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: www.phylosoft.org/forester
27 package org.forester.surfacing;
29 import java.io.BufferedWriter;
31 import java.io.FileWriter;
32 import java.io.IOException;
33 import java.io.Writer;
34 import java.text.DecimalFormat;
35 import java.text.NumberFormat;
36 import java.util.ArrayList;
37 import java.util.Arrays;
38 import java.util.Collections;
39 import java.util.Comparator;
40 import java.util.HashMap;
41 import java.util.HashSet;
42 import java.util.List;
44 import java.util.Map.Entry;
45 import java.util.PriorityQueue;
47 import java.util.SortedMap;
48 import java.util.SortedSet;
49 import java.util.TreeMap;
50 import java.util.TreeSet;
51 import java.util.regex.Matcher;
52 import java.util.regex.Pattern;
54 import org.forester.application.surfacing;
55 import org.forester.evoinference.distance.NeighborJoining;
56 import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
57 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
58 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
59 import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
60 import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
61 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
62 import org.forester.evoinference.matrix.distance.DistanceMatrix;
63 import org.forester.go.GoId;
64 import org.forester.go.GoNameSpace;
65 import org.forester.go.GoTerm;
66 import org.forester.go.PfamToGoMapping;
67 import org.forester.io.parsers.nexus.NexusConstants;
68 import org.forester.io.writers.PhylogenyWriter;
69 import org.forester.msa.MsaCompactor.SORT_BY;
70 import org.forester.phylogeny.Phylogeny;
71 import org.forester.phylogeny.PhylogenyMethods;
72 import org.forester.phylogeny.PhylogenyNode;
73 import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
74 import org.forester.phylogeny.data.BinaryCharacters;
75 import org.forester.phylogeny.data.Confidence;
76 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
77 import org.forester.protein.BasicDomain;
78 import org.forester.protein.BasicProtein;
79 import org.forester.protein.BinaryDomainCombination;
80 import org.forester.protein.Domain;
81 import org.forester.protein.DomainId;
82 import org.forester.protein.Protein;
83 import org.forester.species.Species;
84 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
85 import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
86 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
87 import org.forester.util.AsciiHistogram;
88 import org.forester.util.BasicDescriptiveStatistics;
89 import org.forester.util.BasicTable;
90 import org.forester.util.BasicTableParser;
91 import org.forester.util.DescriptiveStatistics;
92 import org.forester.util.ForesterUtil;
94 public final class SurfacingUtil {
96 private final static NumberFormat FORMATTER = new DecimalFormat( "0.0E0" );
97 private final static NumberFormat FORMATTER_3 = new DecimalFormat( "0.000" );
98 private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
101 public int compare( final Domain d1,
103 if ( d1.getPerSequenceEvalue() < d2
104 .getPerSequenceEvalue() ) {
108 .getPerSequenceEvalue() > d2
109 .getPerSequenceEvalue() ) {
113 return d1.compareTo( d2 );
117 public final static Pattern PATTERN_SP_STYLE_TAXONOMY = Pattern.compile( "^[A-Z0-9]{3,5}$" );
118 private static final boolean USE_LAST = true;
120 private SurfacingUtil() {
121 // Hidden constructor.
124 public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
125 final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
126 final SortedMap<DomainId, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
127 for( final DomainId domain_id : all_cd.keySet() ) {
128 binary_domain_combinations.addAll( all_cd.get( domain_id ).toBinaryDomainCombinations() );
132 public static void addAllDomainIdsToSet( final GenomeWideCombinableDomains genome,
133 final SortedSet<DomainId> domain_ids ) {
134 final SortedSet<DomainId> domains = genome.getAllDomainIds();
135 for( final DomainId domain : domains ) {
136 domain_ids.add( domain );
140 public static void addHtmlHead( final Writer w, final String title ) throws IOException {
141 w.write( SurfacingConstants.NL );
143 w.write( "<title>" );
145 w.write( "</title>" );
146 w.write( SurfacingConstants.NL );
147 w.write( "<style>" );
148 w.write( SurfacingConstants.NL );
149 w.write( "a:visited { color : #6633FF; text-decoration : none; }" );
150 w.write( SurfacingConstants.NL );
151 w.write( "a:link { color : #6633FF; text-decoration : none; }" );
152 w.write( SurfacingConstants.NL );
153 w.write( "a:active { color : #99FF00; text-decoration : none; }" );
154 w.write( SurfacingConstants.NL );
155 w.write( "a:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; }" );
156 w.write( SurfacingConstants.NL );
157 w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
158 w.write( SurfacingConstants.NL );
159 w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
160 w.write( SurfacingConstants.NL );
161 w.write( "h2 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" );
162 w.write( SurfacingConstants.NL );
163 w.write( "</style>" );
164 w.write( SurfacingConstants.NL );
165 w.write( "</head>" );
166 w.write( SurfacingConstants.NL );
169 public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
170 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
171 for( final DomainSimilarity similarity : similarities ) {
172 stats.addValue( similarity.getMeanSimilarityScore() );
177 private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
178 final String outfilename_for_counts,
179 final String outfilename_for_dc,
180 final String outfilename_for_dc_for_go_mapping,
181 final String outfilename_for_dc_for_go_mapping_unique,
182 final String outfilename_for_rank_counts,
183 final String outfilename_for_ancestor_species_counts,
184 final String outfilename_for_protein_stats,
185 final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
186 final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
187 final Map<String, DescriptiveStatistics> domain_length_stats_by_domain ) {
190 // if ( protein_length_stats_by_dc != null ) {
191 // for( final Entry<?, DescriptiveStatistics> entry : protein_length_stats_by_dc.entrySet() ) {
192 // System.out.print( entry.getKey().toString() );
193 // System.out.print( ": " );
194 // double[] a = entry.getValue().getDataAsDoubleArray();
195 // for( int i = 0; i < a.length; i++ ) {
196 // System.out.print( a[ i ] + " " );
198 // System.out.println();
201 // if ( domain_number_stats_by_dc != null ) {
202 // for( final Entry<?, DescriptiveStatistics> entry : domain_number_stats_by_dc.entrySet() ) {
203 // System.out.print( entry.getKey().toString() );
204 // System.out.print( ": " );
205 // double[] a = entry.getValue().getDataAsDoubleArray();
206 // for( int i = 0; i < a.length; i++ ) {
207 // System.out.print( a[ i ] + " " );
209 // System.out.println();
213 final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
214 final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
215 final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) );
216 final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) );
217 final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
218 for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
219 final PhylogenyNode n = it.next();
220 final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
221 for( final String dc : gained_dc ) {
222 if ( dc_gain_counts.containsKey( dc ) ) {
223 dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
226 dc_gain_counts.put( dc, 1 );
230 final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
231 final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
232 final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_protein_length_stats = new TreeMap<Integer, DescriptiveStatistics>();
233 final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_number_stats = new TreeMap<Integer, DescriptiveStatistics>();
234 final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_lengths_stats = new TreeMap<Integer, DescriptiveStatistics>();
235 final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
236 final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
237 final Set<String> dcs = dc_gain_counts.keySet();
238 final SortedSet<String> more_than_once = new TreeSet<String>();
239 final DescriptiveStatistics gained_once_lengths_stats = new BasicDescriptiveStatistics();
240 final DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics();
241 final DescriptiveStatistics gained_multiple_times_lengths_stats = new BasicDescriptiveStatistics();
242 final DescriptiveStatistics gained_multiple_times_domain_count_stats = new BasicDescriptiveStatistics();
243 long gained_multiple_times_domain_length_sum = 0;
244 long gained_once_domain_length_sum = 0;
245 long gained_multiple_times_domain_length_count = 0;
246 long gained_once_domain_length_count = 0;
247 for( final String dc : dcs ) {
248 final int count = dc_gain_counts.get( dc );
249 if ( histogram.containsKey( count ) ) {
250 histogram.put( count, histogram.get( count ) + 1 );
251 domain_lists.get( count ).append( ", " + dc );
252 domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) );
253 domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) );
256 histogram.put( count, 1 );
257 domain_lists.put( count, new StringBuilder( dc ) );
258 final PriorityQueue<String> q = new PriorityQueue<String>();
259 q.addAll( splitDomainCombination( dc ) );
260 domain_lists_go.put( count, q );
261 final SortedSet<String> set = new TreeSet<String>();
262 set.addAll( splitDomainCombination( dc ) );
263 domain_lists_go_unique.put( count, set );
265 if ( protein_length_stats_by_dc != null ) {
266 if ( !dc_reapp_counts_to_protein_length_stats.containsKey( count ) ) {
267 dc_reapp_counts_to_protein_length_stats.put( count, new BasicDescriptiveStatistics() );
269 dc_reapp_counts_to_protein_length_stats.get( count ).addValue( protein_length_stats_by_dc.get( dc )
272 if ( domain_number_stats_by_dc != null ) {
273 if ( !dc_reapp_counts_to_domain_number_stats.containsKey( count ) ) {
274 dc_reapp_counts_to_domain_number_stats.put( count, new BasicDescriptiveStatistics() );
276 dc_reapp_counts_to_domain_number_stats.get( count ).addValue( domain_number_stats_by_dc.get( dc )
279 if ( domain_length_stats_by_domain != null ) {
280 if ( !dc_reapp_counts_to_domain_lengths_stats.containsKey( count ) ) {
281 dc_reapp_counts_to_domain_lengths_stats.put( count, new BasicDescriptiveStatistics() );
283 final String[] ds = dc.split( "=" );
284 dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
285 .get( ds[ 0 ] ).arithmeticMean() );
286 dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
287 .get( ds[ 1 ] ).arithmeticMean() );
290 more_than_once.add( dc );
291 if ( protein_length_stats_by_dc != null ) {
292 final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
293 for( final double element : s.getData() ) {
294 gained_multiple_times_lengths_stats.addValue( element );
297 if ( domain_number_stats_by_dc != null ) {
298 final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
299 for( final double element : s.getData() ) {
300 gained_multiple_times_domain_count_stats.addValue( element );
303 if ( domain_length_stats_by_domain != null ) {
304 final String[] ds = dc.split( "=" );
305 final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
306 final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
307 for( final double element : s0.getData() ) {
308 gained_multiple_times_domain_length_sum += element;
