRG_NAME, "species code " + input_file_properties[ i ][ 1 ]
1554 + " is not unique" );
1556 specs.add( input_file_properties[ i ][ 1 ] );
1557 if ( paths.contains( input_file_properties[ i ][ 0 ] ) ) {
1558 ForesterUtil.fatalError( surfacing.PRG_NAME, "path " + input_file_properties[ i ][ 0 ]
1559 + " is not unique" );
1561 paths.add( input_file_properties[ i ][ 0 ] );
1562 final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
1563 if ( !ForesterUtil.isEmpty( error ) ) {
1564 ForesterUtil.fatalError( surfacing.PRG_NAME, error );
1567 return input_file_properties;
1570 public static void processPlusMinusAnalysisOption( final CommandLineArguments cla,
1571 final List<String> high_copy_base,
1572 final List<String> high_copy_target,
1573 final List<String> low_copy,
1574 final List<Object> numbers ) {
1575 if ( cla.isOptionSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
1576 if ( !cla.isOptionValueSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
1577 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for 'plus-minus' file: -"
1578 + surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>" );
1580 final File plus_minus_file = new File( cla.getOptionValue( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) );
1581 final String msg = ForesterUtil.isReadableFile( plus_minus_file );
1582 if ( !ForesterUtil.isEmpty( msg ) ) {
1583 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + plus_minus_file + "\": " + msg );
1585 processPlusMinusFile( plus_minus_file, high_copy_base, high_copy_target, low_copy, numbers );
1589 // First numbers is minimal difference, second is factor.
1590 public static void processPlusMinusFile( final File plus_minus_file,
1591 final List<String> high_copy_base,
1592 final List<String> high_copy_target,
1593 final List<String> low_copy,
1594 final List<Object> numbers ) {
1595 Set<String> species_set = null;
1596 int min_diff = surfacing.PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT;
1597 double factor = surfacing.PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT;
1599 species_set = ForesterUtil.file2set( plus_minus_file );
1601 catch ( final IOException e ) {
1602 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1604 if ( species_set != null ) {
1605 for( final String species : species_set ) {
1606 final String species_trimmed = species.substring( 1 );
1607 if ( species.startsWith( "+" ) ) {
1608 if ( low_copy.contains( species_trimmed ) ) {
1609 ForesterUtil.fatalError( surfacing.PRG_NAME,
1610 "species/genome names can not appear with both '+' and '-' suffix, as appears the case for: \""
1611 + species_trimmed + "\"" );
1613 high_copy_base.add( species_trimmed );
1615 else if ( species.startsWith( "*" ) ) {
1616 if ( low_copy.contains( species_trimmed ) ) {
1617 ForesterUtil.fatalError( surfacing.PRG_NAME,
1618 "species/genome names can not appear with both '*' and '-' suffix, as appears the case for: \""
1619 + species_trimmed + "\"" );
1621 high_copy_target.add( species_trimmed );
1623 else if ( species.startsWith( "-" ) ) {
1624 if ( high_copy_base.contains( species_trimmed ) || high_copy_target.contains( species_trimmed ) ) {
1625 ForesterUtil.fatalError( surfacing.PRG_NAME,
1626 "species/genome names can not appear with both '+' or '*' and '-' suffix, as appears the case for: \""
1627 + species_trimmed + "\"" );
1629 low_copy.add( species_trimmed );
1631 else if ( species.startsWith( "$D" ) ) {
1633 min_diff = Integer.parseInt( species.substring( 3 ) );
1635 catch ( final NumberFormatException e ) {
1636 ForesterUtil.fatalError( surfacing.PRG_NAME,
1637 "could not parse integer value for minimal difference from: \""
1638 + species.substring( 3 ) + "\"" );
1641 else if ( species.startsWith( "$F" ) ) {
1643 factor = Double.parseDouble( species.substring( 3 ) );
1645 catch ( final NumberFormatException e ) {
1646 ForesterUtil.fatalError( surfacing.PRG_NAME, "could not parse double value for factor from: \""
1647 + species.substring( 3 ) + "\"" );
1650 else if ( species.startsWith( "#" ) ) {
1655 .fatalError( surfacing.PRG_NAME,
1656 "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=<integer>' minimal Difference (default is 1), '$F=<double>' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \""
1659 numbers.add( new Integer( min_diff + "" ) );
1660 numbers.add( new Double( factor + "" ) );
1664 ForesterUtil.fatalError( surfacing.PRG_NAME, "'plus minus' file [" + plus_minus_file + "] appears empty" );
1669 * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
1673 static public StringBuffer proteinToDomainCombinations( final Protein protein,
1674 final String protein_id,
1675 final String separator ) {
1676 final StringBuffer sb = new StringBuffer();
1677 if ( protein.getSpecies() == null ) {
1678 throw new IllegalArgumentException( "species must not be null" );
1680 if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
1681 throw new IllegalArgumentException( "species id must not be empty" );
1683 final List<Domain> domains = protein.getProteinDomains();
1684 if ( domains.size() > 1 ) {
1685 final Map<String, Integer> counts = new HashMap<String, Integer>();
1686 for( final Domain domain : domains ) {
1687 final String id = domain.getDomainId();
1688 if ( counts.containsKey( id ) ) {
1689 counts.put( id, counts.get( id ) + 1 );
1692 counts.put( id, 1 );
1695 final Set<String> dcs = new HashSet<String>();
1696 for( int i = 1; i < domains.size(); ++i ) {
1697 for( int j = 0; j < i; ++j ) {
1698 Domain domain_n = domains.get( i );
1699 Domain domain_c = domains.get( j );
1700 if ( domain_n.getFrom() > domain_c.getFrom() ) {
1701 domain_n = domains.get( j );
1702 domain_c = domains.get( i );
1704 final String dc = domain_n.getDomainId() + domain_c.getDomainId();
1705 if ( !dcs.contains( dc ) ) {
1707 sb.append( protein.getSpecies() );
1708 sb.append( separator );
1709 sb.append( protein_id );
1710 sb.append( separator );
1711 sb.append( domain_n.getDomainId() );
1712 sb.append( separator );
1713 sb.append( domain_c.getDomainId() );
1714 sb.append( separator );
1715 sb.append( domain_n.getPerDomainEvalue() );
1716 sb.append( separator );
1717 sb.append( domain_c.getPerDomainEvalue() );
1718 sb.append( separator );
1719 sb.append( counts.get( domain_n.getDomainId() ) );
1720 sb.append( separator );
1721 sb.append( counts.get( domain_c.getDomainId() ) );
1722 sb.append( ForesterUtil.LINE_SEPARATOR );
1727 else if ( domains.size() == 1 ) {
1728 sb.append( protein.getSpecies() );
1729 sb.append( separator );
1730 sb.append( protein_id );
1731 sb.append( separator );
1732 sb.append( domains.get( 0 ).getDomainId() );
1733 sb.append( separator );
1734 sb.append( separator );
1735 sb.append( domains.get( 0 ).getPerDomainEvalue() );
1736 sb.append( separator );
1737 sb.append( separator );
1739 sb.append( separator );
1740 sb.append( ForesterUtil.LINE_SEPARATOR );
1743 sb.append( protein.getSpecies() );
1744 sb.append( separator );
1745 sb.append( protein_id );
1746 sb.append( separator );
1747 sb.append( separator );
1748 sb.append( separator );
1749 sb.append( separator );
1750 sb.append( separator );
1751 sb.append( separator );
1752 sb.append( ForesterUtil.LINE_SEPARATOR );
1757 public static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
1758 final List<Domain> domains = new ArrayList<Domain>();
1759 for( final Domain d : protein.getProteinDomains() ) {
1762 Collections.sort( domains, SurfacingUtil.ASCENDING_CONFIDENCE_VALUE_ORDER );
1766 public static int storeDomainArchitectures( final String genome,
1767 final SortedMap<String, Set<String>> domain_architecutures,
1768 final List<Protein> protein_list,
1769 final Map<String, Integer> distinct_domain_architecuture_counts ) {
1770 final Set<String> da = new HashSet<String>();
1771 domain_architecutures.put( genome, da );
1772 for( final Protein protein : protein_list ) {
1773 final String da_str = ( ( BasicProtein ) protein ).toDomainArchitectureString( "~", 3, "=" );
1774 if ( !da.contains( da_str ) ) {
1775 if ( !distinct_domain_architecuture_counts.containsKey( da_str ) ) {
1776 distinct_domain_architecuture_counts.put( da_str, 1 );
1779 distinct_domain_architecuture_counts.put( da_str,
1780 distinct_domain_architecuture_counts.get( da_str ) + 1 );
1788 public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
1789 final boolean get_gains,
1790 final String outdir,
1791 final String suffix_for_filename ) throws IOException {
1792 CharacterStateMatrix.GainLossStates state = CharacterStateMatrix.GainLossStates.GAIN;
1794 state = CharacterStateMatrix.GainLossStates.LOSS;
1796 final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
1800 for( final PhylogenyNodeIterator it = p.iteratorPostorder(); it.hasNext(); ) {
1801 final PhylogenyNode node = it.next();
