// $Id: SurfacingUtil.java,v 1.124 2010/09/29 23:50:18 cmzmasek Exp $
//
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: cmzmasek@yahoo.com
// WWW: www.phylosoft.org/forester
package org.forester.surfacing;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.Writer;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.SortedMap;
import java.util.SortedSet;
import java.util.TreeMap;
import java.util.TreeSet;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.forester.application.surfacing_old;
import org.forester.evoinference.distance.NeighborJoining;
import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
import org.forester.evoinference.matrix.character.CharacterStateMatrix;
import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
import org.forester.evoinference.matrix.distance.DistanceMatrix;
import org.forester.go.GoId;
import org.forester.go.GoNameSpace;
import org.forester.go.GoTerm;
import org.forester.go.GoUtils;
import org.forester.go.PfamToGoMapping;
import org.forester.io.parsers.nexus.NexusConstants;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.BinaryCharacters;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
import org.forester.util.AsciiHistogram;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.BasicTable;
import org.forester.util.BasicTableParser;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
public final class SurfacingUtil {
private final static NumberFormat FORMATTER = new DecimalFormat( "0.0E0" );
private final static NumberFormat FORMATTER_3 = new DecimalFormat( "0.000" );
private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
public int compare( final Domain d1,
final Domain d2 ) {
if ( d1.getPerSequenceEvalue() < d2
.getPerSequenceEvalue() ) {
return -1;
}
else if ( d1
.getPerSequenceEvalue() > d2
.getPerSequenceEvalue() ) {
return 1;
}
else {
return d1.compareTo( d2 );
}
}
};
public final static Pattern PATTERN_SP_STYLE_TAXONOMY = Pattern.compile( "^[A-Z0-9]{3,5}$" );
private SurfacingUtil() {
// Hidden constructor.
}
public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
final SortedMap<DomainId, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
for( final DomainId domain_id : all_cd.keySet() ) {
binary_domain_combinations.addAll( all_cd.get( domain_id ).toBinaryDomainCombinations() );
}
}
public static void addAllDomainIdsToSet( final GenomeWideCombinableDomains genome,
final SortedSet<DomainId> domain_ids ) {
final SortedSet<DomainId> domains = genome.getAllDomainIds();
for( final DomainId domain : domains ) {
domain_ids.add( domain );
}
}
public static void addHtmlHead( final Writer w, final String title ) throws IOException {
w.write( SurfacingConstants.NL );
w.write( "<head>" );
w.write( "<title>" );
w.write( title );
w.write( "</title>" );
w.write( SurfacingConstants.NL );
w.write( "<style>" );
w.write( SurfacingConstants.NL );
w.write( "a:visited { color : #6633FF; text-decoration : none; }" );
w.write( SurfacingConstants.NL );
w.write( "a:link { color : #6633FF; text-decoration : none; }" );
w.write( SurfacingConstants.NL );
w.write( "a:active { color : #99FF00; text-decoration : none; }" );
w.write( SurfacingConstants.NL );
w.write( "a:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; }" );
w.write( SurfacingConstants.NL );
w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
w.write( SurfacingConstants.NL );
w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
w.write( SurfacingConstants.NL );
w.write( "h2 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" );
w.write( SurfacingConstants.NL );
w.write( "</style>" );
w.write( SurfacingConstants.NL );
w.write( "</head>" );
w.write( SurfacingConstants.NL );
}
public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
for( final DomainSimilarity similarity : similarities ) {
stats.addValue( similarity.getMeanSimilarityScore() );
}
return stats;
}
public static int calculateOverlap( final Domain domain, final List<Boolean> covered_positions ) {
int overlap_count = 0;
for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) {
++overlap_count;
}
}
return overlap_count;
}
public static void checkForOutputFileWriteability( final File outfile ) {
final String error = ForesterUtil.isWritableFile( outfile );
if ( !ForesterUtil.isEmpty( error ) ) {
ForesterUtil.fatalError( surfacing_old.PRG_NAME, error );
}
}
private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
final boolean get_gains ) {
final SortedSet<String> domains = new TreeSet<String>();
for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
if ( get_gains ) {
domains.addAll( chars.getGainedCharacters() );
}
else {
domains.addAll( chars.getLostCharacters() );
}
}
return domains;
}
public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
final BinaryDomainCombination.DomainCombinationType dc_type,
final List<BinaryDomainCombination> all_binary_domains_combination_gained,
final boolean get_gains ) {
final SortedSet<String> sorted_ids = new TreeSet<String>();
for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
sorted_ids.add( matrix.getIdentifier( i ) );
}
for( final String id : sorted_ids ) {
for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
|| ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
.createInstance( matrix.getCharacter( c ) ) );
}
else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
.createInstance( matrix.getCharacter( c ) ) );
}
else {
all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
.getCharacter( c ) ) );
}
}
}
}
}
private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
final boolean domain_combinations,
final CharacterStateMatrix.GainLossStates state,
final String outfile ) {
File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
+ ForesterUtil.FILE_SEPARATOR + base_dir );
if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
}
if ( domain_combinations ) {
per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+ ForesterUtil.FILE_SEPARATOR + "DC" );
}
else {
per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+ ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
}
if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
}
if ( state == GainLossStates.GAIN ) {
per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+ ForesterUtil.FILE_SEPARATOR + "GAINS" );
}
else if ( state == GainLossStates.LOSS ) {
per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+ ForesterUtil.FILE_SEPARATOR + "LOSSES" );
}
else {
per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+ ForesterUtil.FILE_SEPARATOR + "PRESENT" );
}
if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
}
return per_node_go_mapped_domain_gain_loss_files_base_dir;
}
public static Map<DomainId, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
final Map<DomainId, List<GoId>> domain_id_to_go_ids_map = new HashMap<DomainId, List<GoId>>( pfam_to_go_mappings
.size() );
for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
}
domain_id_to_go_ids_map.get( pfam_to_go.getKey() ).add( pfam_to_go.getValue() );
}
return domain_id_to_go_ids_map;
}
public static Map<DomainId, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
throws IOException {
final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, "\t" );
final Map<DomainId, Set<String>> map = new TreeMap<DomainId, Set<String>>();
for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
final DomainId domain_id = new DomainId( primary_table.getValue( 0, r ) );
if ( !map.containsKey( domain_id ) ) {
map.put( domain_id, new HashSet<String>() );
}
map.get( domain_id ).add( primary_table.getValue( 1, r ) );
}
return map;
}
public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
checkForOutputFileWriteability( nj_tree_outfile );
final NeighborJoining nj = NeighborJoining.createInstance();
final Phylogeny phylogeny = nj.execute( distance );
phylogeny.setName( nj_tree_outfile.getName() );
writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
return phylogeny;
}
private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
final SortedMap<DomainId, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
for( final DomainId domain_id : cds.keySet() ) {
final CombinableDomains cd = cds.get( domain_id );
binary_combinations.addAll( cd.toBinaryDomainCombinations() );
}
return binary_combinations;
}
public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
final Detailedness detailedness,
final GoAnnotationOutput go_annotation_output,
final Map<GoId, GoTerm> go_id_to_term_map,
final GoNameSpace go_namespace_limit ) {
if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) ) {
