" ); - w.write( title );

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FSurfacingUtil.java;h=e646ba4b40603d395cb35d555a05043896180e58;hb=7e567e18a5ba32035a8db4ca041023c9e862d25b;hp=cb9df26cb4350a58e1dc1eb5b5d4136c2c931d7e;hpb=d50df2f5d6b60fe01541a576de2519e047858294;p=jalview.git diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java index cb9df26..e646ba4 100644 --- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java +++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java @@ -26,6 +26,7 @@ package org.forester.surfacing; +import java.awt.Color; import java.io.BufferedWriter; import java.io.File; import java.io.FileWriter; @@ -66,6 +67,8 @@ import org.forester.go.GoNameSpace; import org.forester.go.GoTerm; import org.forester.go.PfamToGoMapping; import org.forester.io.parsers.nexus.NexusConstants; +import org.forester.io.parsers.phyloxml.PhyloXmlUtil; +import org.forester.io.parsers.util.ParserUtils; import org.forester.io.writers.PhylogenyWriter; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; @@ -74,6 +77,7 @@ import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE; import org.forester.phylogeny.data.BinaryCharacters; import org.forester.phylogeny.data.Confidence; import org.forester.phylogeny.data.Taxonomy; +import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.protein.BasicDomain; import org.forester.protein.BasicProtein; @@ -81,39 +85,42 @@ import org.forester.protein.BinaryDomainCombination; import org.forester.protein.Domain; import org.forester.protein.Protein; import org.forester.species.Species; +import org.forester.surfacing.DomainSimilarity.PRINT_OPTION; 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.CommandLineArguments; import org.forester.util.DescriptiveStatistics; import org.forester.util.ForesterUtil; +import org.forester.util.TaxonomyColors; public final class SurfacingUtil { - private final static NumberFormat FORMATTER_3 = new DecimalFormat( "0.000" ); - private static final Comparator ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator() { - - @Override - 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}$" ); + public final static Pattern PATTERN_SP_STYLE_TAXONOMY = Pattern.compile( "^[A-Z0-9]{3,5}$" ); + private final static Map _TAXCODE_HEXCOLORSTRING_MAP = new HashMap(); + private final static Map _TAXCODE_TAXGROUP_MAP = new HashMap(); + private static final Comparator ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator() { + + @Override + public int compare( final Domain d1, + final Domain d2 ) { + if ( d1.getPerDomainEvalue() < d2 + .getPerDomainEvalue() ) { + return -1; + } + else if ( d1.getPerDomainEvalue() > d2 + .getPerDomainEvalue() ) { + return 1; + } + else { + return d1.compareTo( d2 ); + } + } + }; + private final static NumberFormat FORMATTER_3 = new DecimalFormat( "0.000" ); private SurfacingUtil() { // Hidden constructor. @@ -135,35 +142,6 @@ public final class SurfacingUtil { } } - public static void addHtmlHead( final Writer w, final String title ) throws IOException { - w.write( SurfacingConstants.NL ); - w.write( "" ); - w.write( "" ); - w.write( title ); - w.write( "" ); - w.write( SurfacingConstants.NL ); - w.write( "" ); - w.write( SurfacingConstants.NL ); - w.write( "" ); - w.write( SurfacingConstants.NL ); - } - public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set similarities ) { final DescriptiveStatistics stats = new BasicDescriptiveStatistics(); for( final DomainSimilarity similarity : similarities ) { @@ -172,16 +150,6 @@ public final class SurfacingUtil { return stats; } - public static int calculateOverlap( final Domain domain, final List 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 ) ) { @@ -189,6 +157,33 @@ public final class SurfacingUtil { } } + public static void checkWriteabilityForPairwiseComparisons( final DomainSimilarity.PRINT_OPTION domain_similarity_print_option, + final String[][] input_file_properties, + final String automated_pairwise_comparison_suffix, + final File outdir ) { + for( int i = 0; i < input_file_properties.length; ++i ) { + for( int j = 0; j < i; ++j ) { + final String species_i = input_file_properties[ i ][ 1 ]; + final String species_j = input_file_properties[ j ][ 1 ]; + String pairwise_similarities_output_file_str = surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i + + "_" + species_j + automated_pairwise_comparison_suffix; + switch ( domain_similarity_print_option ) { + case HTML: + if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) { + pairwise_similarities_output_file_str += ".html"; + } + break; + } + final String error = ForesterUtil + .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir + + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) ); + if ( !ForesterUtil.isEmpty( error ) ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, error ); + } + } + } + } + public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix matrix, final BinaryDomainCombination.DomainCombinationType dc_type, final List all_binary_domains_combination_gained, @@ -203,14 +198,14 @@ public final class SurfacingUtil { || ( !