309 ++gained_multiple_times_domain_length_count;
311 for( final double element : s1.getData() ) {
312 gained_multiple_times_domain_length_sum += element;
313 ++gained_multiple_times_domain_length_count;
318 if ( protein_length_stats_by_dc != null ) {
319 final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
320 for( final double element : s.getData() ) {
321 gained_once_lengths_stats.addValue( element );
324 if ( domain_number_stats_by_dc != null ) {
325 final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
326 for( final double element : s.getData() ) {
327 gained_once_domain_count_stats.addValue( element );
330 if ( domain_length_stats_by_domain != null ) {
331 final String[] ds = dc.split( "=" );
332 final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
333 final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
334 for( final double element : s0.getData() ) {
335 gained_once_domain_length_sum += element;
336 ++gained_once_domain_length_count;
338 for( final double element : s1.getData() ) {
339 gained_once_domain_length_sum += element;
340 ++gained_once_domain_length_count;
345 final Set<Integer> histogram_keys = histogram.keySet();
346 for( final Integer histogram_key : histogram_keys ) {
347 final int count = histogram.get( histogram_key );
348 final StringBuilder dc = domain_lists.get( histogram_key );
349 out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
350 out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
351 out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
352 final Object[] sorted = domain_lists_go.get( histogram_key ).toArray();
353 Arrays.sort( sorted );
354 for( final Object domain : sorted ) {
355 out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR );
357 out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
358 for( final String domain : domain_lists_go_unique.get( histogram_key ) ) {
359 out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR );
364 out_dc_for_go_mapping.close();
365 out_dc_for_go_mapping_unique.close();
366 final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
367 final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
368 for( final String dc : more_than_once ) {
369 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
370 for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
371 final PhylogenyNode n = it.next();
372 if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
376 for( int i = 0; i < nodes.size() - 1; ++i ) {
377 for( int j = i + 1; j < nodes.size(); ++j ) {
378 final PhylogenyNode lca = PhylogenyMethods.obtainLCA( nodes.get( i ),
380 String rank = "unknown";
381 if ( lca.getNodeData().isHasTaxonomy()
382 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
383 rank = lca.getNodeData().getTaxonomy().getRank();
385 addToCountMap( lca_rank_counts, rank );
387 if ( lca.getNodeData().isHasTaxonomy()
388 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
389 lca_species = lca.getNodeData().getTaxonomy().getScientificName();
391 else if ( lca.getNodeData().isHasTaxonomy()
392 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
393 lca_species = lca.getNodeData().getTaxonomy().getCommonName();
396 lca_species = lca.getName();
398 addToCountMap( lca_ancestor_species_counts, lca_species );
402 final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
403 final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
404 ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
405 ForesterUtil.map2writer( out_for_ancestor_species_counts,
406 lca_ancestor_species_counts,
408 ForesterUtil.LINE_SEPARATOR );
409 out_for_rank_counts.close();
410 out_for_ancestor_species_counts.close();
411 if ( !ForesterUtil.isEmpty( outfilename_for_protein_stats )
412 && ( ( domain_length_stats_by_domain != null ) || ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) {
413 final BufferedWriter w = new BufferedWriter( new FileWriter( outfilename_for_protein_stats ) );
414 w.write( "Domain Lengths: " );
416 if ( domain_length_stats_by_domain != null ) {
417 for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_lengths_stats
419 w.write( entry.getKey().toString() );
420 w.write( "\t" + entry.getValue().arithmeticMean() );
421 w.write( "\t" + entry.getValue().median() );
428 w.write( "Protein Lengths: " );
430 if ( protein_length_stats_by_dc != null ) {
431 for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_protein_length_stats
433 w.write( entry.getKey().toString() );
434 w.write( "\t" + entry.getValue().arithmeticMean() );
435 w.write( "\t" + entry.getValue().median() );
442 w.write( "Number of domains: " );
444 if ( domain_number_stats_by_dc != null ) {
445 for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_number_stats
447 w.write( entry.getKey().toString() );
448 w.write( "\t" + entry.getValue().arithmeticMean() );
449 w.write( "\t" + entry.getValue().median() );
456 w.write( "Gained once, domain lengths:" );
458 w.write( "N: " + gained_once_domain_length_count );
460 w.write( "Avg: " + ( ( double ) gained_once_domain_length_sum / gained_once_domain_length_count ) );
463 w.write( "Gained multiple times, domain lengths:" );
465 w.write( "N: " + gained_multiple_times_domain_length_count );
468 + ( ( double ) gained_multiple_times_domain_length_sum / gained_multiple_times_domain_length_count ) );
473 w.write( "Gained once, protein lengths:" );
475 w.write( gained_once_lengths_stats.toString() );
478 w.write( "Gained once, domain counts:" );
480 w.write( gained_once_domain_count_stats.toString() );
483 w.write( "Gained multiple times, protein lengths:" );
485 w.write( gained_multiple_times_lengths_stats.toString() );
488 w.write( "Gained multiple times, domain counts:" );
490 w.write( gained_multiple_times_domain_count_stats.toString() );
495 catch ( final IOException e ) {
496 ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
498 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
499 + outfilename_for_counts + "]" );
500 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
501 + outfilename_for_dc + "]" );
502 ForesterUtil.programMessage( surfacing.PRG_NAME,
503 "Wrote independent domain combination gains fitch lists to (for GO mapping) ["
504 + outfilename_for_dc_for_go_mapping + "]" );
505 ForesterUtil.programMessage( surfacing.PRG_NAME,
506 "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) ["
507 + outfilename_for_dc_for_go_mapping_unique + "]" );
510 private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
511 if ( map.containsKey( s ) ) {
512 map.put( s, map.get( s ) + 1 );
519 public static int calculateOverlap( final Domain domain, final List<Boolean> covered_positions ) {
520 int overlap_count = 0;
521 for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
522 if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) {
526 return overlap_count;
529 public static void checkForOutputFileWriteability( final File outfile ) {
530 final String error = ForesterUtil.isWritableFile( outfile );
531 if ( !ForesterUtil.isEmpty( error ) ) {
532 ForesterUtil.fatalError( surfacing.PRG_NAME, error );
536 private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
537 final boolean get_gains ) {
538 final SortedSet<String> domains = new TreeSet<String>();
539 for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
540 final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
542 domains.addAll( chars.getGainedCharacters() );
545 domains.addAll( chars.getLostCharacters() );
551 public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
552 final BinaryDomainCombination.DomainCombinationType dc_type,
553 final List<BinaryDomainCombination> all_binary_domains_combination_gained,
554 final boolean get_gains ) {
555 final SortedSet<String> sorted_ids = new TreeSet<String>();
556 for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
557 sorted_ids.add( matrix.getIdentifier( i ) );
559 for( final String id : sorted_ids ) {
560 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
561 if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
562 || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
563 if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
564 all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
565 .createInstance( matrix.getCharacter( c ) ) );
567 else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
568 all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
569 .createInstance( matrix.getCharacter( c ) ) );
572 all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
573 .getCharacter( c ) ) );
580 private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
581 final boolean domain_combinations,
582 final CharacterStateMatrix.GainLossStates state,
583 final String outfile ) {
584 File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
585 + ForesterUtil.FILE_SEPARATOR + base_dir );
586 if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
587 per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
589 if ( domain_combinations ) {
590 per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
591 + ForesterUtil.FILE_SEPARATOR + "DC" );
594 per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
595 + ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
597 if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
598 per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
600 if ( state == GainLossStates.GAIN ) {
601 per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
602 + ForesterUtil.FILE_SEPARATOR + "GAINS" );
604 else if ( state == GainLossStates.LOSS ) {
605 per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
606 + ForesterUtil.FILE_SEPARATOR + "LOSSES" );
609 per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
610 + ForesterUtil.FILE_SEPARATOR + "PRESENT" );
612 if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
613 per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
615 return per_node_go_mapped_domain_gain_loss_files_base_dir;
618 public static Map<DomainId, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
619 final Map<DomainId, List<GoId>> domain_id_to_go_ids_map = new HashMap<DomainId, List<GoId>>( pfam_to_go_mappings
621 for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
622 if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
623 domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
625 domain_id_to_go_ids_map.get( pfam_to_go.getKey() ).add( pfam_to_go.getValue() );
627 return domain_id_to_go_ids_map;
630 public static Map<DomainId, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
632 final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, "\t" );
633 final Map<DomainId, Set<String>> map = new TreeMap<DomainId, Set<String>>();
634 for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
635 final DomainId domain_id = new DomainId( primary_table.getValue( 0, r ) );
636 if ( !map.containsKey( domain_id ) ) {
637 map.put( domain_id, new HashSet<String>() );
639 map.get( domain_id ).add( primary_table.getValue( 1, r ) );
644 public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
645 checkForOutputFileWriteability( nj_tree_outfile );
646 final NeighborJoining nj = NeighborJoining.createInstance();
647 final Phylogeny phylogeny = nj.execute( ( BasicSymmetricalDistanceMatrix ) distance );
648 phylogeny.setName( nj_tree_outfile.getName() );
649 writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
653 private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
654 final SortedMap<DomainId, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
655 final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