1802 if ( !node.isExternal() ) {
1803 final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
1804 if ( domains.size() > 0 ) {
1805 final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
1806 + node.getName() + suffix_for_filename );
1807 for( final String domain : domains ) {
1808 writer.write( domain );
1809 writer.write( ForesterUtil.LINE_SEPARATOR );
1817 public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
1818 final File output_dir,
1819 final GenomeWideCombinableDomains gwcd,
1821 final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1822 File dc_outfile_dot = new File( input_file_properties[ i ][ 1 ]
1823 + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
1824 if ( output_dir != null ) {
1825 dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
1827 checkForOutputFileWriteability( dc_outfile_dot );
1828 final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
1830 final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
1831 for( final BinaryDomainCombination bdc : binary_combinations ) {
1832 out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
1834 out_dot.write( SurfacingConstants.NL );
1838 catch ( final IOException e ) {
1839 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1841 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
1842 + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1843 + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
1846 public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1847 final CharacterStateMatrix.GainLossStates state,
1848 final String filename,
1849 final String indentifier_characters_separator,
1850 final String character_separator,
1851 final Map<String, String> descriptions ) {
1852 final File outfile = new File( filename );
1853 checkForOutputFileWriteability( outfile );
1854 final SortedSet<String> sorted_ids = new TreeSet<String>();
1855 for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1856 sorted_ids.add( matrix.getIdentifier( i ) );
1859 final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1860 for( final String id : sorted_ids ) {
1861 out.write( indentifier_characters_separator );
1862 out.write( "#" + id );
1863 out.write( indentifier_characters_separator );
1864 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1866 // using null to indicate either UNCHANGED_PRESENT or GAIN.
1867 if ( ( matrix.getState( id, c ) == state )
1868 || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1869 .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1870 out.write( matrix.getCharacter( c ) );
1871 if ( ( descriptions != null ) && !descriptions.isEmpty()
1872 && descriptions.containsKey( matrix.getCharacter( c ) ) ) {
1874 out.write( descriptions.get( matrix.getCharacter( c ) ) );
1876 out.write( character_separator );
1883 catch ( final IOException e ) {
1884 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1886 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1889 public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1890 final CharacterStateMatrix.GainLossStates state,
1891 final String filename,
1892 final String indentifier_characters_separator,
1893 final String character_separator,
1894 final BinaryDomainCombination.OutputFormat bc_output_format ) {
1895 final File outfile = new File( filename );
1896 checkForOutputFileWriteability( outfile );
1897 final SortedSet<String> sorted_ids = new TreeSet<String>();
1898 for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1899 sorted_ids.add( matrix.getIdentifier( i ) );
1902 final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1903 for( final String id : sorted_ids ) {
1904 out.write( indentifier_characters_separator );
1905 out.write( "#" + id );
1906 out.write( indentifier_characters_separator );
1907 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1909 // using null to indicate either UNCHANGED_PRESENT or GAIN.
1910 if ( ( matrix.getState( id, c ) == state )
1911 || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1912 .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1913 BinaryDomainCombination bdc = null;
1915 bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
1917 catch ( final Exception e ) {
1918 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
1920 out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
1921 out.write( character_separator );
1928 catch ( final IOException e ) {
1929 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1931 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1934 public static void writeBinaryStatesMatrixToList( final Map<String, List<GoId>> domain_id_to_go_ids_map,
1935 final Map<GoId, GoTerm> go_id_to_term_map,
1936 final GoNameSpace go_namespace_limit,
1937 final boolean domain_combinations,
1938 final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1939 final CharacterStateMatrix.GainLossStates state,
1940 final String filename,
1941 final String indentifier_characters_separator,
1942 final String character_separator,
1943 final String title_for_html,
1944 final String prefix_for_html,
1945 final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
1946 final SortedSet<String> all_pfams_encountered,
1947 final SortedSet<String> pfams_gained_or_lost,
1948 final String suffix_for_per_node_events_file,
1949 final Map<String, Integer> tax_code_to_id_map ) {
1950 if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1951 throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
1953 else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
1954 throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
1956 else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1957 throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
1959 final File outfile = new File( filename );
1960 checkForOutputFileWriteability( outfile );
1961 final SortedSet<String> sorted_ids = new TreeSet<String>();
1962 for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1963 sorted_ids.add( matrix.getIdentifier( i ) );
1966 final Writer out = new BufferedWriter( new FileWriter( outfile ) );
1967 final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
1968 domain_combinations,
1971 Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1972 File per_node_go_mapped_domain_gain_loss_outfile = null;
1973 int per_node_counter = 0;
1974 out.write( "<html>" );
1975 out.write( SurfacingConstants.NL );
1976 writeHtmlHead( out, title_for_html );
1977 out.write( SurfacingConstants.NL );
1978 out.write( "<body>" );
1979 out.write( SurfacingConstants.NL );
1980 out.write( "<h1>" );
1981 out.write( SurfacingConstants.NL );
1982 out.write( title_for_html );
1983 out.write( SurfacingConstants.NL );
1984 out.write( "</h1>" );
1985 out.write( SurfacingConstants.NL );
1986 out.write( "<table>" );
1987 out.write( SurfacingConstants.NL );
1988 for( final String id : sorted_ids ) {
1989 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1990 if ( matcher.matches() ) {
1993 out.write( "<tr>" );
1994 out.write( "<td>" );
1995 out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
1996 out.write( "</td>" );
1997 out.write( "</tr>" );
1998 out.write( SurfacingConstants.NL );
2000 out.write( "</table>" );
2001 out.write( SurfacingConstants.NL );
2002 for( final String id : sorted_ids ) {
2003 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
2004 if ( matcher.matches() ) {
2007 out.write( SurfacingConstants.NL );
2008 out.write( "<h2>" );
2009 out.write( "<a name=\"" + id + "\">" + id + "</a>" );
2010 writeTaxonomyLinks( out, id, tax_code_to_id_map );
2011 out.write( "</h2>" );
2012 out.write( SurfacingConstants.NL );
2013 out.write( "<table>" );
2014 out.write( SurfacingConstants.NL );
2015 out.write( "<tr>" );
2016 out.write( "<td><b>" );
2017 out.write( "Pfam domain(s)" );
2018 out.write( "</b></td><td><b>" );
2019 out.write( "GO term acc" );
2020 out.write( "</b></td><td><b>" );
2021 out.write( "GO term" );
2022 out.write( "</b></td><td><b>" );
2023 out.write( "GO namespace" );
2024 out.write( "</b></td>" );
2025 out.write( "</tr>" );
2026 out.write( SurfacingConstants.NL );
2027 out.write( "</tr>" );
2028 out.write( SurfacingConstants.NL );
2029 per_node_counter = 0;
2030 if ( matrix.getNumberOfCharacters() > 0 ) {
2031 per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2032 + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
2033 SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
2034 per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
2035 .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
2038 per_node_go_mapped_domain_gain_loss_outfile = null;
2039 per_node_go_mapped_domain_gain_loss_outfile_writer = null;
2041 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
2043 // using null to indicate either UNCHANGED_PRESENT or GAIN.