throw new IllegalArgumentException( "attempt to use a GO namespace limit without a GO id to term map" );
}
for( final DomainSimilarity domain_similarity : domain_similarities ) {
if ( domain_similarity instanceof PrintableDomainSimilarity ) {
final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
printable_domain_similarity.setDetailedness( detailedness );
printable_domain_similarity.setGoAnnotationOutput( go_annotation_output );
printable_domain_similarity.setGoIdToTermMap( go_id_to_term_map );
printable_domain_similarity.setGoNamespaceLimit( go_namespace_limit );
}
}
}
public static void executeDomainLengthAnalysis( final String[][] input_file_properties,
final int number_of_genomes,
final DomainLengthsTable domain_lengths_table,
final File outfile ) throws IOException {
final DecimalFormat df = new DecimalFormat( "#.00" );
checkForOutputFileWriteability( outfile );
final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
out.write( "MEAN BASED STATISTICS PER SPECIES" );
out.write( ForesterUtil.LINE_SEPARATOR );
out.write( domain_lengths_table.createMeanBasedStatisticsPerSpeciesTable().toString() );
out.write( ForesterUtil.LINE_SEPARATOR );
out.write( ForesterUtil.LINE_SEPARATOR );
final List<DomainLengths> domain_lengths_list = domain_lengths_table.getDomainLengthsList();
out.write( "OUTLIER SPECIES PER DOMAIN (Z>=1.5)" );
out.write( ForesterUtil.LINE_SEPARATOR );
for( final DomainLengths domain_lengths : domain_lengths_list ) {
final List<Species> species_list = domain_lengths.getMeanBasedOutlierSpecies( 1.5 );
if ( species_list.size() > 0 ) {
out.write( domain_lengths.getDomainId() + "\t" );
for( final Species species : species_list ) {
out.write( species + "\t" );
}
out.write( ForesterUtil.LINE_SEPARATOR );
// DescriptiveStatistics stats_for_domain = domain_lengths
// .calculateMeanBasedStatistics();
//AsciiHistogram histo = new AsciiHistogram( stats_for_domain );
//System.out.println( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
}
}
out.write( ForesterUtil.LINE_SEPARATOR );
out.write( ForesterUtil.LINE_SEPARATOR );
out.write( "OUTLIER SPECIES (Z 1.0)" );
out.write( ForesterUtil.LINE_SEPARATOR );
final DescriptiveStatistics stats_for_all_species = domain_lengths_table
.calculateMeanBasedStatisticsForAllSpecies();
out.write( stats_for_all_species.asSummary() );
out.write( ForesterUtil.LINE_SEPARATOR );
final AsciiHistogram histo = new AsciiHistogram( stats_for_all_species );
out.write( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
out.write( ForesterUtil.LINE_SEPARATOR );
final double population_sd = stats_for_all_species.sampleStandardDeviation();
final double population_mean = stats_for_all_species.arithmeticMean();
for( final Species species : domain_lengths_table.getSpecies() ) {
final double x = domain_lengths_table.calculateMeanBasedStatisticsForSpecies( species ).arithmeticMean();
final double z = ( x - population_mean ) / population_sd;
out.write( species + "\t" + z );
out.write( ForesterUtil.LINE_SEPARATOR );
}
out.write( ForesterUtil.LINE_SEPARATOR );
for( final Species species : domain_lengths_table.getSpecies() ) {
final DescriptiveStatistics stats_for_species = domain_lengths_table
.calculateMeanBasedStatisticsForSpecies( species );
final double x = stats_for_species.arithmeticMean();
final double z = ( x - population_mean ) / population_sd;
if ( ( z <= -1.0 ) || ( z >= 1.0 ) ) {
out.write( species + "\t" + df.format( z ) + "\t" + stats_for_species.asSummary() );
out.write( ForesterUtil.LINE_SEPARATOR );
}
}
out.close();
// final List<HistogramData> histogram_datas = new ArrayList<HistogramData>();
// for( int i = 0; i < number_of_genomes; ++i ) {
// final Species species = new BasicSpecies( input_file_properties[ i ][ 0 ] );
// histogram_datas
// .add( new HistogramData( species.toString(), domain_lengths_table
// .calculateMeanBasedStatisticsForSpecies( species )
// .getDataAsDoubleArray(), 5, 600, null, 60 ) );
// }
// final HistogramsFrame hf = new HistogramsFrame( histogram_datas );
// hf.setVisible( true );
System.gc();
}
/**
*
* @param all_binary_domains_combination_lost_fitch
* @param consider_directedness_and_adjacency_for_bin_combinations
* @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
* which were gained under unweighted (Fitch) parsimony.
*/
public static void executeParsimonyAnalysis( final long random_number_seed_for_fitch_parsimony,
final boolean radomize_fitch_parsimony,
final String outfile_name,
final DomainParsimonyCalculator domain_parsimony,
final Phylogeny phylogeny,
final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
final Map<GoId, GoTerm> go_id_to_term_map,
final GoNameSpace go_namespace_limit,
final String parameters_str,
final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
final SortedSet<DomainId> positive_filter,
final boolean output_binary_domain_combinations_for_graphs,
final List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch,
final List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch,
final BinaryDomainCombination.DomainCombinationType dc_type ) {
final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
final String date_time = ForesterUtil.getCurrentDateTime();
final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
final SortedSet<String> all_pfams_gained_as_domains = new TreeSet<String>();
final SortedSet<String> all_pfams_lost_as_domains = new TreeSet<String>();
final SortedSet<String> all_pfams_gained_as_dom_combinations = new TreeSet<String>();
final SortedSet<String> all_pfams_lost_as_dom_combinations = new TreeSet<String>();
writeToNexus( outfile_name, domain_parsimony, phylogeny );
// DOLLO DOMAINS
// -------------
Phylogeny local_phylogeny_l = phylogeny.copy();
if ( ( positive_filter != null ) && ( positive_filter.size() > 0 ) ) {
domain_parsimony.executeDolloParsimonyOnDomainPresence( positive_filter );
}
else {
domain_parsimony.executeDolloParsimonyOnDomainPresence();
}
SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
+ surfacing_old.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
+ surfacing_old.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.GAIN,
outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
SurfacingUtil
.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.LOSS,
outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
+ surfacing_old.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
//HTML:
writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
go_id_to_term_map,
go_namespace_limit,
false,
domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.GAIN,
outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
sep,
ForesterUtil.LINE_SEPARATOR,
"Dollo Parsimony | Gains | Domains",
"+",
domain_id_to_secondary_features_maps,
all_pfams_encountered,
all_pfams_gained_as_domains,
"_dollo_gains_d" );
writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
go_id_to_term_map,
go_namespace_limit,
false,
domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.LOSS,
outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
sep,
ForesterUtil.LINE_SEPARATOR,
"Dollo Parsimony | Losses | Domains",
"-",
domain_id_to_secondary_features_maps,
all_pfams_encountered,
all_pfams_lost_as_domains,
"_dollo_losses_d" );
writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
go_id_to_term_map,
go_namespace_limit,
false,
domain_parsimony.getGainLossMatrix(),
null,
outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
sep,
ForesterUtil.LINE_SEPARATOR,
"Dollo Parsimony | Present | Domains",
"",
domain_id_to_secondary_features_maps,
all_pfams_encountered,
null,
"_dollo_present_d" );
preparePhylogeny( local_phylogeny_l,
domain_parsimony,
date_time,
"Dollo parsimony on domain presence/absence",
"dollo_on_domains_" + outfile_name,
parameters_str );
SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
+ surfacing_old.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
try {
writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
}
catch ( final IOException e ) {
e.printStackTrace();
ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() );
}
if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
// FITCH DOMAIN COMBINATIONS
// -------------------------
local_phylogeny_l = phylogeny.copy();
String randomization = "no";
if ( radomize_fitch_parsimony ) {
domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( random_number_seed_for_fitch_parsimony );
randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
}
else {
domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( false );
}
SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