656 for( final DomainId domain_id : cds.keySet() ) {
657 final CombinableDomains cd = cds.get( domain_id );
658 binary_combinations.addAll( cd.toBinaryDomainCombinations() );
660 return binary_combinations;
663 public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
664 final Detailedness detailedness,
665 final GoAnnotationOutput go_annotation_output,
666 final Map<GoId, GoTerm> go_id_to_term_map,
667 final GoNameSpace go_namespace_limit ) {
668 if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) ) {
669 throw new IllegalArgumentException( "attempt to use a GO namespace limit without a GO id to term map" );
671 for( final DomainSimilarity domain_similarity : domain_similarities ) {
672 if ( domain_similarity instanceof PrintableDomainSimilarity ) {
673 final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
674 printable_domain_similarity.setDetailedness( detailedness );
675 printable_domain_similarity.setGoAnnotationOutput( go_annotation_output );
676 printable_domain_similarity.setGoIdToTermMap( go_id_to_term_map );
677 printable_domain_similarity.setGoNamespaceLimit( go_namespace_limit );
682 public static void executeDomainLengthAnalysis( final String[][] input_file_properties,
683 final int number_of_genomes,
684 final DomainLengthsTable domain_lengths_table,
685 final File outfile ) throws IOException {
686 final DecimalFormat df = new DecimalFormat( "#.00" );
687 checkForOutputFileWriteability( outfile );
688 final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
689 out.write( "MEAN BASED STATISTICS PER SPECIES" );
690 out.write( ForesterUtil.LINE_SEPARATOR );
691 out.write( domain_lengths_table.createMeanBasedStatisticsPerSpeciesTable().toString() );
692 out.write( ForesterUtil.LINE_SEPARATOR );
693 out.write( ForesterUtil.LINE_SEPARATOR );
694 final List<DomainLengths> domain_lengths_list = domain_lengths_table.getDomainLengthsList();
695 out.write( "OUTLIER SPECIES PER DOMAIN (Z>=1.5)" );
696 out.write( ForesterUtil.LINE_SEPARATOR );
697 for( final DomainLengths domain_lengths : domain_lengths_list ) {
698 final List<Species> species_list = domain_lengths.getMeanBasedOutlierSpecies( 1.5 );
699 if ( species_list.size() > 0 ) {
700 out.write( domain_lengths.getDomainId() + "\t" );
701 for( final Species species : species_list ) {
702 out.write( species + "\t" );
704 out.write( ForesterUtil.LINE_SEPARATOR );
705 // DescriptiveStatistics stats_for_domain = domain_lengths
706 // .calculateMeanBasedStatistics();
707 //AsciiHistogram histo = new AsciiHistogram( stats_for_domain );
708 //System.out.println( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
711 out.write( ForesterUtil.LINE_SEPARATOR );
712 out.write( ForesterUtil.LINE_SEPARATOR );
713 out.write( "OUTLIER SPECIES (Z 1.0)" );
714 out.write( ForesterUtil.LINE_SEPARATOR );
715 final DescriptiveStatistics stats_for_all_species = domain_lengths_table
716 .calculateMeanBasedStatisticsForAllSpecies();
717 out.write( stats_for_all_species.asSummary() );
718 out.write( ForesterUtil.LINE_SEPARATOR );
719 final AsciiHistogram histo = new AsciiHistogram( stats_for_all_species );
720 out.write( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
721 out.write( ForesterUtil.LINE_SEPARATOR );
722 final double population_sd = stats_for_all_species.sampleStandardDeviation();
723 final double population_mean = stats_for_all_species.arithmeticMean();
724 for( final Species species : domain_lengths_table.getSpecies() ) {
725 final double x = domain_lengths_table.calculateMeanBasedStatisticsForSpecies( species ).arithmeticMean();
726 final double z = ( x - population_mean ) / population_sd;
727 out.write( species + "\t" + z );
728 out.write( ForesterUtil.LINE_SEPARATOR );
730 out.write( ForesterUtil.LINE_SEPARATOR );
731 for( final Species species : domain_lengths_table.getSpecies() ) {
732 final DescriptiveStatistics stats_for_species = domain_lengths_table
733 .calculateMeanBasedStatisticsForSpecies( species );
734 final double x = stats_for_species.arithmeticMean();
735 final double z = ( x - population_mean ) / population_sd;
736 if ( ( z <= -1.0 ) || ( z >= 1.0 ) ) {
737 out.write( species + "\t" + df.format( z ) + "\t" + stats_for_species.asSummary() );
738 out.write( ForesterUtil.LINE_SEPARATOR );
742 // final List<HistogramData> histogram_datas = new ArrayList<HistogramData>();
743 // for( int i = 0; i < number_of_genomes; ++i ) {
744 // final Species species = new BasicSpecies( input_file_properties[ i ][ 0 ] );
746 // .add( new HistogramData( species.toString(), domain_lengths_table
747 // .calculateMeanBasedStatisticsForSpecies( species )
748 // .getDataAsDoubleArray(), 5, 600, null, 60 ) );
750 // final HistogramsFrame hf = new HistogramsFrame( histogram_datas );
751 // hf.setVisible( true );
757 * @param all_binary_domains_combination_lost_fitch
758 * @param consider_directedness_and_adjacency_for_bin_combinations
759 * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
760 * which were gained under unweighted (Fitch) parsimony.
762 public static void executeParsimonyAnalysis( final long random_number_seed_for_fitch_parsimony,
763 final boolean radomize_fitch_parsimony,
764 final String outfile_name,
765 final DomainParsimonyCalculator domain_parsimony,
766 final Phylogeny phylogeny,
767 final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
768 final Map<GoId, GoTerm> go_id_to_term_map,
769 final GoNameSpace go_namespace_limit,
770 final String parameters_str,
771 final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
772 final SortedSet<DomainId> positive_filter,
773 final boolean output_binary_domain_combinations_for_graphs,
774 final List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch,
775 final List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch,
776 final BinaryDomainCombination.DomainCombinationType dc_type,
777 final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
778 final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
779 final Map<String, DescriptiveStatistics> domain_length_stats_by_domain ) {
780 final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
781 final String date_time = ForesterUtil.getCurrentDateTime();
782 final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
783 final SortedSet<String> all_pfams_gained_as_domains = new TreeSet<String>();
784 final SortedSet<String> all_pfams_lost_as_domains = new TreeSet<String>();
785 final SortedSet<String> all_pfams_gained_as_dom_combinations = new TreeSet<String>();
786 final SortedSet<String> all_pfams_lost_as_dom_combinations = new TreeSet<String>();
787 writeToNexus( outfile_name, domain_parsimony, phylogeny );
790 Phylogeny local_phylogeny_l = phylogeny.copy();
791 if ( ( positive_filter != null ) && ( positive_filter.size() > 0 ) ) {
792 domain_parsimony.executeDolloParsimonyOnDomainPresence( positive_filter );
795 domain_parsimony.executeDolloParsimonyOnDomainPresence();
797 SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
798 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
799 SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
800 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
801 SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
802 CharacterStateMatrix.GainLossStates.GAIN,
803 outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
805 ForesterUtil.LINE_SEPARATOR,
807 SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
808 CharacterStateMatrix.GainLossStates.LOSS,
809 outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
811 ForesterUtil.LINE_SEPARATOR,
813 SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
814 + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
816 writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
820 domain_parsimony.getGainLossMatrix(),
821 CharacterStateMatrix.GainLossStates.GAIN,
822 outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
824 ForesterUtil.LINE_SEPARATOR,
825 "Dollo Parsimony | Gains | Domains",
827 domain_id_to_secondary_features_maps,
828 all_pfams_encountered,
829 all_pfams_gained_as_domains,
831 writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
835 domain_parsimony.getGainLossMatrix(),
836 CharacterStateMatrix.GainLossStates.LOSS,
837 outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
839 ForesterUtil.LINE_SEPARATOR,
840 "Dollo Parsimony | Losses | Domains",
842 domain_id_to_secondary_features_maps,
843 all_pfams_encountered,
844 all_pfams_lost_as_domains,
846 writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
850 domain_parsimony.getGainLossMatrix(),
852 outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
854 ForesterUtil.LINE_SEPARATOR,
855 "Dollo Parsimony | Present | Domains",
857 domain_id_to_secondary_features_maps,
858 all_pfams_encountered,
860 "_dollo_present_d" );
861 preparePhylogeny( local_phylogeny_l,
864 "Dollo parsimony on domain presence/absence",
865 "dollo_on_domains_" + outfile_name,
867 SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
868 + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
870 writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
871 writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
873 catch ( final IOException e ) {
875 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
877 if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
878 // FITCH DOMAIN COMBINATIONS
879 // -------------------------
880 local_phylogeny_l = phylogeny.copy();
881 String randomization = "no";
882 if ( radomize_fitch_parsimony ) {
883 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( random_number_seed_for_fitch_parsimony );
884 randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
887 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( USE_LAST );
889 SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
890 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
891 SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
892 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
894 .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
895 CharacterStateMatrix.GainLossStates.GAIN,
896 outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
898 ForesterUtil.LINE_SEPARATOR,
900 SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
901 CharacterStateMatrix.GainLossStates.LOSS,
903 + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
905 ForesterUtil.LINE_SEPARATOR,
907 SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
908 + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
909 if ( all_binary_domains_combination_gained_fitch != null ) {
910 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
912 all_binary_domains_combination_gained_fitch,
915 if ( all_binary_domains_combination_lost_fitch != null ) {
916 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
918 all_binary_domains_combination_lost_fitch,
921 if ( output_binary_domain_combinations_for_graphs ) {
923 .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
924 .getGainLossMatrix(),
927 + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
929 ForesterUtil.LINE_SEPARATOR,
930 BinaryDomainCombination.OutputFormat.DOT );
933 writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
937 domain_parsimony.getGainLossMatrix(),
938 CharacterStateMatrix.GainLossStates.GAIN,
939 outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
941 ForesterUtil.LINE_SEPARATOR,
942 "Fitch Parsimony | Gains | Domain Combinations",
945 all_pfams_encountered,
946 all_pfams_gained_as_dom_combinations,
948 writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
952 domain_parsimony.getGainLossMatrix(),