2044 if ( ( matrix.getState( id, c ) == state )
2045 || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
2046 .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
2047 final String character = matrix.getCharacter( c );
2048 String domain_0 = "";
2049 String domain_1 = "";
2050 if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
2051 final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
2052 if ( s.length != 2 ) {
2053 throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
2054 + character + "]" );
2060 domain_0 = character;
2062 writeDomainData( domain_id_to_go_ids_map,
2069 character_separator,
2070 domain_id_to_secondary_features_maps,
2072 all_pfams_encountered.add( domain_0 );
2073 if ( pfams_gained_or_lost != null ) {
2074 pfams_gained_or_lost.add( domain_0 );
2076 if ( !ForesterUtil.isEmpty( domain_1 ) ) {
2077 all_pfams_encountered.add( domain_1 );
2078 if ( pfams_gained_or_lost != null ) {
2079 pfams_gained_or_lost.add( domain_1 );
2082 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
2083 writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
2090 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
2091 per_node_go_mapped_domain_gain_loss_outfile_writer.close();
2092 if ( per_node_counter < 1 ) {
2093 per_node_go_mapped_domain_gain_loss_outfile.delete();
2095 per_node_counter = 0;
2097 out.write( "</table>" );
2098 out.write( SurfacingConstants.NL );
2099 out.write( "<hr>" );
2100 out.write( SurfacingConstants.NL );
2101 } // for( final String id : sorted_ids ) {
2102 out.write( "</body>" );
2103 out.write( SurfacingConstants.NL );
2104 out.write( "</html>" );
2105 out.write( SurfacingConstants.NL );
2109 catch ( final IOException e ) {
2110 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2112 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
2115 public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
2116 final File output_dir,
2117 final Writer per_genome_domain_promiscuity_statistics_writer,
2118 final GenomeWideCombinableDomains gwcd,
2120 final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
2121 File dc_outfile = new File( input_file_properties[ i ][ 1 ]
2122 + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
2123 if ( output_dir != null ) {
2124 dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
2126 checkForOutputFileWriteability( dc_outfile );
2128 final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
2129 out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
2132 catch ( final IOException e ) {
2133 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2135 final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
2137 per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 1 ] + "\t" );
2138 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
2139 if ( stats.getN() < 2 ) {
2140 per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
2143 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
2144 .sampleStandardDeviation() ) + "\t" );
2146 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
2147 per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
2148 per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
2149 per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
2150 final SortedSet<String> mpds = gwcd.getMostPromiscuosDomain();
2151 for( final String mpd : mpds ) {
2152 per_genome_domain_promiscuity_statistics_writer.write( mpd + " " );
2154 per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
2156 catch ( final IOException e ) {
2157 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2159 if ( input_file_properties[ i ].length == 3 ) {
2160 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
2161 + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
2162 + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
2165 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
2166 + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
2167 + dc_outfile + "\"" );
2171 public static void writeDomainSimilaritiesToFile( final StringBuilder html_desc,
2172 final StringBuilder html_title,
2173 final Writer simple_tab_writer,
2174 final Writer single_writer,
2175 Map<Character, Writer> split_writers,
2176 final SortedSet<DomainSimilarity> similarities,
2177 final boolean treat_as_binary,
2178 final List<Species> species_order,
2179 final PrintableDomainSimilarity.PRINT_OPTION print_option,
2180 final DomainSimilarity.DomainSimilarityScoring scoring,
2181 final boolean verbose,
2182 final Map<String, Integer> tax_code_to_id_map,
2183 final Phylogeny phy ) throws IOException {
2184 if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
2185 split_writers = new HashMap<Character, Writer>();
2186 split_writers.put( '_', single_writer );
2188 switch ( print_option ) {
2189 case SIMPLE_TAB_DELIMITED:
2192 for( final Character key : split_writers.keySet() ) {
2193 final Writer w = split_writers.get( key );
2194 w.write( "<html>" );
2195 w.write( SurfacingConstants.NL );
2197 writeHtmlHead( w, "DC analysis (" + html_title + ") " + key.toString().toUpperCase() );
2200 writeHtmlHead( w, "DC analysis (" + html_title + ")" );
2202 w.write( SurfacingConstants.NL );
2203 w.write( "<body>" );
2204 w.write( SurfacingConstants.NL );
2205 w.write( html_desc.toString() );
2206 w.write( SurfacingConstants.NL );
2208 w.write( SurfacingConstants.NL );
2210 w.write( SurfacingConstants.NL );
2211 w.write( "<table>" );
2212 w.write( SurfacingConstants.NL );
2213 w.write( "<tr><td><b>Domains:</b></td></tr>" );
2214 w.write( SurfacingConstants.NL );
2219 for( final DomainSimilarity similarity : similarities ) {
2220 if ( ( species_order != null ) && !species_order.isEmpty() ) {
2221 ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
2223 if ( single_writer != null ) {
2224 single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
2225 + similarity.getDomainId() + "</a></b></td></tr>" );
2226 single_writer.write( SurfacingConstants.NL );
2229 Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
2231 if ( local_writer == null ) {
2232 local_writer = split_writers.get( '0' );
2234 local_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
2235 + similarity.getDomainId() + "</a></b></td></tr>" );
2236 local_writer.write( SurfacingConstants.NL );
2239 for( final Writer w : split_writers.values() ) {
2240 w.write( "</table>" );
2241 w.write( SurfacingConstants.NL );
2243 w.write( SurfacingConstants.NL );
2245 w.write( "<table>" );
2246 w.write( SurfacingConstants.NL );
2247 w.write( "<tr><td><b>" );
2248 w.write( "Species group colors:" );
2249 w.write( "</b></td></tr>" );
2250 w.write( SurfacingConstants.NL );
2251 writeColorLabels( "Deuterostomia", TaxonomyColors.DEUTEROSTOMIA_COLOR, w );
2252 writeColorLabels( "Protostomia", TaxonomyColors.PROTOSTOMIA_COLOR, w );
2253 writeColorLabels( "Cnidaria", TaxonomyColors.CNIDARIA_COLOR, w );
2254 writeColorLabels( "Placozoa", TaxonomyColors.PLACOZOA_COLOR, w );
2255 writeColorLabels( "Ctenophora (comb jellies)", TaxonomyColors.CTENOPHORA_COLOR, w );
2256 writeColorLabels( "Porifera (sponges)", TaxonomyColors.PORIFERA_COLOR, w );
2257 writeColorLabels( "Choanoflagellida", TaxonomyColors.CHOANOFLAGELLIDA, w );
2258 writeColorLabels( "Ichthyosporea & Filasterea", TaxonomyColors.ICHTHYOSPOREA_AND_FILASTEREA, w );
2259 writeColorLabels( "Fungi", TaxonomyColors.FUNGI_COLOR, w );
2260 writeColorLabels( "Nucleariidae and Fonticula group",
2261 TaxonomyColors.NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR,
2263 writeColorLabels( "Amoebozoa", TaxonomyColors.AMOEBOZOA_COLOR, w );
2264 writeColorLabels( "Embryophyta (plants)", TaxonomyColors.EMBRYOPHYTA_COLOR, w );
2265 writeColorLabels( "Chlorophyta (green algae)", TaxonomyColors.CHLOROPHYTA_COLOR, w );
2266 writeColorLabels( "Rhodophyta (red algae)", TaxonomyColors.RHODOPHYTA_COLOR, w );
2267 writeColorLabels( "Glaucocystophyce (Glaucophyta)", TaxonomyColors.GLAUCOPHYTA_COLOR, w );
2268 writeColorLabels( "Hacrobia (Cryptophyta & Haptophyceae & Centroheliozoa)",
2269 TaxonomyColors.HACROBIA_COLOR,
2271 writeColorLabels( "Stramenopiles (Chromophyta, heterokonts)", TaxonomyColors.STRAMENOPILES_COLOR, w );