+ surfacing_old.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
+ surfacing_old.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.GAIN,
outfile_name
+ surfacing_old.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
SurfacingUtil
.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.LOSS,
outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
+ surfacing_old.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
if ( all_binary_domains_combination_gained_fitch != null ) {
collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony
.getGainLossMatrix(), dc_type, all_binary_domains_combination_gained_fitch, true );
}
if ( all_binary_domains_combination_lost_fitch != null ) {
collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony
.getGainLossMatrix(), dc_type, all_binary_domains_combination_lost_fitch, false );
}
if ( output_binary_domain_combinations_for_graphs ) {
SurfacingUtil
.writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
.getGainLossMatrix(),
null,
outfile_name
+ surfacing_old.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
sep,
ForesterUtil.LINE_SEPARATOR,
BinaryDomainCombination.OutputFormat.DOT );
}
// HTML:
writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
go_id_to_term_map,
go_namespace_limit,
true,
domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.GAIN,
outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
sep,
ForesterUtil.LINE_SEPARATOR,
"Fitch Parsimony | Gains | Domain Combinations",
"+",
null,
all_pfams_encountered,
all_pfams_gained_as_dom_combinations,
"_fitch_gains_dc" );
writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
go_id_to_term_map,
go_namespace_limit,
true,
domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.LOSS,
outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
sep,
ForesterUtil.LINE_SEPARATOR,
"Fitch Parsimony | Losses | Domain Combinations",
"-",
null,
all_pfams_encountered,
all_pfams_lost_as_dom_combinations,
"_fitch_losses_dc" );
writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
go_id_to_term_map,
go_namespace_limit,
true,
domain_parsimony.getGainLossMatrix(),
null,
outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
sep,
ForesterUtil.LINE_SEPARATOR,
"Fitch Parsimony | Present | Domain Combinations",
"",
null,
all_pfams_encountered,
null,
"_fitch_present_dc" );
writeAllEncounteredPfamsToFile( domain_id_to_go_ids_map,
go_id_to_term_map,
outfile_name,
all_pfams_encountered );
writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX,
all_pfams_gained_as_domains );
writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
all_pfams_gained_as_dom_combinations );
writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_LOST_AS_DC_SUFFIX,
all_pfams_lost_as_dom_combinations );
preparePhylogeny( local_phylogeny_l,
domain_parsimony,
date_time,
"Fitch parsimony on binary domain combination presence/absence randomization: "
+ randomization,
"fitch_on_binary_domain_combinations_" + outfile_name,
parameters_str );
SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
+ surfacing_old.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
}
}
public static void executeParsimonyAnalysisForSecondaryFeatures( final String outfile_name,
final DomainParsimonyCalculator secondary_features_parsimony,
final Phylogeny phylogeny,
final String parameters_str,
final Map<Species, MappingResults> mapping_results_map ) {
final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
final String date_time = ForesterUtil.getCurrentDateTime();
System.out.println();
writeToNexus( outfile_name + surfacing_old.NEXUS_SECONDARY_FEATURES, secondary_features_parsimony
.createMatrixOfSecondaryFeaturePresenceOrAbsence( null ), phylogeny );
final Phylogeny local_phylogeny_copy = phylogeny.copy();
secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
+ surfacing_old.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
+ surfacing_old.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
SurfacingUtil
.writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.GAIN,
outfile_name
+ surfacing_old.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
SurfacingUtil
.writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.LOSS,
outfile_name
+ surfacing_old.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
SurfacingUtil
.writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
null,
outfile_name
+ surfacing_old.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
preparePhylogeny( local_phylogeny_copy,
secondary_features_parsimony,
date_time,
"Dollo parsimony on secondary feature presence/absence",
"dollo_on_secondary_features_" + outfile_name,
parameters_str );
SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
+ surfacing_old.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
}
public static void extractProteinNames( final List<Protein> proteins,
final List<DomainId> query_domain_ids_nc_order,
final Writer out,
final String separator ) throws IOException {
for( final Protein protein : proteins ) {
if ( protein.contains( query_domain_ids_nc_order, true ) ) {
out.write( protein.getSpecies().getSpeciesId() );
out.write( separator );
out.write( protein.getProteinId().getId() );
out.write( separator );
out.write( "[" );
final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
boolean first = true;
for( final Domain domain : protein.getProteinDomains() ) {
if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
visited_domain_ids.add( domain.getDomainId() );
if ( first ) {
first = false;
}
else {
out.write( " " );
}
out.write( domain.getDomainId().getId() );
out.write( " {" );
out.write( "" + domain.getTotalCount() );
out.write( "}" );
}
}
out.write( "]" );
out.write( separator );
if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
.equals( SurfacingConstants.NONE ) ) ) {
out.write( protein.getDescription() );
}
out.write( separator );
if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
.equals( SurfacingConstants.NONE ) ) ) {
out.write( protein.getAccession() );
}
out.write( SurfacingConstants.NL );
}
}
out.flush();
}
public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
final DomainId domain_id,
final Writer out,
final String separator ) throws IOException {
for( final Species species : protein_lists_per_species.keySet() ) {
for( final Protein protein : protein_lists_per_species.get( species ) ) {
final List<Domain> domains = protein.getProteinDomains( domain_id );
if ( domains.size() > 0 ) {
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
for( final Domain domain : domains ) {
stats.addValue( domain.getPerSequenceEvalue() );
}
out.write( protein.getSpecies().getSpeciesId() );
out.write( separator );
out.write( protein.getProteinId().getId() );
out.write( separator );
out.write( "[" + FORMATTER.format( stats.median() ) + "]" );
out.write( separator );
if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
.equals( SurfacingConstants.NONE ) ) ) {
out.write( protein.getDescription() );
}
out.write( separator );
if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
.equals( SurfacingConstants.NONE ) ) ) {
out.write( protein.getAccession() );
}
out.write( SurfacingConstants.NL );
}
}
}
out.flush();
}
public static SortedSet<DomainId> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
final SortedSet<DomainId> all_domains_ids = new TreeSet<DomainId>();
for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
final Set<DomainId> all_domains = gwcd.getAllDomainIds();
// for( final Domain domain : all_domains ) {
all_domains_ids.addAll( all_domains );
// }
}
return all_domains_ids;
}
public static SortedMap<String, Integer> getDomainCounts( final List<Protein> protein_domain_collections ) {
final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
for( final Protein protein_domain_collection : protein_domain_collections ) {
for( final Object name : protein_domain_collection.getProteinDomains() ) {
final BasicDomain protein_domain = ( BasicDomain ) name;
final String id = protein_domain.getDomainId().getId();
if ( map.containsKey( id ) ) {
map.put( id, map.get( id ) + 1 );
}
else {
map.put( id, 1 );
}
}
}
return map;
}
public static int getNumberOfNodesLackingName( final Phylogeny p, final StringBuilder names ) {
final PhylogenyNodeIterator it = p.iteratorPostorder();
int c = 0;
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();
if ( ForesterUtil.isEmpty( n.getNodeName() ) ) {
if ( n.getParent() != null ) {
names.append( " " );
names.append( n.getParent().getNodeName() );
}
++c;
}
}
return c;
}
/**
* Returns true is Domain domain falls in an uninterrupted stretch of
* covered positions.