953 CharacterStateMatrix.GainLossStates.LOSS,
954 outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
956 ForesterUtil.LINE_SEPARATOR,
957 "Fitch Parsimony | Losses | Domain Combinations",
960 all_pfams_encountered,
961 all_pfams_lost_as_dom_combinations,
962 "_fitch_losses_dc" );
963 writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
967 domain_parsimony.getGainLossMatrix(),
969 outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
971 ForesterUtil.LINE_SEPARATOR,
972 "Fitch Parsimony | Present | Domain Combinations",
975 all_pfams_encountered,
977 "_fitch_present_dc" );
978 writeAllEncounteredPfamsToFile( domain_id_to_go_ids_map,
981 all_pfams_encountered );
982 writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX, all_pfams_gained_as_domains );
983 writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
984 writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
985 all_pfams_gained_as_dom_combinations );
986 writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DC_SUFFIX, all_pfams_lost_as_dom_combinations );
987 preparePhylogeny( local_phylogeny_l,
990 "Fitch parsimony on binary domain combination presence/absence randomization: "
992 "fitch_on_binary_domain_combinations_" + outfile_name,
994 SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
995 + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
996 calculateIndependentDomainCombinationGains( local_phylogeny_l,
998 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX,
1000 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX,
1002 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX,
1004 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX,
1005 outfile_name + "_indep_dc_gains_fitch_lca_ranks.txt",
1006 outfile_name + "_indep_dc_gains_fitch_lca_taxonomies.txt",
1007 outfile_name + "_indep_dc_gains_fitch_protein_statistics.txt",
1008 protein_length_stats_by_dc,
1009 domain_number_stats_by_dc,
1010 domain_length_stats_by_domain );
1014 public static void executeParsimonyAnalysisForSecondaryFeatures( final String outfile_name,
1015 final DomainParsimonyCalculator secondary_features_parsimony,
1016 final Phylogeny phylogeny,
1017 final String parameters_str,
1018 final Map<Species, MappingResults> mapping_results_map ) {
1019 final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
1020 final String date_time = ForesterUtil.getCurrentDateTime();
1021 System.out.println();
1022 writeToNexus( outfile_name + surfacing.NEXUS_SECONDARY_FEATURES,
1023 secondary_features_parsimony.createMatrixOfSecondaryFeaturePresenceOrAbsence( null ),
1025 Phylogeny local_phylogeny_copy = phylogeny.copy();
1026 secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
1027 SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
1028 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
1029 SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
1030 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
1032 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
1033 CharacterStateMatrix.GainLossStates.GAIN,
1035 + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
1037 ForesterUtil.LINE_SEPARATOR,
1040 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
1041 CharacterStateMatrix.GainLossStates.LOSS,
1043 + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
1045 ForesterUtil.LINE_SEPARATOR,
1048 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
1051 + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
1053 ForesterUtil.LINE_SEPARATOR,
1055 preparePhylogeny( local_phylogeny_copy,
1056 secondary_features_parsimony,
1058 "Dollo parsimony on secondary feature presence/absence",
1059 "dollo_on_secondary_features_" + outfile_name,
1061 SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
1062 + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
1063 // FITCH DOMAIN COMBINATIONS
1064 // -------------------------
1065 local_phylogeny_copy = phylogeny.copy();
1066 final String randomization = "no";
1067 secondary_features_parsimony.executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( USE_LAST );
1068 preparePhylogeny( local_phylogeny_copy,
1069 secondary_features_parsimony,
1071 "Fitch parsimony on secondary binary domain combination presence/absence randomization: "
1073 "fitch_on_binary_domain_combinations_" + outfile_name,
1075 SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
1076 + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED );
1077 calculateIndependentDomainCombinationGains( local_phylogeny_copy, outfile_name
1078 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name
1079 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
1080 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
1081 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
1082 + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name
1083 + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null );
1086 public static void doit( final List<Protein> proteins,
1087 final List<DomainId> query_domain_ids_nc_order,
1089 final String separator,
1090 final String limit_to_species,
1091 final Map<String, List<Integer>> average_protein_lengths_by_dc ) throws IOException {
1092 for( final Protein protein : proteins ) {
1093 if ( ForesterUtil.isEmpty( limit_to_species )
1094 || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
1095 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
1096 out.write( protein.getSpecies().getSpeciesId() );
1097 out.write( separator );
1098 out.write( protein.getProteinId().getId() );
1099 out.write( separator );
1101 final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
1102 boolean first = true;
1103 for( final Domain domain : protein.getProteinDomains() ) {
1104 if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
1105 visited_domain_ids.add( domain.getDomainId() );
1112 out.write( domain.getDomainId().getId() );
1114 out.write( "" + domain.getTotalCount() );
1119 out.write( separator );
1120 if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
1121 .equals( SurfacingConstants.NONE ) ) ) {
1122 out.write( protein.getDescription() );
1124 out.write( separator );
1125 if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
1126 .equals( SurfacingConstants.NONE ) ) ) {
1127 out.write( protein.getAccession() );
1129 out.write( SurfacingConstants.NL );
1136 public static void extractProteinNames( final List<Protein> proteins,
1137 final List<DomainId> query_domain_ids_nc_order,
1139 final String separator,
1140 final String limit_to_species ) throws IOException {
1141 for( final Protein protein : proteins ) {
1142 if ( ForesterUtil.isEmpty( limit_to_species )
1143 || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
1144 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
1145 out.write( protein.getSpecies().getSpeciesId() );
1146 out.write( separator );
1147 out.write( protein.getProteinId().getId() );
1148 out.write( separator );
1150 final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
1151 boolean first = true;
1152 for( final Domain domain : protein.getProteinDomains() ) {
1153 if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
1154 visited_domain_ids.add( domain.getDomainId() );
1161 out.write( domain.getDomainId().getId() );
1163 out.write( "" + domain.getTotalCount() );
1168 out.write( separator );
1169 if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
1170 .equals( SurfacingConstants.NONE ) ) ) {
1171 out.write( protein.getDescription() );
1173 out.write( separator );
1174 if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
1175 .equals( SurfacingConstants.NONE ) ) ) {
1176 out.write( protein.getAccession() );
1178 out.write( SurfacingConstants.NL );
1185 public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
1186 final DomainId domain_id,
1188 final String separator,
1189 final String limit_to_species,
1190 final double domain_e_cutoff ) throws IOException {
1191 for( final Species species : protein_lists_per_species.keySet() ) {
1192 for( final Protein protein : protein_lists_per_species.get( species ) ) {
1193 if ( ForesterUtil.isEmpty( limit_to_species )
1194 || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
1195 final List<Domain> domains = protein.getProteinDomains( domain_id );
1196 if ( domains.size() > 0 ) {
1197 out.write( protein.getSpecies().getSpeciesId() );
1198 out.write( separator );
1199 out.write( protein.getProteinId().getId() );
1200 out.write( separator );
1201 out.write( domain_id.toString() );
1202 out.write( separator );
1203 for( final Domain domain : domains ) {
1204 if ( domain_e_cutoff < 0 || domain.getPerDomainEvalue() <= domain_e_cutoff ) {
1206 out.write( domain.getFrom() + "-" + domain.getTo() );
1210 out.write( separator );
1212 final List<Domain> domain_list = new ArrayList<Domain>();
1214 for( final Domain domain : protein.getProteinDomains() ) {
1215 if ( domain_e_cutoff < 0 || domain.getPerDomainEvalue() <= domain_e_cutoff ) {
1216 domain_list.add( domain );
1220 Domain domain_ary[] = new Domain[ domain_list.size() ];
1222 for( int i = 0; i < domain_list.size(); ++i ) {
1223 domain_ary[ i ] = domain_list.get( i );
1226 Arrays.sort( domain_ary, new DomainComparator( true ) );
1229 boolean first = true;
1231 for( final Domain domain : domain_ary ) {
1238 out.write( domain.getDomainId().toString() );
1239 out.write( ":" + domain.getFrom() + "-" + domain.getTo() );
1240 out.write( ":" + domain.getPerDomainEvalue() );
1243 if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
1244 .equals( SurfacingConstants.NONE ) ) ) {
1245 out.write( protein.getDescription() );
1247 out.write( separator );
1248 if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
1249 .equals( SurfacingConstants.NONE ) ) ) {
1250 out.write( protein.getAccession() );
1252 out.write( SurfacingConstants.NL );
1260 public static SortedSet<DomainId> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
1261 final SortedSet<DomainId> all_domains_ids = new TreeSet<DomainId>();
1262 for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
1263 final Set<DomainId> all_domains = gwcd.getAllDomainIds();
1264 // for( final Domain domain : all_domains ) {
1265 all_domains_ids.addAll( all_domains );
1268 return all_domains_ids;
1271 public static SortedMap<String, Integer> getDomainCounts( final List<Protein> protein_domain_collections ) {
1272 final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
1273 for( final Protein protein_domain_collection : protein_domain_collections ) {
1274 for( final Object name : protein_domain_collection.getProteinDomains() ) {
1275 final BasicDomain protein_domain = ( BasicDomain ) name;
1276 final String id = protein_domain.getDomainId().getId();
1277 if ( map.containsKey( id ) ) {
1278 map.put( id, map.get( id ) + 1 );
1288 public static int getNumberOfNodesLackingName( final Phylogeny p, final StringBuilder names ) {
1289 final PhylogenyNodeIterator it = p.iteratorPostorder();
1291 while ( it.hasNext() ) {
1292 final PhylogenyNode n = it.next();
1293 if ( ForesterUtil.isEmpty( n.getName() )
1294 && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1295 .getScientificName() ) )
1296 && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1297 .getCommonName() ) ) ) {
1298 if ( n.getParent() != null ) {
1299 names.append( " " );
1300 names.append( n.getParent().getName() );
1302 final List l = n.getAllExternalDescendants();
1303 for( final Object object : l ) {
1304 System.out.println( l.toString() );
1313 * Returns true is Domain domain falls in an uninterrupted stretch of
1314 * covered positions.