2272 writeColorLabels( "Alveolata", TaxonomyColors.ALVEOLATA_COLOR, w );
2273 writeColorLabels( "Rhizaria", TaxonomyColors.RHIZARIA_COLOR, w );
2274 writeColorLabels( "Excavata", TaxonomyColors.EXCAVATA_COLOR, w );
2275 writeColorLabels( "Apusozoa", TaxonomyColors.APUSOZOA_COLOR, w );
2276 writeColorLabels( "Archaea", TaxonomyColors.ARCHAEA_COLOR, w );
2277 writeColorLabels( "Bacteria", TaxonomyColors.BACTERIA_COLOR, w );
2278 w.write( "</table>" );
2279 w.write( SurfacingConstants.NL );
2282 w.write( SurfacingConstants.NL );
2283 w.write( "<table>" );
2284 w.write( SurfacingConstants.NL );
2287 for( final DomainSimilarity similarity : similarities ) {
2288 if ( ( species_order != null ) && !species_order.isEmpty() ) {
2289 ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
2291 if ( simple_tab_writer != null ) {
2292 simple_tab_writer.write( similarity.toStringBuffer( PRINT_OPTION.SIMPLE_TAB_DELIMITED,
2294 null ).toString() );
2296 if ( single_writer != null ) {
2297 single_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map, phy ).toString() );
2298 single_writer.write( SurfacingConstants.NL );
2301 Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
2303 if ( local_writer == null ) {
2304 local_writer = split_writers.get( '0' );
2306 local_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map, phy ).toString() );
2307 local_writer.write( SurfacingConstants.NL );
2310 switch ( print_option ) {
2312 for( final Writer w : split_writers.values() ) {
2313 w.write( SurfacingConstants.NL );
2314 w.write( "</table>" );
2315 w.write( SurfacingConstants.NL );
2316 w.write( "</font>" );
2317 w.write( SurfacingConstants.NL );
2318 w.write( "</body>" );
2319 w.write( SurfacingConstants.NL );
2320 w.write( "</html>" );
2321 w.write( SurfacingConstants.NL );
2327 for( final Writer w : split_writers.values() ) {
2332 public static void writeHtmlHead( final Writer w, final String title ) throws IOException {
2333 w.write( SurfacingConstants.NL );
2334 w.write( "<head>" );
2335 w.write( "<title>" );
2337 w.write( "</title>" );
2338 w.write( SurfacingConstants.NL );
2339 w.write( "<style>" );
2340 w.write( SurfacingConstants.NL );
2341 w.write( "a:visited { color : #000066; text-decoration : none; }" );
2342 w.write( SurfacingConstants.NL );
2343 w.write( "a:link { color : #000066; text-decoration : none; }" );
2344 w.write( SurfacingConstants.NL );
2345 w.write( "a:active { color : ##000066; text-decoration : none; }" );
2346 w.write( SurfacingConstants.NL );
2347 w.write( "a:hover { color : #FFFFFF; background-color : #000000; text-decoration : none; }" );
2348 w.write( SurfacingConstants.NL );
2350 w.write( "a.pl:visited { color : #505050; text-decoration : none; font-size: 7px;}" );
2351 w.write( SurfacingConstants.NL );
2352 w.write( "a.pl:link { color : #505050; text-decoration : none; font-size: 7px;}" );
2353 w.write( SurfacingConstants.NL );
2354 w.write( "a.pl:active { color : #505050; text-decoration : none; font-size: 7px;}" );
2355 w.write( SurfacingConstants.NL );
2356 w.write( "a.pl:hover { color : #FFFFFF; background-color : #000000; text-decoration : none; font-size: 7px;}" );
2357 w.write( SurfacingConstants.NL );
2359 w.write( "a.ps:visited { color : #707070; text-decoration : none; font-size: 7px;}" );
2360 w.write( SurfacingConstants.NL );
2361 w.write( "a.ps:link { color : #707070; text-decoration : none; font-size: 7px;}" );
2362 w.write( SurfacingConstants.NL );
2363 w.write( "a.ps:active { color : #707070; text-decoration : none; font-size: 7px;}" );
2364 w.write( SurfacingConstants.NL );
2365 w.write( "a.ps:hover { color : #FFFFFF; background-color : #000000; text-decoration : none; font-size: 7px;}" );
2366 w.write( SurfacingConstants.NL );
2368 w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
2369 w.write( SurfacingConstants.NL );
2370 w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
2371 w.write( SurfacingConstants.NL );
2372 w.write( "h2 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" );
2373 w.write( SurfacingConstants.NL );
2374 w.write( "</style>" );
2375 w.write( SurfacingConstants.NL );
2376 w.write( "</head>" );
2377 w.write( SurfacingConstants.NL );
2380 public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
2381 final String filename,
2382 final Format format ) {
2383 final File outfile = new File( filename );
2384 checkForOutputFileWriteability( outfile );
2386 final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
2387 matrix.toWriter( out, format );
2391 catch ( final IOException e ) {
2392 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2394 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
2397 public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
2398 checkForOutputFileWriteability( matrix_outfile );
2400 final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
2401 for( final DistanceMatrix distance_matrix : matrices ) {
2402 out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
2403 out.write( ForesterUtil.LINE_SEPARATOR );
2408 catch ( final IOException e ) {
2409 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2411 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
2414 public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
2415 final PhylogenyWriter writer = new PhylogenyWriter();
2417 writer.toPhyloXML( new File( filename ), phylogeny, 1 );
2419 catch ( final IOException e ) {
2420 ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
2423 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
2426 public static void writePresentToNexus( final File output_file,
2427 final File positive_filter_file,
2428 final SortedSet<String> filter,
2429 final List<GenomeWideCombinableDomains> gwcd_list ) {
2431 writeMatrixToFile( DomainParsimonyCalculator.createMatrixOfDomainPresenceOrAbsence( gwcd_list,
2432 positive_filter_file == null ? null
2434 output_file + surfacing.DOMAINS_PRESENT_NEXUS,
2435 Format.NEXUS_BINARY );
2436 writeMatrixToFile( DomainParsimonyCalculator.createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ),
2437 output_file + surfacing.BDC_PRESENT_NEXUS,
2438 Format.NEXUS_BINARY );
2440 catch ( final Exception e ) {
2441 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
2445 public static void writeProteinListsForAllSpecies( final File output_dir,
2446 final SortedMap<Species, List<Protein>> protein_lists_per_species,
2447 final List<GenomeWideCombinableDomains> gwcd_list,
2448 final double domain_e_cutoff ) {
2449 final SortedSet<String> all_domains = new TreeSet<String>();
2450 for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
2451 all_domains.addAll( gwcd.getAllDomainIds() );
2453 for( final String domain : all_domains ) {
2454 final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + surfacing.SEQ_EXTRACT_SUFFIX );
2455 checkForOutputFileWriteability( out );
2457 final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
2458 extractProteinNames( protein_lists_per_species,
2460 proteins_file_writer,
2462 surfacing.LIMIT_SPEC_FOR_PROT_EX,
2464 proteins_file_writer.close();
2466 catch ( final IOException e ) {
2467 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
2469 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
2473 public static void writeTaxonomyLinks( final Writer writer,
2474 final String species,
2475 final Map<String, Integer> tax_code_to_id_map ) throws IOException {
2476 if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
2477 writer.write( " [" );
2478 if ( ( tax_code_to_id_map != null ) && tax_code_to_id_map.containsKey( species ) ) {
2479 writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_TAXONOMY_ID_LINK
2480 + tax_code_to_id_map.get( species ) + "\" target=\"taxonomy_window\">uniprot</a>" );
2483 writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
2484 + "\" target=\"taxonomy_window\">eol</a>" );
2485 writer.write( "|" );
2486 writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_SEARCH + species
2487 + "\" target=\"taxonomy_window\">scholar</a>" );
2488 writer.write( "|" );