*
* @param domain
* @param covered_positions
* @return
*/
public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
return false;
}
}
return true;
}
public static void preparePhylogeny( final Phylogeny p,
final DomainParsimonyCalculator domain_parsimony,
final String date_time,
final String method,
final String name,
final String parameters_str ) {
domain_parsimony.decoratePhylogenyWithDomains( p );
final StringBuilder desc = new StringBuilder();
desc.append( "[Method: " + method + "] [Date: " + date_time + "] " );
desc.append( "[Cost: " + domain_parsimony.getCost() + "] " );
desc.append( "[Gains: " + domain_parsimony.getTotalGains() + "] " );
desc.append( "[Losses: " + domain_parsimony.getTotalLosses() + "] " );
desc.append( "[Unchanged: " + domain_parsimony.getTotalUnchanged() + "] " );
desc.append( "[Parameters: " + parameters_str + "]" );
p.setName( name );
p.setDescription( desc.toString() );
p.setConfidence( new Confidence( domain_parsimony.getCost(), "parsimony" ) );
p.setRerootable( false );
p.setRooted( true );
}
/**
*
* Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
* domain with 0.3 is ignored
*
* -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
*
*
* ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
* ignored
*
* @param max_allowed_overlap
* maximal allowed overlap (inclusive) to be still considered not
* overlapping (zero or negative value to allow any overlap)
* @param remove_engulfed_domains
* to remove domains which are completely engulfed by coverage of
* domains with better support
* @param protein
* @return
*/
public static Protein removeOverlappingDomains( final int max_allowed_overlap,
final boolean remove_engulfed_domains,
final Protein protein ) {
final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
.getSpeciesId() );
final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
final List<Boolean> covered_positions = new ArrayList<Boolean>();
for( final Domain domain : sorted ) {
if ( ( ( max_allowed_overlap < 0 ) || ( SurfacingUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
&& ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
final int covered_positions_size = covered_positions.size();
for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
covered_positions.add( false );
}
final int new_covered_positions_size = covered_positions.size();
for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
if ( i < new_covered_positions_size ) {
covered_positions.set( i, true );
}
else {
covered_positions.add( true );
}
}
pruned_protein.addProteinDomain( domain );
}
}
return pruned_protein;
}
static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
final List<Domain> domains = new ArrayList<Domain>();
for( final Domain d : protein.getProteinDomains() ) {
domains.add( d );
}
Collections.sort( domains, SurfacingUtil.ASCENDING_CONFIDENCE_VALUE_ORDER );
return domains;
}
public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
final boolean get_gains,
final String outdir,
final String suffix_for_filename ) throws IOException {
CharacterStateMatrix.GainLossStates state = CharacterStateMatrix.GainLossStates.GAIN;
if ( !get_gains ) {
state = CharacterStateMatrix.GainLossStates.LOSS;
}
final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing_old.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
false,
state,
outdir );
for( final PhylogenyNodeIterator it = p.iteratorPostorder(); it.hasNext(); ) {
final PhylogenyNode node = it.next();
if ( !node.isExternal() ) {
final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
if ( domains.size() > 0 ) {
final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
+ node.getNodeName() + suffix_for_filename );
for( final String domain : domains ) {
writer.write( domain );
writer.write( ForesterUtil.LINE_SEPARATOR );
}
writer.close();
}
}
}
}
private static void writeAllEncounteredPfamsToFile( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
final Map<GoId, GoTerm> go_id_to_term_map,
final String outfile_name,
final SortedSet<String> all_pfams_encountered ) {
final File all_pfams_encountered_file = new File( outfile_name + surfacing_old.ALL_PFAMS_ENCOUNTERED_SUFFIX );
final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
+ surfacing_old.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
final File encountered_pfams_summary_file = new File( outfile_name
+ surfacing_old.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
int biological_process_counter = 0;
int cellular_component_counter = 0;
int molecular_function_counter = 0;
int pfams_with_mappings_counter = 0;
int pfams_without_mappings_counter = 0;
int pfams_without_mappings_to_bp_or_mf_counter = 0;
int pfams_with_mappings_to_bp_or_mf_counter = 0;
try {
final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
summary_writer.write( "# Pfam to GO mapping summary" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Actual summary is at the end of this file." );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Encountered Pfams without a GO mapping:" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
for( final String pfam : all_pfams_encountered ) {
all_pfams_encountered_writer.write( pfam );
all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
final DomainId domain_id = new DomainId( pfam );
if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
++pfams_with_mappings_counter;
all_pfams_encountered_with_go_annotation_writer.write( pfam );
all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
boolean maps_to_bp = false;
boolean maps_to_cc = false;
boolean maps_to_mf = false;
for( final GoId go_id : go_ids ) {
final GoTerm go_term = go_id_to_term_map.get( go_id );
if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
maps_to_bp = true;
}
else if ( go_term.getGoNameSpace().isCellularComponent() ) {
maps_to_cc = true;
}
else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
maps_to_mf = true;
}
}
if ( maps_to_bp ) {
++biological_process_counter;
}
if ( maps_to_cc ) {
++cellular_component_counter;
}
if ( maps_to_mf ) {
++molecular_function_counter;
}
if ( maps_to_bp || maps_to_mf ) {
++pfams_with_mappings_to_bp_or_mf_counter;
}
else {
++pfams_without_mappings_to_bp_or_mf_counter;
}
}
else {
++pfams_without_mappings_to_bp_or_mf_counter;
++pfams_without_mappings_counter;
summary_writer.write( pfam );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
}
}
all_pfams_encountered_writer.close();
all_pfams_encountered_with_go_annotation_writer.close();
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
+ "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
+ "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
+ "\"" );
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote summary (including all ["
+ pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
+ encountered_pfams_summary_file + "\"" );
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Sum of Pfams encountered : "
+ all_pfams_encountered.size() );
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams without a mapping : "
+ pfams_without_mappings_counter + " ["
+ ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams without mapping to proc. or func. : "
+ pfams_without_mappings_to_bp_or_mf_counter + " ["
+ ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams with a mapping : "
+ pfams_with_mappings_counter + " ["
+ ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() ) + "%]" );
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams with a mapping to proc. or func. : "