1317 * @param covered_positions
1320 public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
1321 for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1322 if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
1329 public static void preparePhylogeny( final Phylogeny p,
1330 final DomainParsimonyCalculator domain_parsimony,
1331 final String date_time,
1332 final String method,
1334 final String parameters_str ) {
1335 domain_parsimony.decoratePhylogenyWithDomains( p );
1336 final StringBuilder desc = new StringBuilder();
1337 desc.append( "[Method: " + method + "] [Date: " + date_time + "] " );
1338 desc.append( "[Cost: " + domain_parsimony.getCost() + "] " );
1339 desc.append( "[Gains: " + domain_parsimony.getTotalGains() + "] " );
1340 desc.append( "[Losses: " + domain_parsimony.getTotalLosses() + "] " );
1341 desc.append( "[Unchanged: " + domain_parsimony.getTotalUnchanged() + "] " );
1342 desc.append( "[Parameters: " + parameters_str + "]" );
1344 p.setDescription( desc.toString() );
1345 p.setConfidence( new Confidence( domain_parsimony.getCost(), "parsimony" ) );
1346 p.setRerootable( false );
1347 p.setRooted( true );
1351 * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
1355 static public StringBuffer proteinToDomainCombinations( final Protein protein,
1356 final String protein_id,
1357 final String separator ) {
1358 final StringBuffer sb = new StringBuffer();
1359 if ( protein.getSpecies() == null ) {
1360 throw new IllegalArgumentException( "species must not be null" );
1362 if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
1363 throw new IllegalArgumentException( "species id must not be empty" );
1365 final List<Domain> domains = protein.getProteinDomains();
1366 if ( domains.size() > 1 ) {
1367 final Map<String, Integer> counts = new HashMap<String, Integer>();
1368 for( final Domain domain : domains ) {
1369 final String id = domain.getDomainId().getId();
1370 if ( counts.containsKey( id ) ) {
1371 counts.put( id, counts.get( id ) + 1 );
1374 counts.put( id, 1 );
1377 final Set<String> dcs = new HashSet<String>();
1378 for( int i = 1; i < domains.size(); ++i ) {
1379 for( int j = 0; j < i; ++j ) {
1380 Domain domain_n = domains.get( i );
1381 Domain domain_c = domains.get( j );
1382 if ( domain_n.getFrom() > domain_c.getFrom() ) {
1383 domain_n = domains.get( j );
1384 domain_c = domains.get( i );
1386 final String dc = domain_n.getDomainId().getId() + domain_c.getDomainId().getId();
1387 if ( !dcs.contains( dc ) ) {
1389 sb.append( protein.getSpecies() );
1390 sb.append( separator );
1391 sb.append( protein_id );
1392 sb.append( separator );
1393 sb.append( domain_n.getDomainId().getId() );
1394 sb.append( separator );
1395 sb.append( domain_c.getDomainId().getId() );
1396 sb.append( separator );
1397 sb.append( domain_n.getPerDomainEvalue() );
1398 sb.append( separator );
1399 sb.append( domain_c.getPerDomainEvalue() );
1400 sb.append( separator );
1401 sb.append( counts.get( domain_n.getDomainId().getId() ) );
1402 sb.append( separator );
1403 sb.append( counts.get( domain_c.getDomainId().getId() ) );
1404 sb.append( ForesterUtil.LINE_SEPARATOR );
1409 else if ( domains.size() == 1 ) {
1410 sb.append( protein.getSpecies() );
1411 sb.append( separator );
1412 sb.append( protein_id );
1413 sb.append( separator );
1414 sb.append( domains.get( 0 ).getDomainId().getId() );
1415 sb.append( separator );
1416 sb.append( separator );
1417 sb.append( domains.get( 0 ).getPerDomainEvalue() );
1418 sb.append( separator );
1419 sb.append( separator );
1421 sb.append( separator );
1422 sb.append( ForesterUtil.LINE_SEPARATOR );
1425 sb.append( protein.getSpecies() );
1426 sb.append( separator );
1427 sb.append( protein_id );
1428 sb.append( separator );
1429 sb.append( separator );
1430 sb.append( separator );
1431 sb.append( separator );
1432 sb.append( separator );
1433 sb.append( separator );
1434 sb.append( ForesterUtil.LINE_SEPARATOR );
1441 * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
1442 * domain with 0.3 is ignored
1444 * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
1447 * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
1450 * @param max_allowed_overlap
1451 * maximal allowed overlap (inclusive) to be still considered not
1452 * overlapping (zero or negative value to allow any overlap)
1453 * @param remove_engulfed_domains
1454 * to remove domains which are completely engulfed by coverage of
1455 * domains with better support
1459 public static Protein removeOverlappingDomains( final int max_allowed_overlap,
1460 final boolean remove_engulfed_domains,
1461 final Protein protein ) {
1462 final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
1463 .getSpeciesId(), protein.getLength() );
1464 final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
1465 final List<Boolean> covered_positions = new ArrayList<Boolean>();
1466 for( final Domain domain : sorted ) {
1467 if ( ( ( max_allowed_overlap < 0 ) || ( SurfacingUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
1468 && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
1469 final int covered_positions_size = covered_positions.size();
1470 for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
1471 covered_positions.add( false );
1473 final int new_covered_positions_size = covered_positions.size();
1474 for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1475 if ( i < new_covered_positions_size ) {
1476 covered_positions.set( i, true );
1479 covered_positions.add( true );
1482 pruned_protein.addProteinDomain( domain );
1485 return pruned_protein;
1488 public static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
1489 final List<Domain> domains = new ArrayList<Domain>();
1490 for( final Domain d : protein.getProteinDomains() ) {
1493 Collections.sort( domains, SurfacingUtil.ASCENDING_CONFIDENCE_VALUE_ORDER );
1497 private static List<String> splitDomainCombination( final String dc ) {
1498 final String[] s = dc.split( "=" );
1499 if ( s.length != 2 ) {
1500 ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: "
1504 final List<String> l = new ArrayList<String>( 2 );
1510 public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
1511 final boolean get_gains,
1512 final String outdir,
1513 final String suffix_for_filename ) throws IOException {
1514 CharacterStateMatrix.GainLossStates state = CharacterStateMatrix.GainLossStates.GAIN;
1516 state = CharacterStateMatrix.GainLossStates.LOSS;
1518 final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
1522 for( final PhylogenyNodeIterator it = p.iteratorPostorder(); it.hasNext(); ) {
1523 final PhylogenyNode node = it.next();
1524 if ( !node.isExternal() ) {
1525 final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
1526 if ( domains.size() > 0 ) {
1527 final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
1528 + node.getName() + suffix_for_filename );
1529 for( final String domain : domains ) {
1530 writer.write( domain );
1531 writer.write( ForesterUtil.LINE_SEPARATOR );
1539 private static void writeAllEncounteredPfamsToFile( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1540 final Map<GoId, GoTerm> go_id_to_term_map,
1541 final String outfile_name,
1542 final SortedSet<String> all_pfams_encountered ) {
1543 final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
1544 final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
1545 + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
1546 final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
1547 int biological_process_counter = 0;
1548 int cellular_component_counter = 0;
1549 int molecular_function_counter = 0;
1550 int pfams_with_mappings_counter = 0;
1551 int pfams_without_mappings_counter = 0;
1552 int pfams_without_mappings_to_bp_or_mf_counter = 0;
1553 int pfams_with_mappings_to_bp_or_mf_counter = 0;
1555 final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
1556 final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
1557 final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
1558 summary_writer.write( "# Pfam to GO mapping summary" );
1559 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1560 summary_writer.write( "# Actual summary is at the end of this file." );
1561 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1562 summary_writer.write( "# Encountered Pfams without a GO mapping:" );
1563 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1564 for( final String pfam : all_pfams_encountered ) {
1565 all_pfams_encountered_writer.write( pfam );
1566 all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
1567 final DomainId domain_id = new DomainId( pfam );
1568 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
1569 ++pfams_with_mappings_counter;
1570 all_pfams_encountered_with_go_annotation_writer.write( pfam );
1571 all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
1572 final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
1573 boolean maps_to_bp = false;
1574 boolean maps_to_cc = false;
1575 boolean maps_to_mf = false;
1576 for( final GoId go_id : go_ids ) {
1577 final GoTerm go_term = go_id_to_term_map.get( go_id );
1578 if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
1581 else if ( go_term.getGoNameSpace().isCellularComponent() ) {
1584 else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
1589 ++biological_process_counter;
1592 ++cellular_component_counter;
1595 ++molecular_function_counter;
1597 if ( maps_to_bp || maps_to_mf ) {
1598 ++pfams_with_mappings_to_bp_or_mf_counter;
1601 ++pfams_without_mappings_to_bp_or_mf_counter;
1605 ++pfams_without_mappings_to_bp_or_mf_counter;
1606 ++pfams_without_mappings_counter;
1607 summary_writer.write( pfam );
1608 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1611 all_pfams_encountered_writer.close();
1612 all_pfams_encountered_with_go_annotation_writer.close();
1613 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
1614 + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
1615 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
1616 + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
1618 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
1619 + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
1620 + encountered_pfams_summary_file + "\"" );
1621 ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered : "
1622 + all_pfams_encountered.size() );
1623 ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping : "
1624 + pfams_without_mappings_counter + " ["
1625 + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
1626 ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
1627 + pfams_without_mappings_to_bp_or_mf_counter + " ["
1628 + ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1629 ForesterUtil.programMessage( surfacing.PRG_NAME,
1630 "Pfams with a mapping : " + pfams_with_mappings_counter
1632 + ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() )
1634 ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func. : "