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 ) ) ); + .obtainInstance( matrix.getCharacter( c ) ) ); } else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) { all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination - .createInstance( matrix.getCharacter( c ) ) ); + .obtainInstance( matrix.getCharacter( c ) ) ); } else { - all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix + all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.obtainInstance( matrix .getCharacter( c ) ) ); } } @@ -252,6 +247,103 @@ public final class SurfacingUtil { return phylogeny; } + public static StringBuilder createParametersAsString( final boolean ignore_dufs, + final double ie_value_max, + final double fs_e_value_max, + final int max_allowed_overlap, + final boolean no_engulfing_overlaps, + final File cutoff_scores_file, + final BinaryDomainCombination.DomainCombinationType dc_type ) { + final StringBuilder parameters_sb = new StringBuilder(); + parameters_sb.append( "iE-value: " + ie_value_max ); + parameters_sb.append( ", FS E-value: " + fs_e_value_max ); + if ( cutoff_scores_file != null ) { + parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file ); + } + else { + parameters_sb.append( ", Cutoff-scores-file: not-set" ); + } + if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) { + parameters_sb.append( ", Max-overlap: " + max_allowed_overlap ); + } + else { + parameters_sb.append( ", Max-overlap: not-set" ); + } + if ( no_engulfing_overlaps ) { + parameters_sb.append( ", Engulfing-overlaps: not-allowed" ); + } + else { + parameters_sb.append( ", Engulfing-overlaps: allowed" ); + } + if ( ignore_dufs ) { + parameters_sb.append( ", Ignore-dufs: true" ); + } + else { + parameters_sb.append( ", Ignore-dufs: false" ); + } + parameters_sb.append( ", DC type (if applicable): " + dc_type ); + return parameters_sb; + } + + public static void createSplitWriters( final File out_dir, + final String my_outfile, + final Map split_writers ) throws IOException { + split_writers.put( 'a', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_A.html" ) ) ); + split_writers.put( 'b', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_B.html" ) ) ); + split_writers.put( 'c', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_C.html" ) ) ); + split_writers.put( 'd', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_D.html" ) ) ); + split_writers.put( 'e', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_E.html" ) ) ); + split_writers.put( 'f', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_F.html" ) ) ); + split_writers.put( 'g', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_G.html" ) ) ); + split_writers.put( 'h', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_H.html" ) ) ); + split_writers.put( 'i', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_I.html" ) ) ); + split_writers.put( 'j', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_J.html" ) ) ); + split_writers.put( 'k', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_K.html" ) ) ); + split_writers.put( 'l', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_L.html" ) ) ); + split_writers.put( 'm', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_M.html" ) ) ); + split_writers.put( 'n', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_N.html" ) ) ); + split_writers.put( 'o', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_O.html" ) ) ); + split_writers.put( 'p', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_P.html" ) ) ); + split_writers.put( 'q', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_Q.html" ) ) ); + split_writers.put( 'r', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_R.html" ) ) ); + split_writers.put( 's', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_S.html" ) ) ); + split_writers.put( 't', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_T.html" ) ) ); + split_writers.put( 'u', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_U.html" ) ) ); + split_writers.put( 'v', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_V.html" ) ) ); + split_writers.put( 'w', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_W.html" ) ) ); + split_writers.put( 'x', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_X.html" ) ) ); + split_writers.put( 'y', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_Y.html" ) ) ); + split_writers.put( 'z', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_Z.html" ) ) ); + split_writers.put( '0', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_0.html" ) ) ); + } + public static Map createTaxCodeToIdMap( final Phylogeny phy ) { final Map m = new HashMap(); for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) { @@ -285,20 +377,11 @@ public final class SurfacingUtil { } public static void decoratePrintableDomainSimilarities( final SortedSet domain_similarities, - final Detailedness detailedness, - final GoAnnotationOutput go_annotation_output, - final Map 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" ); - } + final Detailedness detailedness ) { for( final DomainSimilarity domain_similarity : domain_similarities ) { - if ( domain_similarity instanceof PrintableDomainSimilarity ) { - final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity; + if ( domain_similarity instanceof DomainSimilarity ) { + final DomainSimilarity printable_domain_similarity = 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 ); } } } @@ -461,10 +544,6 @@ public final class SurfacingUtil { 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 ); @@ -498,23 +577,98 @@ public final class SurfacingUtil { } } out.close(); - // final List histogram_datas = new ArrayList(); - // 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(); } /** + * Warning: This side-effects 'all_bin_domain_combinations_encountered'! + * + * + * @param output_file + * @param all_bin_domain_combinations_changed + * @param sum_of_all_domains_encountered + * @param all_bin_domain_combinations_encountered + * @param is_gains_analysis + * @param protein_length_stats_by_dc + * @throws IOException + */ + public static void executeFitchGainsAnalysis( final File output_file, + final List all_bin_domain_combinations_changed, + final int sum_of_all_domains_encountered, + final SortedSet all_bin_domain_combinations_encountered, + final boolean is_gains_analysis ) throws IOException { + checkForOutputFileWriteability( output_file ); + final Writer out = ForesterUtil.createBufferedWriter( output_file ); + final SortedMap bdc_to_counts = ForesterUtil + .listToSortedCountsMap( all_bin_domain_combinations_changed ); + final SortedSet all_domains_in_combination_changed_more_than_once = new TreeSet(); + final SortedSet all_domains_in_combination_changed_only_once = new TreeSet(); + int above_one = 0; + int one = 0; + for( final Object bdc_object : bdc_to_counts.keySet() ) { + final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object; + final int count = bdc_to_counts.get( bdc_object ); + if ( count < 1 ) { + ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "count < 1 " ); + } + out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR ); + if ( count > 1 ) { + all_domains_in_combination_changed_more_than_once.add( bdc.getId0() ); + all_domains_in_combination_changed_more_than_once.add( bdc.getId1() ); + above_one++; + } + else if ( count == 1 ) { + all_domains_in_combination_changed_only_once.add( bdc.getId0() ); + all_domains_in_combination_changed_only_once.add( bdc.getId1() ); + one++; + } + } + final int all = all_bin_domain_combinations_encountered.size(); + int never_lost = -1; + if ( !is_gains_analysis ) { + all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed ); + never_lost = all_bin_domain_combinations_encountered.size(); + for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) { + out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR ); + } + } + if ( is_gains_analysis ) { + out.write( "Sum of all distinct domain combinations appearing once : " + one + + ForesterUtil.LINE_SEPARATOR ); + out.write( "Sum of all distinct domain combinations appearing more than once : " + above_one + + ForesterUtil.LINE_SEPARATOR ); + out.write( "Sum of all distinct domains in combinations apppearing only once : " + + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR ); + out.write( "Sum of all distinct domains in combinations apppearing more than once: " + + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR ); + } + else { + out.write( "Sum of all distinct domain combinations never lost : " + never_lost + + ForesterUtil.LINE_SEPARATOR ); + out.write( "Sum of all distinct domain combinations lost once : " + one + + ForesterUtil.LINE_SEPARATOR ); + out.write( "Sum of all distinct domain combinations lost more than once : " + above_one + + ForesterUtil.LINE_SEPARATOR ); + out.write( "Sum of all distinct domains in combinations lost only once : " + + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR ); + out.write( "Sum of all distinct domains in combinations lost more than once: " + + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR ); + } + out.write( "All binary combinations : " + all + + ForesterUtil.LINE_SEPARATOR ); + out.write( "All domains : " + + sum_of_all_domains_encountered ); + out.close(); + ForesterUtil.programMessage( surfacing.PRG_NAME, + "Wrote fitch domain combination dynamics counts analysis to \"" + output_file + + "\"" ); + } + + /** * * @param all_binary_domains_combination_lost_fitch * @param use_last_in_fitch_parsimony + * @param perform_dc_fich * @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. @@ -539,7 +693,8 @@ public final class SurfacingUtil { final Map domain_length_stats_by_domain, final Map tax_code_to_id_map, final boolean write_to_nexus, - final boolean use_last_in_fitch_parsimony ) { + final boolean use_last_in_fitch_parsimony, + final boolean perform_dc_fich ) { final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR; final String date_time = ForesterUtil.getCurrentDateTime(); final SortedSet all_pfams_encountered = new TreeSet(); @@ -642,7 +797,7 @@ public final class SurfacingUtil { e.printStackTrace(); ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() ); } - if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) { + if ( perform_dc_fich && ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) ) { // FITCH DOMAIN COMBINATIONS // ------------------------- local_phylogeny_l = phylogeny.copy(); @@ -856,6 +1011,60 @@ public final class SurfacingUtil { + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null ); } + public static void executePlusMinusAnalysis( final File output_file, + final List plus_minus_analysis_high_copy_base, + final List plus_minus_analysis_high_copy_target, + final List plus_minus_analysis_low_copy, + final List gwcd_list, + final SortedMap> protein_lists_per_species, + final Map> domain_id_to_go_ids_map, + final Map go_id_to_term_map, + final List

N:	" + stats.getN() + "
Min:	" + stats.getMin() + "
Max:	" + stats.getMax() + "
Mean:	" + stats.arithmeticMean() + "
SD:	" + stats.sampleStandardDeviation() + "
SD:	n/a
Median:	" + stats.median() + "
Pearsonian skewness:	" + stats.pearsonianSkewness() + "
Pearsonian skewness:	n/a

N:	" + stats.getN() + "
Min:	" + stats.getMin() + "
Max:	" + stats.getMax() + "
Mean:	" + stats.arithmeticMean() + "
SD:	" + stats.sampleStandardDeviation() + "
SD:	n/a