+ pfams_with_mappings_to_bp_or_mf_counter + " ["
+ ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams with mapping to biological process: "
+ biological_process_counter + " ["
+ ( 100 * biological_process_counter / all_pfams_encountered.size() ) + "%]" );
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams with mapping to molecular function: "
+ molecular_function_counter + " ["
+ ( 100 * molecular_function_counter / all_pfams_encountered.size() ) + "%]" );
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams with mapping to cellular component: "
+ cellular_component_counter + " ["
+ ( 100 * cellular_component_counter / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Sum of Pfams encountered : " + all_pfams_encountered.size() );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Pfams without a mapping : " + pfams_without_mappings_counter
+ " [" + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Pfams without mapping to proc. or func. : "
+ pfams_without_mappings_to_bp_or_mf_counter + " ["
+ ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Pfams with a mapping : " + pfams_with_mappings_counter + " ["
+ ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Pfams with a mapping to proc. or func. : "
+ pfams_with_mappings_to_bp_or_mf_counter + " ["
+ ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
+ ( 100 * biological_process_counter / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
+ ( 100 * molecular_function_counter / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
+ ( 100 * cellular_component_counter / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.close();
}
catch ( final IOException e ) {
ForesterUtil.printWarningMessage( surfacing_old.PRG_NAME, "Failure to write: " + e );
}
}
public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
final File output_dir,
final GenomeWideCombinableDomains gwcd,
final int i,
final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
File dc_outfile_dot = new File( input_file_properties[ i ][ 0 ]
+ surfacing_old.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
if ( output_dir != null ) {
dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
}
checkForOutputFileWriteability( dc_outfile_dot );
final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
try {
final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
for( final BinaryDomainCombination bdc : binary_combinations ) {
out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
.toString() );
out_dot.write( SurfacingConstants.NL );
}
out_dot.close();
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
}
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote binary domain combination for \""
+ input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
+ input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
}
/*
* species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
*
*
*/
static public StringBuffer proteinToDomainCombinations( final Protein protein,
final String protein_id,
final String separator ) {
final StringBuffer sb = new StringBuffer();
if ( protein.getSpecies() == null ) {
throw new IllegalArgumentException( "species must not be null" );
}
if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
throw new IllegalArgumentException( "species id must not be empty" );
}
final List<Domain> domains = protein.getProteinDomains();
if ( domains.size() > 1 ) {
final Map<String, Integer> counts = new HashMap<String, Integer>();
for( final Domain domain : domains ) {
final String id = domain.getDomainId().getId();
if ( counts.containsKey( id ) ) {
counts.put( id, counts.get( id ) + 1 );
}
else {
counts.put( id, 1 );
}
}
for( int i = 1; i < domains.size(); ++i ) {
for( int j = 0; j < i; ++j ) {
Domain domain_n = domains.get( i );
Domain domain_c = domains.get( j );
if ( domain_n.getFrom() > domain_c.getFrom() ) {
domain_n = domains.get( j );
domain_c = domains.get( i );
}
sb.append( protein.getSpecies() );
sb.append( separator );
sb.append( protein_id );
sb.append( separator );
sb.append( domain_n.getDomainId().getId() );
sb.append( separator );
sb.append( domain_c.getDomainId().getId() );
sb.append( separator );
sb.append( domain_n.getPerDomainEvalue() );
sb.append( separator );
sb.append( domain_c.getPerDomainEvalue() );
sb.append( separator );
sb.append( counts.get( domain_n.getDomainId().getId() ) );
sb.append( separator );
sb.append( counts.get( domain_c.getDomainId().getId() ) );
sb.append( ForesterUtil.LINE_SEPARATOR );
}
}
}
else if ( domains.size() == 1 ) {
sb.append( protein.getSpecies() );
sb.append( separator );
sb.append( protein_id );
sb.append( separator );
sb.append( domains.get( 0 ).getDomainId().getId() );
sb.append( separator );
sb.append( separator );
sb.append( domains.get( 0 ).getPerDomainEvalue() );
sb.append( separator );
sb.append( separator );
sb.append( 1 );
sb.append( separator );
sb.append( ForesterUtil.LINE_SEPARATOR );
}
else {
sb.append( protein.getSpecies() );
sb.append( separator );
sb.append( protein_id );
sb.append( separator );
sb.append( separator );
sb.append( separator );
sb.append( separator );
sb.append( separator );
sb.append( separator );
sb.append( ForesterUtil.LINE_SEPARATOR );
}
return sb;
}
public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
final CharacterStateMatrix.GainLossStates state,
final String filename,
final String indentifier_characters_separator,
final String character_separator,
final Map<String, String> descriptions ) {
final File outfile = new File( filename );
checkForOutputFileWriteability( outfile );
final SortedSet<String> sorted_ids = new TreeSet<String>();
for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
sorted_ids.add( matrix.getIdentifier( i ) );
}
try {
final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
for( final String id : sorted_ids ) {
out.write( indentifier_characters_separator );
out.write( "#" + id );
out.write( indentifier_characters_separator );
for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
// Not nice:
// using null to indicate either UNCHANGED_PRESENT or GAIN.
if ( ( matrix.getState( id, c ) == state )
|| ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
out.write( matrix.getCharacter( c ) );
if ( ( descriptions != null ) && !descriptions.isEmpty()
&& descriptions.containsKey( matrix.getCharacter( c ) ) ) {
out.write( "\t" );
out.write( descriptions.get( matrix.getCharacter( c ) ) );
}
out.write( character_separator );
}
}
}
out.flush();
out.close();
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
}
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
}
public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
final CharacterStateMatrix.GainLossStates state,
final String filename,
final String indentifier_characters_separator,
final String character_separator,
final BinaryDomainCombination.OutputFormat bc_output_format ) {
final File outfile = new File( filename );
checkForOutputFileWriteability( outfile );
final SortedSet<String> sorted_ids = new TreeSet<String>();
for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
sorted_ids.add( matrix.getIdentifier( i ) );
}
try {
final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
for( final String id : sorted_ids ) {
out.write( indentifier_characters_separator );
out.write( "#" + id );
out.write( indentifier_characters_separator );
for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
// Not nice:
// using null to indicate either UNCHANGED_PRESENT or GAIN.