1635 + pfams_with_mappings_to_bp_or_mf_counter + " ["
1636 + ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1637 ForesterUtil.programMessage( surfacing.PRG_NAME,
1638 "Pfams with mapping to biological process: " + biological_process_counter
1640 + ( 100 * biological_process_counter / all_pfams_encountered.size() )
1642 ForesterUtil.programMessage( surfacing.PRG_NAME,
1643 "Pfams with mapping to molecular function: " + molecular_function_counter
1645 + ( 100 * molecular_function_counter / all_pfams_encountered.size() )
1647 ForesterUtil.programMessage( surfacing.PRG_NAME,
1648 "Pfams with mapping to cellular component: " + cellular_component_counter
1650 + ( 100 * cellular_component_counter / all_pfams_encountered.size() )
1652 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1653 summary_writer.write( "# Sum of Pfams encountered : " + all_pfams_encountered.size() );
1654 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1655 summary_writer.write( "# Pfams without a mapping : " + pfams_without_mappings_counter
1656 + " [" + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
1657 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1658 summary_writer.write( "# Pfams without mapping to proc. or func. : "
1659 + pfams_without_mappings_to_bp_or_mf_counter + " ["
1660 + ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1661 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1662 summary_writer.write( "# Pfams with a mapping : " + pfams_with_mappings_counter + " ["
1663 + ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() ) + "%]" );
1664 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1665 summary_writer.write( "# Pfams with a mapping to proc. or func. : "
1666 + pfams_with_mappings_to_bp_or_mf_counter + " ["
1667 + ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1668 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1669 summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
1670 + ( 100 * biological_process_counter / all_pfams_encountered.size() ) + "%]" );
1671 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1672 summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
1673 + ( 100 * molecular_function_counter / all_pfams_encountered.size() ) + "%]" );
1674 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1675 summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
1676 + ( 100 * cellular_component_counter / all_pfams_encountered.size() ) + "%]" );
1677 summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1678 summary_writer.close();
1680 catch ( final IOException e ) {
1681 ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
1685 public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
1686 final File output_dir,
1687 final GenomeWideCombinableDomains gwcd,
1689 final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1690 File dc_outfile_dot = new File( input_file_properties[ i ][ 0 ]
1691 + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
1692 if ( output_dir != null ) {
1693 dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
1695 checkForOutputFileWriteability( dc_outfile_dot );
1696 final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
1698 final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
1699 for( final BinaryDomainCombination bdc : binary_combinations ) {
1700 out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
1702 out_dot.write( SurfacingConstants.NL );
1706 catch ( final IOException e ) {
1707 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1709 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
1710 + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1711 + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
1714 public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1715 final CharacterStateMatrix.GainLossStates state,
1716 final String filename,
1717 final String indentifier_characters_separator,
1718 final String character_separator,
1719 final Map<String, String> descriptions ) {
1720 final File outfile = new File( filename );
1721 checkForOutputFileWriteability( outfile );
1722 final SortedSet<String> sorted_ids = new TreeSet<String>();
1723 for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1724 sorted_ids.add( matrix.getIdentifier( i ) );
1727 final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1728 for( final String id : sorted_ids ) {
1729 out.write( indentifier_characters_separator );
1730 out.write( "#" + id );
1731 out.write( indentifier_characters_separator );
1732 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1734 // using null to indicate either UNCHANGED_PRESENT or GAIN.
1735 if ( ( matrix.getState( id, c ) == state )
1736 || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1737 .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1738 out.write( matrix.getCharacter( c ) );
1739 if ( ( descriptions != null ) && !descriptions.isEmpty()
1740 && descriptions.containsKey( matrix.getCharacter( c ) ) ) {
1742 out.write( descriptions.get( matrix.getCharacter( c ) ) );
1744 out.write( character_separator );
1751 catch ( final IOException e ) {
1752 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1754 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1757 public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1758 final CharacterStateMatrix.GainLossStates state,
1759 final String filename,
1760 final String indentifier_characters_separator,
1761 final String character_separator,
1762 final BinaryDomainCombination.OutputFormat bc_output_format ) {
1763 final File outfile = new File( filename );
1764 checkForOutputFileWriteability( outfile );
1765 final SortedSet<String> sorted_ids = new TreeSet<String>();
1766 for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1767 sorted_ids.add( matrix.getIdentifier( i ) );
1770 final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1771 for( final String id : sorted_ids ) {
1772 out.write( indentifier_characters_separator );
1773 out.write( "#" + id );
1774 out.write( indentifier_characters_separator );
1775 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1777 // using null to indicate either UNCHANGED_PRESENT or GAIN.
1778 if ( ( matrix.getState( id, c ) == state )
1779 || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1780 .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1781 BinaryDomainCombination bdc = null;
1783 bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
1785 catch ( final Exception e ) {
1786 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
1788 out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
1789 out.write( character_separator );
1796 catch ( final IOException e ) {
1797 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1799 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1802 public static void writeBinaryStatesMatrixToList( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1803 final Map<GoId, GoTerm> go_id_to_term_map,
1804 final GoNameSpace go_namespace_limit,
1805 final boolean domain_combinations,
1806 final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1807 final CharacterStateMatrix.GainLossStates state,
1808 final String filename,
1809 final String indentifier_characters_separator,
1810 final String character_separator,
1811 final String title_for_html,
1812 final String prefix_for_html,
1813 final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
1814 final SortedSet<String> all_pfams_encountered,
1815 final SortedSet<String> pfams_gained_or_lost,
1816 final String suffix_for_per_node_events_file ) {
1817 if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1818 throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
1820 else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
1821 throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
1823 else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1824 throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
1826 final File outfile = new File( filename );
1827 checkForOutputFileWriteability( outfile );
1828 final SortedSet<String> sorted_ids = new TreeSet<String>();
1829 for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1830 sorted_ids.add( matrix.getIdentifier( i ) );
1833 final Writer out = new BufferedWriter( new FileWriter( outfile ) );
1834 final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
1835 domain_combinations,
1838 Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1839 File per_node_go_mapped_domain_gain_loss_outfile = null;
1840 int per_node_counter = 0;
1841 out.write( "<html>" );
1842 out.write( SurfacingConstants.NL );
1843 addHtmlHead( out, title_for_html );
1844 out.write( SurfacingConstants.NL );
1845 out.write( "<body>" );
1846 out.write( SurfacingConstants.NL );
1847 out.write( "<h1>" );
1848 out.write( SurfacingConstants.NL );
1849 out.write( title_for_html );
1850 out.write( SurfacingConstants.NL );
1851 out.write( "</h1>" );
1852 out.write( SurfacingConstants.NL );
1853 out.write( "<table>" );
1854 out.write( SurfacingConstants.NL );
1855 for( final String id : sorted_ids ) {
1856 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1857 if ( matcher.matches() ) {
1860 out.write( "<tr>" );
1861 out.write( "<td>" );
1862 out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
1863 out.write( "</td>" );
1864 out.write( "</tr>" );
1865 out.write( SurfacingConstants.NL );
1867 out.write( "</table>" );
1868 out.write( SurfacingConstants.NL );
1869 for( final String id : sorted_ids ) {
1870 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1871 if ( matcher.matches() ) {
1874 out.write( SurfacingConstants.NL );
1875 out.write( "<h2>" );
1876 out.write( "<a name=\"" + id + "\">" + id + "</a>" );
1877 writeTaxonomyLinks( out, id );
1878 out.write( "</h2>" );
1879 out.write( SurfacingConstants.NL );
1880 out.write( "<table>" );
1881 out.write( SurfacingConstants.NL );
1882 out.write( "<tr>" );
1883 out.write( "<td><b>" );
1884 out.write( "Pfam domain(s)" );
1885 out.write( "</b></td><td><b>" );
1886 out.write( "GO term acc" );
1887 out.write( "</b></td><td><b>" );
1888 out.write( "GO term" );
1889 out.write( "</b></td><td><b>" );
1890 out.write( "GO namespace" );
1891 out.write( "</b></td>" );
1892 out.write( "</tr>" );
1893 out.write( SurfacingConstants.NL );
1894 out.write( "</tr>" );
1895 out.write( SurfacingConstants.NL );
1896 per_node_counter = 0;
1897 if ( matrix.getNumberOfCharacters() > 0 ) {
1898 per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
1899 + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
1900 SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
1901 per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
1902 .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
1905 per_node_go_mapped_domain_gain_loss_outfile = null;
1906 per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1908 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1910 // using null to indicate either UNCHANGED_PRESENT or GAIN.