2489 writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_WEB_SEARCH_LINK + species
2490 + "\" target=\"taxonomy_window\">google</a>" );
2492 writer.write( "]" );
2496 private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
2497 if ( map.containsKey( s ) ) {
2498 map.put( s, map.get( s ) + 1 );
2505 private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
2506 final String outfilename_for_counts,
2507 final String outfilename_for_dc,
2508 final String outfilename_for_dc_for_go_mapping,
2509 final String outfilename_for_dc_for_go_mapping_unique,
2510 final String outfilename_for_rank_counts,
2511 final String outfilename_for_ancestor_species_counts,
2512 final String outfilename_for_protein_stats,
2513 final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
2514 final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
2515 final Map<String, DescriptiveStatistics> domain_length_stats_by_domain ) {
2518 // if ( protein_length_stats_by_dc != null ) {
2519 // for( final Entry<?, DescriptiveStatistics> entry : protein_length_stats_by_dc.entrySet() ) {
2520 // System.out.print( entry.getKey().toString() );
2521 // System.out.print( ": " );
2522 // double[] a = entry.getValue().getDataAsDoubleArray();
2523 // for( int i = 0; i < a.length; i++ ) {
2524 // System.out.print( a[ i ] + " " );
2526 // System.out.println();
2529 // if ( domain_number_stats_by_dc != null ) {
2530 // for( final Entry<?, DescriptiveStatistics> entry : domain_number_stats_by_dc.entrySet() ) {
2531 // System.out.print( entry.getKey().toString() );
2532 // System.out.print( ": " );
2533 // double[] a = entry.getValue().getDataAsDoubleArray();
2534 // for( int i = 0; i < a.length; i++ ) {
2535 // System.out.print( a[ i ] + " " );
2537 // System.out.println();
2541 final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
2542 final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
2543 final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) );
2544 final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) );
2545 final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
2546 for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
2547 final PhylogenyNode n = it.next();
2548 final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
2549 for( final String dc : gained_dc ) {
2550 if ( dc_gain_counts.containsKey( dc ) ) {
2551 dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
2554 dc_gain_counts.put( dc, 1 );
2558 final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
2559 final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
2560 final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_protein_length_stats = new TreeMap<Integer, DescriptiveStatistics>();
2561 final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_number_stats = new TreeMap<Integer, DescriptiveStatistics>();
2562 final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_lengths_stats = new TreeMap<Integer, DescriptiveStatistics>();
2563 final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
2564 final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
2565 final Set<String> dcs = dc_gain_counts.keySet();
2566 final SortedSet<String> more_than_once = new TreeSet<String>();
2567 DescriptiveStatistics gained_once_lengths_stats = new BasicDescriptiveStatistics();
2568 DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics();
2569 DescriptiveStatistics gained_multiple_times_lengths_stats = new BasicDescriptiveStatistics();
2570 final DescriptiveStatistics gained_multiple_times_domain_count_stats = new BasicDescriptiveStatistics();
2571 long gained_multiple_times_domain_length_sum = 0;
2572 long gained_once_domain_length_sum = 0;
2573 long gained_multiple_times_domain_length_count = 0;
2574 long gained_once_domain_length_count = 0;
2575 for( final String dc : dcs ) {
2576 final int count = dc_gain_counts.get( dc );
2577 if ( histogram.containsKey( count ) ) {
2578 histogram.put( count, histogram.get( count ) + 1 );
2579 domain_lists.get( count ).append( ", " + dc );
2580 domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) );
2581 domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) );
2584 histogram.put( count, 1 );
2585 domain_lists.put( count, new StringBuilder( dc ) );
2586 final PriorityQueue<String> q = new PriorityQueue<String>();
2587 q.addAll( splitDomainCombination( dc ) );
2588 domain_lists_go.put( count, q );
2589 final SortedSet<String> set = new TreeSet<String>();
2590 set.addAll( splitDomainCombination( dc ) );
2591 domain_lists_go_unique.put( count, set );
2593 if ( protein_length_stats_by_dc != null ) {
2594 if ( !dc_reapp_counts_to_protein_length_stats.containsKey( count ) ) {
2595 dc_reapp_counts_to_protein_length_stats.put( count, new BasicDescriptiveStatistics() );
2597 dc_reapp_counts_to_protein_length_stats.get( count ).addValue( protein_length_stats_by_dc.get( dc )
2598 .arithmeticMean() );
2600 if ( domain_number_stats_by_dc != null ) {
2601 if ( !dc_reapp_counts_to_domain_number_stats.containsKey( count ) ) {
2602 dc_reapp_counts_to_domain_number_stats.put( count, new BasicDescriptiveStatistics() );
2604 dc_reapp_counts_to_domain_number_stats.get( count ).addValue( domain_number_stats_by_dc.get( dc )
2605 .arithmeticMean() );
2607 if ( domain_length_stats_by_domain != null ) {
2608 if ( !dc_reapp_counts_to_domain_lengths_stats.containsKey( count ) ) {
2609 dc_reapp_counts_to_domain_lengths_stats.put( count, new BasicDescriptiveStatistics() );
2611 final String[] ds = dc.split( "=" );
2612 dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
2613 .get( ds[ 0 ] ).arithmeticMean() );
2614 dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
2615 .get( ds[ 1 ] ).arithmeticMean() );
2618 more_than_once.add( dc );
2619 if ( protein_length_stats_by_dc != null ) {
2620 final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
2621 for( final double element : s.getData() ) {
2622 gained_multiple_times_lengths_stats.addValue( element );
2625 if ( domain_number_stats_by_dc != null ) {
2626 final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
2627 for( final double element : s.getData() ) {
2628 gained_multiple_times_domain_count_stats.addValue( element );
2631 if ( domain_length_stats_by_domain != null ) {
2632 final String[] ds = dc.split( "=" );
2633 final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
2634 final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
2635 for( final double element : s0.getData() ) {
2636 gained_multiple_times_domain_length_sum += element;
2637 ++gained_multiple_times_domain_length_count;
2639 for( final double element : s1.getData() ) {
2640 gained_multiple_times_domain_length_sum += element;
2641 ++gained_multiple_times_domain_length_count;
2646 if ( protein_length_stats_by_dc != null ) {
2647 final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
2648 for( final double element : s.getData() ) {
2649 gained_once_lengths_stats.addValue( element );
2652 if ( domain_number_stats_by_dc != null ) {
2653 final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
2654 for( final double element : s.getData() ) {
2655 gained_once_domain_count_stats.addValue( element );
2658 if ( domain_length_stats_by_domain != null ) {
2659 final String[] ds = dc.split( "=" );
2660 final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
2661 final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
2662 for( final double element : s0.getData() ) {
2663 gained_once_domain_length_sum += element;
2664 ++gained_once_domain_length_count;
2666 for( final double element : s1.getData() ) {
2667 gained_once_domain_length_sum += element;
2668 ++gained_once_domain_length_count;
2673 final Set<Integer> histogram_keys = histogram.keySet();
2674 for( final Integer histogram_key : histogram_keys ) {
2675 final int count = histogram.get( histogram_key );
2676 final StringBuilder dc = domain_lists.get( histogram_key );
2677 out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
2678 out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
2679 out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