if ( ( matrix.getState( id, c ) == state )
|| ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
BinaryDomainCombination bdc = null;
try {
bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
}
catch ( final Exception e ) {
ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() );
}
out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
out.write( character_separator );
}
}
}
out.flush();
out.close();
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
}
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
}
public static void writeBinaryStatesMatrixToList( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
final Map<GoId, GoTerm> go_id_to_term_map,
final GoNameSpace go_namespace_limit,
final boolean domain_combinations,
final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
final CharacterStateMatrix.GainLossStates state,
final String filename,
final String indentifier_characters_separator,
final String character_separator,
final String title_for_html,
final String prefix_for_html,
final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
final SortedSet<String> all_pfams_encountered,
final SortedSet<String> pfams_gained_or_lost,
final String suffix_for_per_node_events_file ) {
if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
}
else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
}
else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
}
final File outfile = new File( filename );
checkForOutputFileWriteability( outfile );
final SortedSet<String> sorted_ids = new TreeSet<String>();
for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
sorted_ids.add( matrix.getIdentifier( i ) );
}
try {
final Writer out = new BufferedWriter( new FileWriter( outfile ) );
final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing_old.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
domain_combinations,
state,
filename );
Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
File per_node_go_mapped_domain_gain_loss_outfile = null;
int per_node_counter = 0;
out.write( "<html>" );
out.write( SurfacingConstants.NL );
addHtmlHead( out, title_for_html );
out.write( SurfacingConstants.NL );
out.write( "<body>" );
out.write( SurfacingConstants.NL );
out.write( "<h1>" );
out.write( SurfacingConstants.NL );
out.write( title_for_html );
out.write( SurfacingConstants.NL );
out.write( "</h1>" );
out.write( SurfacingConstants.NL );
out.write( "<table>" );
out.write( SurfacingConstants.NL );
for( final String id : sorted_ids ) {
out.write( "<tr>" );
out.write( "<td>" );
out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
writeTaxonomyLinks( out, id );
out.write( "</td>" );
out.write( "</tr>" );
out.write( SurfacingConstants.NL );
}
out.write( "</table>" );
out.write( SurfacingConstants.NL );
for( final String id : sorted_ids ) {
out.write( SurfacingConstants.NL );
out.write( "<h2>" );
out.write( "<a name=\"" + id + "\">" + id + "</a>" );
writeTaxonomyLinks( out, id );
out.write( "</h2>" );
out.write( SurfacingConstants.NL );
out.write( "<table>" );
out.write( SurfacingConstants.NL );
out.write( "<tr>" );
out.write( "<td><b>" );
out.write( "Pfam domain(s)" );
out.write( "</b></td><td><b>" );
out.write( "GO term acc" );
out.write( "</b></td><td><b>" );
out.write( "GO term" );
out.write( "</b></td><td><b>" );
out.write( "Penultimate GO term" );
out.write( "</b></td><td><b>" );
out.write( "GO namespace" );
out.write( "</b></td>" );
out.write( "</tr>" );
out.write( SurfacingConstants.NL );
out.write( "</tr>" );
out.write( SurfacingConstants.NL );
per_node_counter = 0;
if ( matrix.getNumberOfCharacters() > 0 ) {
per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+ ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
.createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
}
else {
per_node_go_mapped_domain_gain_loss_outfile = null;
per_node_go_mapped_domain_gain_loss_outfile_writer = null;
}
for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
// Not nice:
// using null to indicate either UNCHANGED_PRESENT or GAIN.
if ( ( matrix.getState( id, c ) == state )
|| ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
final String character = matrix.getCharacter( c );
String domain_0 = "";
String domain_1 = "";
if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
if ( s.length != 2 ) {
throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
+ character + "]" );
}
domain_0 = s[ 0 ];
domain_1 = s[ 1 ];
}
else {
domain_0 = character;
}
writeDomainData( domain_id_to_go_ids_map,
go_id_to_term_map,
go_namespace_limit,
out,
domain_0,
domain_1,
prefix_for_html,
character_separator,
domain_id_to_secondary_features_maps,
null );
all_pfams_encountered.add( domain_0 );
if ( pfams_gained_or_lost != null ) {
pfams_gained_or_lost.add( domain_0 );
}
if ( !ForesterUtil.isEmpty( domain_1 ) ) {
all_pfams_encountered.add( domain_1 );
if ( pfams_gained_or_lost != null ) {
pfams_gained_or_lost.add( domain_1 );
}
}
if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
domain_0,
domain_1 );
per_node_counter++;
}
}
}
if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
per_node_go_mapped_domain_gain_loss_outfile_writer.close();
if ( per_node_counter < 1 ) {
per_node_go_mapped_domain_gain_loss_outfile.delete();
}
per_node_counter = 0;
}
out.write( "</table>" );
out.write( SurfacingConstants.NL );
out.write( "<hr>" );
out.write( SurfacingConstants.NL );
} // for( final String id : sorted_ids ) {
out.write( "</body>" );
out.write( SurfacingConstants.NL );
out.write( "</html>" );
out.write( SurfacingConstants.NL );
out.flush();
out.close();
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
}
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename
+ "\"" );
}
public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
final File output_dir,
final Writer per_genome_domain_promiscuity_statistics_writer,
final GenomeWideCombinableDomains gwcd,
final int i,
final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
File dc_outfile = new File( input_file_properties[ i ][ 0 ]
+ surfacing_old.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
if ( output_dir != null ) {
dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
}
checkForOutputFileWriteability( dc_outfile );
try {
final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
out.close();
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
}
final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
try {
per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 0 ] + "\t" );
per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
if ( stats.getN() < 2 ) {
per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
}
else {
per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
.sampleStandardDeviation() )
+ "\t" );
}
per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
final SortedSet<DomainId> mpds = gwcd.getMostPromiscuosDomain();
for( final DomainId mpd : mpds ) {
per_genome_domain_promiscuity_statistics_writer.write( mpd.getId() + " " );
}
per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
}
if ( input_file_properties[ i ].length == 3 ) {
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote domain combination counts for \""
+ input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
+ input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
}
else {
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote domain combination counts for \""
+ input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
+ dc_outfile + "\"" );
}
}
private static void writeDomainData( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
final Map<GoId, GoTerm> go_id_to_term_map,
final GoNameSpace go_namespace_limit,
final Writer out,
final String domain_0,
final String domain_1,
final String prefix_for_html,
final String character_separator_for_non_html_output,
final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
final Set<GoId> all_go_ids ) throws IOException {
boolean any_go_annotation_present = false;
boolean first_has_no_go = false;
int domain_count = 2; // To distinguish between domains and binary domain combinations.
if ( ForesterUtil.isEmpty( domain_1 ) ) {
domain_count = 1;
}
// The following has a difficult to understand logic.