1911 if ( ( matrix.getState( id, c ) == state )
1912 || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
1913 .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
1914 final String character = matrix.getCharacter( c );
1915 String domain_0 = "";
1916 String domain_1 = "";
1917 if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
1918 final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
1919 if ( s.length != 2 ) {
1920 throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
1921 + character + "]" );
1927 domain_0 = character;
1929 writeDomainData( domain_id_to_go_ids_map,
1936 character_separator,
1937 domain_id_to_secondary_features_maps,
1939 all_pfams_encountered.add( domain_0 );
1940 if ( pfams_gained_or_lost != null ) {
1941 pfams_gained_or_lost.add( domain_0 );
1943 if ( !ForesterUtil.isEmpty( domain_1 ) ) {
1944 all_pfams_encountered.add( domain_1 );
1945 if ( pfams_gained_or_lost != null ) {
1946 pfams_gained_or_lost.add( domain_1 );
1949 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1950 writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
1957 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1958 per_node_go_mapped_domain_gain_loss_outfile_writer.close();
1959 if ( per_node_counter < 1 ) {
1960 per_node_go_mapped_domain_gain_loss_outfile.delete();
1962 per_node_counter = 0;
1964 out.write( "</table>" );
1965 out.write( SurfacingConstants.NL );
1966 out.write( "<hr>" );
1967 out.write( SurfacingConstants.NL );
1968 } // for( final String id : sorted_ids ) {
1969 out.write( "</body>" );
1970 out.write( SurfacingConstants.NL );
1971 out.write( "</html>" );
1972 out.write( SurfacingConstants.NL );
1976 catch ( final IOException e ) {
1977 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1979 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
1982 public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
1983 final File output_dir,
1984 final Writer per_genome_domain_promiscuity_statistics_writer,
1985 final GenomeWideCombinableDomains gwcd,
1987 final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1988 File dc_outfile = new File( input_file_properties[ i ][ 0 ]
1989 + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
1990 if ( output_dir != null ) {
1991 dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
1993 checkForOutputFileWriteability( dc_outfile );
1995 final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
1996 out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
1999 catch ( final IOException e ) {
2000 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2002 final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
2004 per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 0 ] + "\t" );
2005 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
2006 if ( stats.getN() < 2 ) {
2007 per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
2010 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
2011 .sampleStandardDeviation() ) + "\t" );
2013 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
2014 per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
2015 per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
2016 per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
2017 final SortedSet<DomainId> mpds = gwcd.getMostPromiscuosDomain();
2018 for( final DomainId mpd : mpds ) {
2019 per_genome_domain_promiscuity_statistics_writer.write( mpd.getId() + " " );
2021 per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
2023 catch ( final IOException e ) {
2024 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2026 if ( input_file_properties[ i ].length == 3 ) {
2027 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
2028 + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
2029 + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
2032 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
2033 + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
2034 + dc_outfile + "\"" );
2038 private static void writeDomainData( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
2039 final Map<GoId, GoTerm> go_id_to_term_map,
2040 final GoNameSpace go_namespace_limit,
2042 final String domain_0,
2043 final String domain_1,
2044 final String prefix_for_html,
2045 final String character_separator_for_non_html_output,
2046 final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
2047 final Set<GoId> all_go_ids ) throws IOException {
2048 boolean any_go_annotation_present = false;
2049 boolean first_has_no_go = false;
2050 int domain_count = 2; // To distinguish between domains and binary domain combinations.
2051 if ( ForesterUtil.isEmpty( domain_1 ) ) {
2054 // The following has a difficult to understand logic.
2055 for( int d = 0; d < domain_count; ++d ) {
2056 List<GoId> go_ids = null;
2057 boolean go_annotation_present = false;
2059 final DomainId domain_id = new DomainId( domain_0 );
2060 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
2061 go_annotation_present = true;
2062 any_go_annotation_present = true;
2063 go_ids = domain_id_to_go_ids_map.get( domain_id );
2066 first_has_no_go = true;
2070 final DomainId domain_id = new DomainId( domain_1 );
2071 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
2072 go_annotation_present = true;
2073 any_go_annotation_present = true;
2074 go_ids = domain_id_to_go_ids_map.get( domain_id );
2077 if ( go_annotation_present ) {
2078 boolean first = ( ( d == 0 ) || ( ( d == 1 ) && first_has_no_go ) );
2079 for( final GoId go_id : go_ids ) {
2080 out.write( "<tr>" );
2083 writeDomainIdsToHtml( out,
2087 domain_id_to_secondary_features_maps );
2090 out.write( "<td></td>" );
2092 if ( !go_id_to_term_map.containsKey( go_id ) ) {
2093 throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
2095 final GoTerm go_term = go_id_to_term_map.get( go_id );
2096 if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
2097 // final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
2098 final String go_id_str = go_id.getId();
2099 out.write( "<td>" );
2100 out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
2101 + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
2102 out.write( "</td><td>" );
2103 out.write( go_term.getName() );
2104 if ( domain_count == 2 ) {
2105 out.write( " (" + d + ")" );
2107 out.write( "</td><td>" );
2108 // out.write( top );
2109 // out.write( "</td><td>" );
2111 out.write( go_term.getGoNameSpace().toShortString() );
2113 out.write( "</td>" );
2114 if ( all_go_ids != null ) {
2115 all_go_ids.add( go_id );
2119 out.write( "<td>" );
2120 out.write( "</td><td>" );
2121 out.write( "</td><td>" );
2122 out.write( "</td><td>" );
2123 out.write( "</td>" );
2125 out.write( "</tr>" );
2126 out.write( SurfacingConstants.NL );
2129 } // for( int d = 0; d < domain_count; ++d )
2130 if ( !any_go_annotation_present ) {
2131 out.write( "<tr>" );
2132 writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
2133 out.write( "<td>" );
2134 out.write( "</td><td>" );
2135 out.write( "</td><td>" );
2136 out.write( "</td><td>" );
2137 out.write( "</td>" );
2138 out.write( "</tr>" );
2139 out.write( SurfacingConstants.NL );
2143 private static void writeDomainIdsToHtml( final Writer out,
2144 final String domain_0,
2145 final String domain_1,
2146 final String prefix_for_detailed_html,
2147 final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps )
2148 throws IOException {
2149 out.write( "<td>" );
2150 if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
2151 out.write( prefix_for_detailed_html );
2154 out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
2155 out.write( "</td>" );
2158 public static DescriptiveStatistics writeDomainSimilaritiesToFile( final StringBuilder html_desc,
2159 final StringBuilder html_title,
2160 final Writer single_writer,
2161 Map<Character, Writer> split_writers,
2162 final SortedSet<DomainSimilarity> similarities,
2163 final boolean treat_as_binary,
2164 final List<Species> species_order,
2165 final PrintableDomainSimilarity.PRINT_OPTION print_option,
2166 final DomainSimilarity.DomainSimilaritySortField sort_field,
2167 final DomainSimilarity.DomainSimilarityScoring scoring,
2168 final boolean verbose ) throws IOException {
2169 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
2170 String histogram_title = null;
2171 switch ( sort_field ) {
2172 case ABS_MAX_COUNTS_DIFFERENCE:
2173 if ( treat_as_binary ) {
2174 histogram_title = "absolute counts difference:";
2177 histogram_title = "absolute (maximal) counts difference:";
2180 case MAX_COUNTS_DIFFERENCE:
2181 if ( treat_as_binary ) {
2182 histogram_title = "counts difference:";
2185 histogram_title = "(maximal) counts difference:";
2189 histogram_title = "score mean:";
2192 histogram_title = "score minimum:";
2195 histogram_title = "score maximum:";
2197 case MAX_DIFFERENCE:
2198 if ( treat_as_binary ) {
2199 histogram_title = "difference:";
2202 histogram_title = "(maximal) difference:";
2206 histogram_title = "score mean:";
2209 histogram_title = "score standard deviation:";
2212 histogram_title = "species number:";
2215 throw new AssertionError( "Unknown sort field: " + sort_field );
2217 for( final DomainSimilarity similarity : similarities ) {
2218 switch ( sort_field ) {
2219 case ABS_MAX_COUNTS_DIFFERENCE:
2220 stats.addValue( Math.abs( similarity.getMaximalDifferenceInCounts() ) );
2222 case MAX_COUNTS_DIFFERENCE:
2223 stats.addValue( similarity.getMaximalDifferenceInCounts() );
2226 stats.addValue( similarity.getMeanSimilarityScore() );
2229 stats.addValue( similarity.getMinimalSimilarityScore() );
2232 stats.addValue( similarity.getMaximalSimilarityScore() );
2234 case MAX_DIFFERENCE:
2235 stats.addValue( similarity.getMaximalDifference() );
2238 stats.addValue( similarity.getMeanSimilarityScore() );
2241 stats.addValue( similarity.getStandardDeviationOfSimilarityScore() );
2244 stats.addValue( similarity.getSpecies().size() );
2247 throw new AssertionError( "Unknown sort field: " + sort_field );
2251 // final HistogramData[] hists = new HistogramData[ 1 ];
2254 // List<HistogramDataItem> data_items = new
2255 // ArrayList<HistogramDataItem>();
2256 // double[] values = stats.getDataAsDoubleArray();
2257 // for( int i = 0; i < values.length; i++ ) {
2258 // HistogramDataItem data_item = new BasicHistogramDataItem( "", values[
2260 // data_items.add( data_item );
2264 // HistogramData hd0 = new HistogramData( "name",
2272 // hists[ 0 ] = hd0;
2274 // final HistogramsFrame hf = new HistogramsFrame( hists );
2275 // hf.setVisible( true );
2277 AsciiHistogram histo = null;
2278 if ( stats.getMin() < stats.getMin() ) {
2279 histo = new AsciiHistogram( stats, histogram_title );
2282 if ( histo != null ) {
2283 System.out.println( histo.toStringBuffer( 20, '|', 40, 5 ) );
2285 System.out.println();
2286 System.out.println( "N : " + stats.getN() );
2287 System.out.println( "Min : " + stats.getMin() );
2288 System.out.println( "Max : " + stats.getMax() );
2289 System.out.println( "Mean : " + stats.arithmeticMean() );
2290 if ( stats.getN() > 1 ) {
2291 System.out.println( "SD : " + stats.sampleStandardDeviation() );
2294 System.out.println( "SD : n/a" );