2680 final Object[] sorted = domain_lists_go.get( histogram_key ).toArray();
2681 Arrays.sort( sorted );
2682 for( final Object domain : sorted ) {
2683 out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR );
2685 out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
2686 for( final String domain : domain_lists_go_unique.get( histogram_key ) ) {
2687 out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR );
2692 out_dc_for_go_mapping.close();
2693 out_dc_for_go_mapping_unique.close();
2694 final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
2695 final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
2696 for( final String dc : more_than_once ) {
2697 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
2698 for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
2699 final PhylogenyNode n = it.next();
2700 if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
2704 for( int i = 0; i < ( nodes.size() - 1 ); ++i ) {
2705 for( int j = i + 1; j < nodes.size(); ++j ) {
2706 final PhylogenyNode lca = PhylogenyMethods.calculateLCA( nodes.get( i ), nodes.get( j ) );
2707 String rank = "unknown";
2708 if ( lca.getNodeData().isHasTaxonomy()
2709 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
2710 rank = lca.getNodeData().getTaxonomy().getRank();
2712 addToCountMap( lca_rank_counts, rank );
2714 if ( lca.getNodeData().isHasTaxonomy()
2715 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
2716 lca_species = lca.getNodeData().getTaxonomy().getScientificName();
2718 else if ( lca.getNodeData().isHasTaxonomy()
2719 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
2720 lca_species = lca.getNodeData().getTaxonomy().getCommonName();
2723 lca_species = lca.getName();
2725 addToCountMap( lca_ancestor_species_counts, lca_species );
2729 final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
2730 final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
2731 ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
2732 ForesterUtil.map2writer( out_for_ancestor_species_counts,
2733 lca_ancestor_species_counts,
2735 ForesterUtil.LINE_SEPARATOR );
2736 out_for_rank_counts.close();
2737 out_for_ancestor_species_counts.close();
2738 if ( !ForesterUtil.isEmpty( outfilename_for_protein_stats )
2739 && ( ( domain_length_stats_by_domain != null ) || ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) {
2740 final BufferedWriter w = new BufferedWriter( new FileWriter( outfilename_for_protein_stats ) );
2741 w.write( "Domain Lengths: " );
2743 if ( domain_length_stats_by_domain != null ) {
2744 for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_lengths_stats
2746 w.write( entry.getKey().toString() );
2747 w.write( "\t" + entry.getValue().arithmeticMean() );
2748 w.write( "\t" + entry.getValue().median() );
2755 w.write( "Protein Lengths: " );
2757 if ( protein_length_stats_by_dc != null ) {
2758 for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_protein_length_stats
2760 w.write( entry.getKey().toString() );
2761 w.write( "\t" + entry.getValue().arithmeticMean() );
2762 w.write( "\t" + entry.getValue().median() );
2769 w.write( "Number of domains: " );
2771 if ( domain_number_stats_by_dc != null ) {
2772 for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_number_stats
2774 w.write( entry.getKey().toString() );
2775 w.write( "\t" + entry.getValue().arithmeticMean() );
2776 w.write( "\t" + entry.getValue().median() );
2783 w.write( "Gained once, domain lengths:" );
2785 w.write( "N: " + gained_once_domain_length_count );
2787 w.write( "Avg: " + ( ( double ) gained_once_domain_length_sum / gained_once_domain_length_count ) );
2790 w.write( "Gained multiple times, domain lengths:" );
2792 w.write( "N: " + gained_multiple_times_domain_length_count );
2795 + ( ( double ) gained_multiple_times_domain_length_sum / gained_multiple_times_domain_length_count ) );
2800 w.write( "Gained once, protein lengths:" );
2802 w.write( gained_once_lengths_stats.toString() );
2803 gained_once_lengths_stats = null;
2806 w.write( "Gained once, domain counts:" );
2808 w.write( gained_once_domain_count_stats.toString() );
2809 gained_once_domain_count_stats = null;
2812 w.write( "Gained multiple times, protein lengths:" );
2814 w.write( gained_multiple_times_lengths_stats.toString() );
2815 gained_multiple_times_lengths_stats = null;
2818 w.write( "Gained multiple times, domain counts:" );
2820 w.write( gained_multiple_times_domain_count_stats.toString() );
2825 catch ( final IOException e ) {
2826 ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2828 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
2829 + outfilename_for_counts + "]" );
2830 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
2831 + outfilename_for_dc + "]" );
2832 ForesterUtil.programMessage( surfacing.PRG_NAME,
2833 "Wrote independent domain combination gains fitch lists to (for GO mapping) ["
2834 + outfilename_for_dc_for_go_mapping + "]" );
2835 ForesterUtil.programMessage( surfacing.PRG_NAME,
2836 "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) ["
2837 + outfilename_for_dc_for_go_mapping_unique + "]" );
2840 private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
2841 final boolean get_gains ) {
2842 final SortedSet<String> domains = new TreeSet<String>();
2843 for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
2844 final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
2846 domains.addAll( chars.getGainedCharacters() );
2849 domains.addAll( chars.getLostCharacters() );
2855 private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
2856 final boolean domain_combinations,
2857 final CharacterStateMatrix.GainLossStates state,
2858 final String outfile ) {
2859 File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
2860 + ForesterUtil.FILE_SEPARATOR + base_dir );
2861 if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2862 per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2864 if ( domain_combinations ) {
2865 per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2866 + ForesterUtil.FILE_SEPARATOR + "DC" );
2869 per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2870 + ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
2872 if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2873 per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2875 if ( state == GainLossStates.GAIN ) {
2876 per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2877 + ForesterUtil.FILE_SEPARATOR + "GAINS" );
2879 else if ( state == GainLossStates.LOSS ) {
2880 per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2881 + ForesterUtil.FILE_SEPARATOR + "LOSSES" );
2884 per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2885 + ForesterUtil.FILE_SEPARATOR + "PRESENT" );
2887 if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2888 per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2890 return per_node_go_mapped_domain_gain_loss_files_base_dir;
2893 private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
2894 final SortedMap<String, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
2895 final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
2896 for( final String domain_id : cds.keySet() ) {
2897 final CombinableDomains cd = cds.get( domain_id );
2898 binary_combinations.addAll( cd.toBinaryDomainCombinations() );
2900 return binary_combinations;
2903 private static void printSomeStats( final DescriptiveStatistics stats, final AsciiHistogram histo, final Writer w )
2904 throws IOException {
2907 w.write( SurfacingConstants.NL );
2908 w.write( "<tt><pre>" );
2909 w.write( SurfacingConstants.NL );
2910 if ( histo != null ) {
2911 w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
2912 w.write( SurfacingConstants.NL );
2914 w.write( "</pre></tt>" );
2915 w.write( SurfacingConstants.NL );
2916 w.write( "<table>" );
2917 w.write( SurfacingConstants.NL );
2918 w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
2919 w.write( SurfacingConstants.NL );
2920 w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
2921 w.write( SurfacingConstants.NL );
2922 w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