for( int d = 0; d < domain_count; ++d ) {
List<GoId> go_ids = null;
boolean go_annotation_present = false;
if ( d == 0 ) {
final DomainId domain_id = new DomainId( domain_0 );
if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
go_annotation_present = true;
any_go_annotation_present = true;
go_ids = domain_id_to_go_ids_map.get( domain_id );
}
else {
first_has_no_go = true;
}
}
else {
final DomainId domain_id = new DomainId( domain_1 );
if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
go_annotation_present = true;
any_go_annotation_present = true;
go_ids = domain_id_to_go_ids_map.get( domain_id );
}
}
if ( go_annotation_present ) {
boolean first = ( ( d == 0 ) || ( ( d == 1 ) && first_has_no_go ) );
for( final GoId go_id : go_ids ) {
out.write( "<tr>" );
if ( first ) {
first = false;
writeDomainIdsToHtml( out,
domain_0,
domain_1,
prefix_for_html,
domain_id_to_secondary_features_maps );
}
else {
out.write( "<td></td>" );
}
if ( !go_id_to_term_map.containsKey( go_id ) ) {
throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
}
final GoTerm go_term = go_id_to_term_map.get( go_id );
if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
final String go_id_str = go_id.getId();
out.write( "<td>" );
out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
+ "\" target=\"amigo_window\">" + go_id_str + "</a>" );
out.write( "</td><td>" );
out.write( go_term.getName() );
if ( domain_count == 2 ) {
out.write( " (" + d + ")" );
}
out.write( "</td><td>" );
out.write( top );
out.write( "</td><td>" );
out.write( "[" );
out.write( go_term.getGoNameSpace().toShortString() );
out.write( "]" );
out.write( "</td>" );
if ( all_go_ids != null ) {
all_go_ids.add( go_id );
}
}
else {
out.write( "<td>" );
out.write( "</td><td>" );
out.write( "</td><td>" );
out.write( "</td><td>" );
out.write( "</td>" );
}
out.write( "</tr>" );
out.write( SurfacingConstants.NL );
}
}
} // for( int d = 0; d < domain_count; ++d )
if ( !any_go_annotation_present ) {
out.write( "<tr>" );
writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
out.write( "<td>" );
out.write( "</td><td>" );
out.write( "</td><td>" );
out.write( "</td><td>" );
out.write( "</td>" );
out.write( "</tr>" );
out.write( SurfacingConstants.NL );
}
}
private static void writeDomainIdsToHtml( final Writer out,
final String domain_0,
final String domain_1,
final String prefix_for_detailed_html,
final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps )
throws IOException {
out.write( "<td>" );
if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
out.write( prefix_for_detailed_html );
out.write( " " );
}
out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
if ( ForesterUtil.isEmpty( domain_1 ) ) {
out.write( " <a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_LINK + domain_0
+ SurfacingConstants.GOOGLE_SCHOLAR_LIMITS + "\">[gs]</a>" );
}
if ( !ForesterUtil.isEmpty( domain_1 ) ) {
out.write( "=" );
out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_1 + "\">" + domain_1 + "</a>" );
}
else if ( ( domain_id_to_secondary_features_maps != null )
&& ( domain_id_to_secondary_features_maps.length > 0 ) ) {
out.write( " [" );
boolean first = true;
for( final Map<DomainId, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
final Set<String> sec_features = domain_id_to_secondary_features_map.get( new DomainId( domain_0 ) );
if ( ( sec_features != null ) && ( sec_features.size() > 0 ) ) {
for( final String sec_feature : sec_features ) {
if ( first ) {
first = false;
}
else {
out.write( ", " );
}
if ( SurfacingConstants.SECONDARY_FEATURES_ARE_SCOP
&& ( SurfacingConstants.SECONDARY_FEATURES_SCOP_LINK != null ) ) {
out.write( "<a href=\"" + SurfacingConstants.SECONDARY_FEATURES_SCOP_LINK + sec_feature
+ "\" target=\"scop_window\">" + sec_feature + "</a>" );
}
else {
out.write( sec_feature );
}
}
}
}
out.write( "]" );
}
out.write( "</td>" );
}
public static DescriptiveStatistics writeDomainSimilaritiesToFile( final StringBuilder html_desc,
final StringBuilder html_title,
final Writer w,
final SortedSet<DomainSimilarity> similarities,
final boolean treat_as_binary,
final List<Species> species_order,
final PrintableDomainSimilarity.PRINT_OPTION print_option,
final DomainSimilarity.DomainSimilaritySortField sort_field,
final DomainSimilarity.DomainSimilarityScoring scoring,
final boolean verbose ) throws IOException {
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
String histogram_title = null;
switch ( sort_field ) {
case ABS_MAX_COUNTS_DIFFERENCE:
if ( treat_as_binary ) {
histogram_title = "absolute counts difference:";
}
else {
histogram_title = "absolute (maximal) counts difference:";
}
break;
case MAX_COUNTS_DIFFERENCE:
if ( treat_as_binary ) {
histogram_title = "counts difference:";
}
else {
histogram_title = "(maximal) counts difference:";
}
break;
case DOMAIN_ID:
histogram_title = "score mean:";
break;
case MIN:
histogram_title = "score minimum:";
break;
case MAX:
histogram_title = "score maximum:";
break;
case MAX_DIFFERENCE:
if ( treat_as_binary ) {
histogram_title = "difference:";
}
else {
histogram_title = "(maximal) difference:";
}
break;
case MEAN:
histogram_title = "score mean:";
break;
case SD:
histogram_title = "score standard deviation:";
break;
case SPECIES_COUNT:
histogram_title = "species number:";
break;
default:
throw new AssertionError( "Unknown sort field: " + sort_field );
}
for( final DomainSimilarity similarity : similarities ) {
switch ( sort_field ) {
case ABS_MAX_COUNTS_DIFFERENCE:
stats.addValue( Math.abs( similarity.getMaximalDifferenceInCounts() ) );
break;
case MAX_COUNTS_DIFFERENCE:
stats.addValue( similarity.getMaximalDifferenceInCounts() );
break;
case DOMAIN_ID:
stats.addValue( similarity.getMeanSimilarityScore() );
break;
case MIN:
stats.addValue( similarity.getMinimalSimilarityScore() );
break;
case MAX:
stats.addValue( similarity.getMaximalSimilarityScore() );
break;
case MAX_DIFFERENCE:
stats.addValue( similarity.getMaximalDifference() );
break;
case MEAN:
stats.addValue( similarity.getMeanSimilarityScore() );
break;
case SD:
stats.addValue( similarity.getStandardDeviationOfSimilarityScore() );
break;
case SPECIES_COUNT:
stats.addValue( similarity.getSpecies().size() );
break;
default:
throw new AssertionError( "Unknown sort field: " + sort_field );
}
}
//
// final HistogramData[] hists = new HistogramData[ 1 ];
//
//
// List<HistogramDataItem> data_items = new
// ArrayList<HistogramDataItem>();
// double[] values = stats.getDataAsDoubleArray();
// for( int i = 0; i < values.length; i++ ) {
// HistogramDataItem data_item = new BasicHistogramDataItem( "", values[
// i ] );
// data_items.add( data_item );
// }
//
//
// HistogramData hd0 = new HistogramData( "name",
// data_items,
// null, 20,
// 40 );
//
//
//
//
// hists[ 0 ] = hd0;
//
// final HistogramsFrame hf = new HistogramsFrame( hists );
// hf.setVisible( true );
//
AsciiHistogram histo = null;
if ( stats.getMin() < stats.getMin() ) {
histo = new AsciiHistogram( stats, histogram_title );
}
if ( verbose ) {
if ( histo != null ) {
System.out.println( histo.toStringBuffer( 20, '|', 40, 5 ) );
}
System.out.println();
System.out.println( "N : " + stats.getN() );
System.out.println( "Min : " + stats.getMin() );
System.out.println( "Max : " + stats.getMax() );
System.out.println( "Mean : " + stats.arithmeticMean() );
if ( stats.getN() > 1 ) {
System.out.println( "SD : " + stats.sampleStandardDeviation() );
}
else {
System.out.println( "SD : n/a" );
}
System.out.println( "Median : " + stats.median() );
if ( stats.getN() > 1 ) {
System.out.println( "Pearsonian skewness : " + stats.pearsonianSkewness() );
}
else {
System.out.println( "Pearsonian skewness : n/a" );