2296 System.out.println( "Median : " + stats.median() );
2297 if ( stats.getN() > 1 ) {
2298 System.out.println( "Pearsonian skewness : " + stats.pearsonianSkewness() );
2301 System.out.println( "Pearsonian skewness : n/a" );
2304 if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
2305 split_writers = new HashMap<Character, Writer>();
2306 split_writers.put( '_', single_writer );
2308 switch ( print_option ) {
2309 case SIMPLE_TAB_DELIMITED:
2312 for( final Character key : split_writers.keySet() ) {
2313 final Writer w = split_writers.get( key );
2314 w.write( "<html>" );
2315 w.write( SurfacingConstants.NL );
2317 addHtmlHead( w, "DCs (" + html_title + ") " + key.toString().toUpperCase() );
2320 addHtmlHead( w, "DCs (" + html_title + ")" );
2322 w.write( SurfacingConstants.NL );
2323 w.write( "<body>" );
2324 w.write( SurfacingConstants.NL );
2325 w.write( html_desc.toString() );
2326 w.write( SurfacingConstants.NL );
2329 w.write( SurfacingConstants.NL );
2330 w.write( "<tt><pre>" );
2331 w.write( SurfacingConstants.NL );
2332 if ( histo != null ) {
2333 w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
2334 w.write( SurfacingConstants.NL );
2336 w.write( "</pre></tt>" );
2337 w.write( SurfacingConstants.NL );
2338 w.write( "<table>" );
2339 w.write( SurfacingConstants.NL );
2340 w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
2341 w.write( SurfacingConstants.NL );
2342 w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
2343 w.write( SurfacingConstants.NL );
2344 w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
2345 w.write( SurfacingConstants.NL );
2346 w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
2347 w.write( SurfacingConstants.NL );
2348 if ( stats.getN() > 1 ) {
2349 w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
2352 w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
2354 w.write( SurfacingConstants.NL );
2355 w.write( "<tr><td>Median: </td><td>" + stats.median() + "</td></tr>" );
2356 w.write( SurfacingConstants.NL );
2357 if ( stats.getN() > 1 ) {
2358 w.write( "<tr><td>Pearsonian skewness: </td><td>" + stats.pearsonianSkewness() + "</td></tr>" );
2361 w.write( "<tr><td>Pearsonian skewness: </td><td>n/a</td></tr>" );
2363 w.write( SurfacingConstants.NL );
2364 w.write( "</table>" );
2365 w.write( SurfacingConstants.NL );
2367 w.write( SurfacingConstants.NL );
2369 w.write( SurfacingConstants.NL );
2371 w.write( SurfacingConstants.NL );
2372 w.write( "<table>" );
2373 w.write( SurfacingConstants.NL );
2377 for( final Writer w : split_writers.values() ) {
2378 w.write( SurfacingConstants.NL );
2380 for( final DomainSimilarity similarity : similarities ) {
2381 if ( ( species_order != null ) && !species_order.isEmpty() ) {
2382 ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
2384 if ( single_writer != null ) {
2385 single_writer.write( similarity.toStringBuffer( print_option ).toString() );
2388 Writer local_writer = split_writers.get( ( similarity.getDomainId().getId().charAt( 0 ) + "" )
2389 .toLowerCase().charAt( 0 ) );
2390 if ( local_writer == null ) {
2391 local_writer = split_writers.get( '0' );
2393 local_writer.write( similarity.toStringBuffer( print_option ).toString() );
2395 for( final Writer w : split_writers.values() ) {
2396 w.write( SurfacingConstants.NL );
2399 switch ( print_option ) {
2401 for( final Writer w : split_writers.values() ) {
2402 w.write( SurfacingConstants.NL );
2403 w.write( "</table>" );
2404 w.write( SurfacingConstants.NL );
2405 w.write( "</font>" );
2406 w.write( SurfacingConstants.NL );
2407 w.write( "</body>" );
2408 w.write( SurfacingConstants.NL );
2409 w.write( "</html>" );
2410 w.write( SurfacingConstants.NL );
2414 for( final Writer w : split_writers.values() ) {
2420 private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
2421 final String domain_0,
2422 final String domain_1 ) throws IOException {
2423 individual_files_writer.write( domain_0 );
2424 individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2425 if ( !ForesterUtil.isEmpty( domain_1 ) ) {
2426 individual_files_writer.write( domain_1 );
2427 individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2431 public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
2432 final String filename,
2433 final Format format ) {
2434 final File outfile = new File( filename );
2435 checkForOutputFileWriteability( outfile );
2437 final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
2438 matrix.toWriter( out, format );
2442 catch ( final IOException e ) {
2443 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2445 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
2448 public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
2449 checkForOutputFileWriteability( matrix_outfile );
2451 final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
2452 for( final DistanceMatrix distance_matrix : matrices ) {
2453 out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
2454 out.write( ForesterUtil.LINE_SEPARATOR );
2459 catch ( final IOException e ) {
2460 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2462 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
2465 private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
2467 final Writer writer = new BufferedWriter( new FileWriter( new File( outfile_name ) ) );
2468 for( final String pfam : pfams ) {
2469 writer.write( pfam );
2470 writer.write( ForesterUtil.LINE_SEPARATOR );
2473 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
2476 catch ( final IOException e ) {
2477 ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2481 public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
2482 final PhylogenyWriter writer = new PhylogenyWriter();
2484 writer.toPhyloXML( new File( filename ), phylogeny, 1 );
2486 catch ( final IOException e ) {
2487 ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
2490 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
2493 public static void writeTaxonomyLinks( final Writer writer, final String species ) throws IOException {
2494 if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
2495 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( species );
2496 writer.write( " [" );
2497 if ( matcher.matches() ) {
2498 writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_LINK + species
2499 + "\" target=\"taxonomy_window\">uniprot</a>" );
2502 writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
2503 + "\" target=\"taxonomy_window\">eol</a>" );
2504 writer.write( "|" );
2505 writer.write( "<a href=\"" + SurfacingConstants.TOL_LINK + species
2506 + "\" target=\"taxonomy_window\">tol</a>" );
2508 writer.write( "]" );
2512 private static void writeToNexus( final String outfile_name,
2513 final CharacterStateMatrix<BinaryStates> matrix,
2514 final Phylogeny phylogeny ) {
2515 if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
2516 throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
2519 final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
2520 final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>( 1 );
2521 phylogenies.add( phylogeny );
2523 final BufferedWriter w = new BufferedWriter( new FileWriter( outfile_name ) );
2524 w.write( NexusConstants.NEXUS );
2525 w.write( ForesterUtil.LINE_SEPARATOR );
2526 my_matrix.writeNexusTaxaBlock( w );
2527 my_matrix.writeNexusBinaryChractersBlock( w );
2528 PhylogenyWriter.writeNexusTreesBlock( w, phylogenies, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
2531 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
2533 catch ( final IOException e ) {
2534 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2538 private static void writeToNexus( final String outfile_name,
2539 final DomainParsimonyCalculator domain_parsimony,
2540 final Phylogeny phylogeny ) {
2541 writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAINS,
2542 domain_parsimony.createMatrixOfDomainPresenceOrAbsence(),
2544 writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
2545 domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(),
2549 public static void domainsPerProteinsStatistics( final String genome,
2550 final List<Protein> protein_list,
2551 final DescriptiveStatistics all_genomes_domains_per_potein_stats,
2552 final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
2553 final SortedSet<String> domains_which_are_always_single,
2554 final SortedSet<String> domains_which_are_sometimes_single_sometimes_not,
2555 final SortedSet<String> domains_which_never_single,
2556 final Writer writer ) {
2557 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
2558 for( final Protein protein : protein_list ) {
2559 final int domains = protein.getNumberOfProteinDomains();
2560 //System.out.println( domains );
2561 stats.addValue( domains );
2562 all_genomes_domains_per_potein_stats.addValue( domains );
2563 if ( !all_genomes_domains_per_potein_histo.containsKey( domains ) ) {
2564 all_genomes_domains_per_potein_histo.put( domains, 1 );
2567 all_genomes_domains_per_potein_histo.put( domains,
2568 1 + all_genomes_domains_per_potein_histo.get( domains ) );
2570 if ( domains == 1 ) {
2571 final String domain = protein.getProteinDomain( 0 ).getDomainId().getId();
2572 if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
2573 if ( domains_which_never_single.contains( domain ) ) {
2574 domains_which_never_single.remove( domain );
2575 domains_which_are_sometimes_single_sometimes_not.add( domain );
2578 domains_which_are_always_single.add( domain );
2582 else if ( domains > 1 ) {
2583 for( final Domain d : protein.getProteinDomains() ) {
2584 final String domain = d.getDomainId().getId();
2585 // System.out.println( domain );
2586 if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
2587 if ( domains_which_are_always_single.contains( domain ) ) {
2588 domains_which_are_always_single.remove( domain );
2589 domains_which_are_sometimes_single_sometimes_not.add( domain );
2592 domains_which_never_single.add( domain );
2599 writer.write( genome );
2600 writer.write( "\t" );
2601 if ( stats.getN() >= 1 ) {
2602 writer.write( stats.arithmeticMean() + "" );
2603 writer.write( "\t" );
2604 if ( stats.getN() >= 2 ) {
2605 writer.write( stats.sampleStandardDeviation() + "" );
2610 writer.write( "\t" );
2611 writer.write( stats.median() + "" );
2612 writer.write( "\t" );
2613 writer.write( stats.getN() + "" );
2614 writer.write( "\t" );
2615 writer.write( stats.getMin() + "" );
2616 writer.write( "\t" );
2617 writer.write( stats.getMax() + "" );
2620 writer.write( "\t" );
2621 writer.write( "\t" );
2622 writer.write( "\t" );
2623 writer.write( "0" );
2624 writer.write( "\t" );
2625 writer.write( "\t" );
2627 writer.write( "\n" );
2629 catch ( final IOException e ) {
2630 e.printStackTrace();
2634 final static class DomainComparator implements Comparator<Domain> {
2636 final private boolean _ascending;
2638 public DomainComparator( final boolean ascending ) {
2639 _ascending = ascending;
2643 public final int compare( final Domain d0, final Domain d1 ) {
2645 if ( d0.getFrom() < d1.getFrom() ) {
2646 return _ascending ? -1 : 1;
2648 else if ( d0.getFrom() > d1.getFrom() ) {
2649 return _ascending ? 1 : -1;