2923 w.write( SurfacingConstants.NL );
2924 w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
2925 w.write( SurfacingConstants.NL );
2926 if ( stats.getN() > 1 ) {
2927 w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
2930 w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
2932 w.write( SurfacingConstants.NL );
2933 w.write( "</table>" );
2934 w.write( SurfacingConstants.NL );
2936 w.write( SurfacingConstants.NL );
2939 private static List<String> splitDomainCombination( final String dc ) {
2940 final String[] s = dc.split( "=" );
2941 if ( s.length != 2 ) {
2942 ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: "
2946 final List<String> l = new ArrayList<String>( 2 );
2952 private static void writeAllEncounteredPfamsToFile( final Map<String, List<GoId>> domain_id_to_go_ids_map,
2953 final Map<GoId, GoTerm> go_id_to_term_map,
2954 final String outfile_name,
2955 final SortedSet<String> all_pfams_encountered ) {
2956 final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
2957 final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
2958 + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
2959 final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
2960 int biological_process_counter = 0;
2961 int cellular_component_counter = 0;
2962 int molecular_function_counter = 0;
2963 int pfams_with_mappings_counter = 0;
2964 int pfams_without_mappings_counter = 0;
2965 int pfams_without_mappings_to_bp_or_mf_counter = 0;
2966 int pfams_with_mappings_to_bp_or_mf_counter = 0;
2968 final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
2969 final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
2970 final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
2971 summary_writer.write( "# Pfam to GO mapping summary" );
2972 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2973 summary_writer.write( "# Actual summary is at the end of this file." );
2974 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2975 summary_writer.write( "# Encountered Pfams without a GO mapping:" );
2976 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2977 for( final String pfam : all_pfams_encountered ) {
2978 all_pfams_encountered_writer.write( pfam );
2979 all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
2980 final String domain_id = new String( pfam );
2981 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
2982 ++pfams_with_mappings_counter;
2983 all_pfams_encountered_with_go_annotation_writer.write( pfam );
2984 all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
2985 final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
2986 boolean maps_to_bp = false;
2987 boolean maps_to_cc = false;
2988 boolean maps_to_mf = false;
2989 for( final GoId go_id : go_ids ) {
2990 final GoTerm go_term = go_id_to_term_map.get( go_id );
2991 if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
2994 else if ( go_term.getGoNameSpace().isCellularComponent() ) {
2997 else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
3002 ++biological_process_counter;
3005 ++cellular_component_counter;
3008 ++molecular_function_counter;
3010 if ( maps_to_bp || maps_to_mf ) {
3011 ++pfams_with_mappings_to_bp_or_mf_counter;
3014 ++pfams_without_mappings_to_bp_or_mf_counter;
3018 ++pfams_without_mappings_to_bp_or_mf_counter;
3019 ++pfams_without_mappings_counter;
3020 summary_writer.write( pfam );
3021 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3024 all_pfams_encountered_writer.close();
3025 all_pfams_encountered_with_go_annotation_writer.close();
3026 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
3027 + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
3028 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
3029 + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
3031 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
3032 + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
3033 + encountered_pfams_summary_file + "\"" );
3034 ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered : "
3035 + all_pfams_encountered.size() );
3036 ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping : "
3037 + pfams_without_mappings_counter + " ["
3038 + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
3039 ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
3040 + pfams_without_mappings_to_bp_or_mf_counter + " ["
3041 + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
3042 ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping : "
3043 + pfams_with_mappings_counter + " ["
3044 + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
3045 ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func. : "
3046 + pfams_with_mappings_to_bp_or_mf_counter + " ["
3047 + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
3048 ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to biological process: "
3049 + biological_process_counter + " ["
3050 + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
3051 ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to molecular function: "
3052 + molecular_function_counter + " ["
3053 + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
3054 ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to cellular component: "
3055 + cellular_component_counter + " ["
3056 + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
3057 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3058 summary_writer.write( "# Sum of Pfams encountered : " + all_pfams_encountered.size() );
3059 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3060 summary_writer.write( "# Pfams without a mapping : " + pfams_without_mappings_counter
3061 + " [" + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
3062 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3063 summary_writer.write( "# Pfams without mapping to proc. or func. : "
3064 + pfams_without_mappings_to_bp_or_mf_counter + " ["
3065 + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
3066 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3067 summary_writer.write( "# Pfams with a mapping : " + pfams_with_mappings_counter + " ["
3068 + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
3069 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3070 summary_writer.write( "# Pfams with a mapping to proc. or func. : "
3071 + pfams_with_mappings_to_bp_or_mf_counter + " ["
3072 + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
3073 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3074 summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
3075 + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
3076 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3077 summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
3078 + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
3079 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3080 summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
3081 + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
3082 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3083 summary_writer.close();
3085 catch ( final IOException e ) {
3086 ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
3090 private final static void writeColorLabels( final String l, final Color c, final Writer w ) throws IOException {
3091 w.write( "<tr><td><b><span style=\"color:" );
3092 w.write( String.format( "#%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue() ) );
3095 w.write( "</span></b></td></tr>" );
3096 w.write( SurfacingConstants.NL );
3099 private static void writeDomainData( final Map<String, List<GoId>> domain_id_to_go_ids_map,
3100 final Map<GoId, GoTerm> go_id_to_term_map,
3101 final GoNameSpace go_namespace_limit,
3103 final String domain_0,
3104 final String domain_1,
3105 final String prefix_for_html,
3106 final String character_separator_for_non_html_output,
3107 final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
3108 final Set<GoId> all_go_ids ) throws IOException {
3109 boolean any_go_annotation_present = false;
3110 boolean first_has_no_go = false;
3111 int domain_count = 2; // To distinguish between domains and binary domain combinations.