}
}
switch ( print_option ) {
case SIMPLE_TAB_DELIMITED:
break;
case HTML:
w.write( "<html>" );
w.write( SurfacingConstants.NL );
addHtmlHead( w, "SURFACING :: " + html_title );
w.write( SurfacingConstants.NL );
w.write( "<body>" );
w.write( SurfacingConstants.NL );
w.write( html_desc.toString() );
w.write( SurfacingConstants.NL );
w.write( "<hr>" );
w.write( "<br>" );
w.write( SurfacingConstants.NL );
w.write( "<tt><pre>" );
w.write( SurfacingConstants.NL );
if ( histo != null ) {
w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
w.write( SurfacingConstants.NL );
}
w.write( "</pre></tt>" );
w.write( SurfacingConstants.NL );
w.write( "<table>" );
w.write( SurfacingConstants.NL );
w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
w.write( SurfacingConstants.NL );
w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
w.write( SurfacingConstants.NL );
w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
w.write( SurfacingConstants.NL );
w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
w.write( SurfacingConstants.NL );
if ( stats.getN() > 1 ) {
w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
}
else {
w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
}
w.write( SurfacingConstants.NL );
w.write( "<tr><td>Median: </td><td>" + stats.median() + "</td></tr>" );
w.write( SurfacingConstants.NL );
if ( stats.getN() > 1 ) {
w.write( "<tr><td>Pearsonian skewness: </td><td>" + stats.pearsonianSkewness() + "</td></tr>" );
}
else {
w.write( "<tr><td>Pearsonian skewness: </td><td>n/a</td></tr>" );
}
w.write( SurfacingConstants.NL );
w.write( "</table>" );
w.write( SurfacingConstants.NL );
w.write( "<br>" );
w.write( SurfacingConstants.NL );
w.write( "<hr>" );
w.write( SurfacingConstants.NL );
w.write( "<br>" );
w.write( SurfacingConstants.NL );
w.write( "<table>" );
w.write( SurfacingConstants.NL );
break;
}
w.write( SurfacingConstants.NL );
for( final DomainSimilarity similarity : similarities ) {
if ( ( species_order != null ) && !species_order.isEmpty() ) {
( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
}
w.write( similarity.toStringBuffer( print_option ).toString() );
w.write( SurfacingConstants.NL );
}
switch ( print_option ) {
case HTML:
w.write( SurfacingConstants.NL );
w.write( "</table>" );
w.write( SurfacingConstants.NL );
w.write( "</font>" );
w.write( SurfacingConstants.NL );
w.write( "</body>" );
w.write( SurfacingConstants.NL );
w.write( "</html>" );
w.write( SurfacingConstants.NL );
break;
}
w.flush();
w.close();
return stats;
}
private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
final String domain_0,
final String domain_1 ) throws IOException {
individual_files_writer.write( domain_0 );
individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
if ( !ForesterUtil.isEmpty( domain_1 ) ) {
individual_files_writer.write( domain_1 );
individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
}
}
public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
final String filename,
final Format format ) {
final File outfile = new File( filename );
checkForOutputFileWriteability( outfile );
try {
final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
matrix.toWriter( out, format );
out.flush();
out.close();
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
}
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
}
public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
checkForOutputFileWriteability( matrix_outfile );
try {
final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
for( final DistanceMatrix distance_matrix : matrices ) {
out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
out.write( ForesterUtil.LINE_SEPARATOR );
out.flush();
}
out.close();
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
}
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
}
private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
try {
final Writer writer = new BufferedWriter( new FileWriter( new File( outfile_name ) ) );
for( final String pfam : pfams ) {
writer.write( pfam );
writer.write( ForesterUtil.LINE_SEPARATOR );
}
writer.close();
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
+ "]" );
}
catch ( final IOException e ) {
ForesterUtil.printWarningMessage( surfacing_old.PRG_NAME, "Failure to write: " + e );
}
}
public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
final PhylogenyWriter writer = new PhylogenyWriter();
try {
writer.toPhyloXML( new File( filename ), phylogeny, 1 );
}
catch ( final IOException e ) {
ForesterUtil.printWarningMessage( surfacing_old.PRG_NAME, "failed to write phylogeny to \"" + filename
+ "\": " + e );
}
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
}
public static void writeTaxonomyLinks( final Writer writer, final String species ) throws IOException {
if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( species );
writer.write( " [" );
if ( matcher.matches() ) {
writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_LINK + species
+ "\" target=\"taxonomy_window\">uniprot</a>" );
}
else {
writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
+ "\" target=\"taxonomy_window\">eol</a>" );
writer.write( "|" );
writer.write( "<a href=\"" + SurfacingConstants.TOL_LINK + species
+ "\" target=\"taxonomy_window\">tol</a>" );
writer.write( "|" );
writer.write( "<a href=\"" + SurfacingConstants.WIKIPEDIA_LINK + species
+ "\" target=\"taxonomy_window\">wikipedia</a>" );
writer.write( "|" );
writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_LINK + species
+ "\" target=\"taxonomy_window\">gs</a>" );
}
writer.write( "]" );
}
}
private static void writeToNexus( final String outfile_name, final CharacterStateMatrix<BinaryStates> matrix ) {
if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
+ "] to nexus" );
}
final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
try {
final BufferedWriter w = new BufferedWriter( new FileWriter( outfile_name ) );
w.write( NexusConstants.NEXUS );
w.write( ForesterUtil.LINE_SEPARATOR );
my_matrix.writeNexusTaxaBlock( w );
my_matrix.writeNexusBinaryChractersBlock( w );
w.flush();
w.close();
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
}
}
private static void writeToNexus( final String outfile_name,
final CharacterStateMatrix<BinaryStates> matrix,
final Phylogeny phylogeny ) {
if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
+ "] to nexus" );
}
final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>( 1 );
phylogenies.add( phylogeny );
try {
final BufferedWriter w = new BufferedWriter( new FileWriter( outfile_name ) );
w.write( NexusConstants.NEXUS );
w.write( ForesterUtil.LINE_SEPARATOR );
my_matrix.writeNexusTaxaBlock( w );
my_matrix.writeNexusBinaryChractersBlock( w );
PhylogenyWriter.writeNexusTreesBlock( w, phylogenies );
w.flush();
w.close();
ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
}
}
private static void writeToNexus( final String outfile_name, final DomainParsimonyCalculator domain_parsimony ) {
writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAINS, domain_parsimony
.createMatrixOfDomainPresenceOrAbsence() );
writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS, domain_parsimony
.createMatrixOfBinaryDomainCombinationPresenceOrAbsence() );
}
private static void writeToNexus( final String outfile_name,
final DomainParsimonyCalculator domain_parsimony,
final Phylogeny phylogeny ) {
writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAINS, domain_parsimony
.createMatrixOfDomainPresenceOrAbsence(), phylogeny );
writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS, domain_parsimony
.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(), phylogeny );
}
}