3112 if ( ForesterUtil.isEmpty( domain_1 ) ) {
3115 // The following has a difficult to understand logic.
3116 for( int d = 0; d < domain_count; ++d ) {
3117 List<GoId> go_ids = null;
3118 boolean go_annotation_present = false;
3120 if ( domain_id_to_go_ids_map.containsKey( domain_0 ) ) {
3121 go_annotation_present = true;
3122 any_go_annotation_present = true;
3123 go_ids = domain_id_to_go_ids_map.get( domain_0 );
3126 first_has_no_go = true;
3130 if ( domain_id_to_go_ids_map.containsKey( domain_1 ) ) {
3131 go_annotation_present = true;
3132 any_go_annotation_present = true;
3133 go_ids = domain_id_to_go_ids_map.get( domain_1 );
3136 if ( go_annotation_present ) {
3137 boolean first = ( ( d == 0 ) || ( ( d == 1 ) && first_has_no_go ) );
3138 for( final GoId go_id : go_ids ) {
3139 out.write( "<tr>" );
3142 writeDomainIdsToHtml( out,
3146 domain_id_to_secondary_features_maps );
3149 out.write( "<td></td>" );
3151 if ( !go_id_to_term_map.containsKey( go_id ) ) {
3152 throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
3154 final GoTerm go_term = go_id_to_term_map.get( go_id );
3155 if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
3156 // final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
3157 final String go_id_str = go_id.getId();
3158 out.write( "<td>" );
3159 out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
3160 + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
3161 out.write( "</td><td>" );
3162 out.write( go_term.getName() );
3163 if ( domain_count == 2 ) {
3164 out.write( " (" + d + ")" );
3166 out.write( "</td><td>" );
3167 // out.write( top );
3168 // out.write( "</td><td>" );
3170 out.write( go_term.getGoNameSpace().toShortString() );
3172 out.write( "</td>" );
3173 if ( all_go_ids != null ) {
3174 all_go_ids.add( go_id );
3178 out.write( "<td>" );
3179 out.write( "</td><td>" );
3180 out.write( "</td><td>" );
3181 out.write( "</td><td>" );
3182 out.write( "</td>" );
3184 out.write( "</tr>" );
3185 out.write( SurfacingConstants.NL );
3188 } // for( int d = 0; d < domain_count; ++d )
3189 if ( !any_go_annotation_present ) {
3190 out.write( "<tr>" );
3191 writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
3192 out.write( "<td>" );
3193 out.write( "</td><td>" );
3194 out.write( "</td><td>" );
3195 out.write( "</td><td>" );
3196 out.write( "</td>" );
3197 out.write( "</tr>" );
3198 out.write( SurfacingConstants.NL );
3202 private static void writeDomainIdsToHtml( final Writer out,
3203 final String domain_0,
3204 final String domain_1,
3205 final String prefix_for_detailed_html,
3206 final Map<String, Set<String>>[] domain_id_to_secondary_features_maps )
3207 throws IOException {
3208 out.write( "<td>" );
3209 if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
3210 out.write( prefix_for_detailed_html );
3213 out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
3214 out.write( "</td>" );
3217 private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
3218 final String domain_0,
3219 final String domain_1 ) throws IOException {
3220 individual_files_writer.write( domain_0 );
3221 individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
3222 if ( !ForesterUtil.isEmpty( domain_1 ) ) {
3223 individual_files_writer.write( domain_1 );
3224 individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
3228 private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
3230 final Writer writer = new BufferedWriter( new FileWriter( new File( outfile_name ) ) );
3231 for( final String pfam : pfams ) {
3232 writer.write( pfam );
3233 writer.write( ForesterUtil.LINE_SEPARATOR );
3236 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
3239 catch ( final IOException e ) {
3240 ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
3244 private static void writeToNexus( final String outfile_name,
3245 final CharacterStateMatrix<BinaryStates> matrix,
3246 final Phylogeny phylogeny ) {
3247 if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
3248 throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
3251 final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
3252 final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>( 1 );
3253 phylogenies.add( phylogeny );
3255 final BufferedWriter w = new BufferedWriter( new FileWriter( outfile_name ) );
3256 w.write( NexusConstants.NEXUS );
3257 w.write( ForesterUtil.LINE_SEPARATOR );
3258 my_matrix.writeNexusTaxaBlock( w );
3259 my_matrix.writeNexusBinaryChractersBlock( w );
3260 PhylogenyWriter.writeNexusTreesBlock( w, phylogenies, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
3263 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
3265 catch ( final IOException e ) {
3266 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
3270 private static void writeToNexus( final String outfile_name,
3271 final DomainParsimonyCalculator domain_parsimony,
3272 final Phylogeny phylogeny ) {
3273 writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAINS,
3274 domain_parsimony.createMatrixOfDomainPresenceOrAbsence(),
3276 writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
3277 domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(),
3281 final static class DomainComparator implements Comparator<Domain> {
3283 final private boolean _ascending;
3285 public DomainComparator( final boolean ascending ) {
3286 _ascending = ascending;
3290 public final int compare( final Domain d0, final Domain d1 ) {
3291 if ( d0.getFrom() < d1.getFrom() ) {
3292 return _ascending ? -1 : 1;
3294 else if ( d0.getFrom() > d1.getFrom() ) {
3295 return _ascending ? 1 : -1;