X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FSurfacingUtil.java;h=abcd31f67e309e1a5547e289d0bb1d6e00c33cdf;hb=3491e0d3c56167d6f6e8f291572e40367efd7fca;hp=974409d614eb201246c6c7a4f29560efaf492831;hpb=07d2b6864846c6c95ec1d4f1b083c248ffbcc591;p=jalview.git diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java index 974409d..abcd31f 100644 --- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java +++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; @@ -39,6 +39,7 @@ import java.util.Collections; import java.util.Comparator; import java.util.HashMap; import java.util.HashSet; +import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Map.Entry; @@ -58,6 +59,7 @@ 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.BasicSymmetricalDistanceMatrix; import org.forester.evoinference.matrix.distance.DistanceMatrix; import org.forester.go.GoId; import org.forester.go.GoNameSpace; @@ -68,7 +70,7 @@ 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.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE; +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.iterators.PhylogenyNodeIterator; @@ -119,6 +121,75 @@ public final class SurfacingUtil { // Hidden constructor. } + public static void performDomainArchitectureAnalysis( final SortedMap> domain_architecutures, + final SortedMap domain_architecuture_counts, + final int min_count, + final File da_counts_outfile, + final File unique_da_outfile ) { + checkForOutputFileWriteability( da_counts_outfile ); + checkForOutputFileWriteability( unique_da_outfile ); + try { + final BufferedWriter da_counts_out = new BufferedWriter( new FileWriter( da_counts_outfile ) ); + final BufferedWriter unique_da_out = new BufferedWriter( new FileWriter( unique_da_outfile ) ); + final Iterator> it = domain_architecuture_counts.entrySet().iterator(); + while ( it.hasNext() ) { + final Map.Entry e = it.next(); + final String da = e.getKey(); + final int count = e.getValue(); + if ( count >= min_count ) { + da_counts_out.write( da ); + da_counts_out.write( "\t" ); + da_counts_out.write( String.valueOf( count ) ); + da_counts_out.write( ForesterUtil.LINE_SEPARATOR ); + } + if ( count == 1 ) { + final Iterator>> it2 = domain_architecutures.entrySet().iterator(); + while ( it2.hasNext() ) { + final Map.Entry> e2 = it2.next(); + final String genome = e2.getKey(); + final Set das = e2.getValue(); + if ( das.contains( da ) ) { + unique_da_out.write( genome ); + unique_da_out.write( "\t" ); + unique_da_out.write( da ); + unique_da_out.write( ForesterUtil.LINE_SEPARATOR ); + } + } + } + } + unique_da_out.close(); + da_counts_out.close(); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() ); + } + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + da_counts_outfile + "\"" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + unique_da_outfile + "\"" ); + // + } + + public static int storeDomainArchitectures( final String genome, + final SortedMap> domain_architecutures, + final List protein_list, + final Map distinct_domain_architecuture_counts ) { + final Set da = new HashSet(); + domain_architecutures.put( genome, da ); + for( final Protein protein : protein_list ) { + final String da_str = ( ( BasicProtein ) protein ).toDomainArchitectureString( "~", 3, "=" ); + if ( !da.contains( da_str ) ) { + if ( !distinct_domain_architecuture_counts.containsKey( da_str ) ) { + distinct_domain_architecuture_counts.put( da_str, 1 ); + } + else { + distinct_domain_architecuture_counts.put( da_str, + distinct_domain_architecuture_counts.get( da_str ) + 1 ); + } + da.add( da_str ); + } + } + return da.size(); + } + public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome, final SortedSet binary_domain_combinations ) { final SortedMap all_cd = genome.getAllCombinableDomainsIds(); @@ -238,8 +309,10 @@ public final class SurfacingUtil { final DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics(); final DescriptiveStatistics gained_multiple_times_lengths_stats = new BasicDescriptiveStatistics(); final DescriptiveStatistics gained_multiple_times_domain_count_stats = new BasicDescriptiveStatistics(); - final DescriptiveStatistics gained_multiple_times_domain_length_stats = new BasicDescriptiveStatistics(); - final DescriptiveStatistics gained_once_domain_length_stats = new BasicDescriptiveStatistics(); + long gained_multiple_times_domain_length_sum = 0; + long gained_once_domain_length_sum = 0; + long gained_multiple_times_domain_length_count = 0; + long gained_once_domain_length_count = 0; for( final String dc : dcs ) { final int count = dc_gain_counts.get( dc ); if ( histogram.containsKey( count ) ) { @@ -286,15 +359,13 @@ public final class SurfacingUtil { more_than_once.add( dc ); if ( protein_length_stats_by_dc != null ) { final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc ); - final double[] a = s.getDataAsDoubleArray(); - for( final double element : a ) { + for( final double element : s.getData() ) { gained_multiple_times_lengths_stats.addValue( element ); } } if ( domain_number_stats_by_dc != null ) { final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc ); - final double[] a = s.getDataAsDoubleArray(); - for( final double element : a ) { + for( final double element : s.getData() ) { gained_multiple_times_domain_count_stats.addValue( element ); } } @@ -302,28 +373,26 @@ public final class SurfacingUtil { final String[] ds = dc.split( "=" ); final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] ); final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] ); - final double[] a0 = s0.getDataAsDoubleArray(); - final double[] a1 = s1.getDataAsDoubleArray(); - for( final double element : a0 ) { - gained_multiple_times_domain_length_stats.addValue( element ); + for( final double element : s0.getData() ) { + gained_multiple_times_domain_length_sum += element; + ++gained_multiple_times_domain_length_count; } - for( final double element : a1 ) { - gained_multiple_times_domain_length_stats.addValue( element ); + for( final double element : s1.getData() ) { + gained_multiple_times_domain_length_sum += element; + ++gained_multiple_times_domain_length_count; } } } else { if ( protein_length_stats_by_dc != null ) { final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc ); - final double[] a = s.getDataAsDoubleArray(); - for( final double element : a ) { + for( final double element : s.getData() ) { gained_once_lengths_stats.addValue( element ); } } if ( domain_number_stats_by_dc != null ) { final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc ); - final double[] a = s.getDataAsDoubleArray(); - for( final double element : a ) { + for( final double element : s.getData() ) { gained_once_domain_count_stats.addValue( element ); } } @@ -331,13 +400,13 @@ public final class SurfacingUtil { final String[] ds = dc.split( "=" ); final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] ); final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] ); - final double[] a0 = s0.getDataAsDoubleArray(); - final double[] a1 = s1.getDataAsDoubleArray(); - for( final double element : a0 ) { - gained_once_domain_length_stats.addValue( element ); + for( final double element : s0.getData() ) { + gained_once_domain_length_sum += element; + ++gained_once_domain_length_count; } - for( final double element : a1 ) { - gained_once_domain_length_stats.addValue( element ); + for( final double element : s1.getData() ) { + gained_once_domain_length_sum += element; + ++gained_once_domain_length_count; } } } @@ -373,10 +442,9 @@ public final class SurfacingUtil { nodes.add( n ); } } - for( int i = 0; i < nodes.size() - 1; ++i ) { + for( int i = 0; i < ( nodes.size() - 1 ); ++i ) { for( int j = i + 1; j < nodes.size(); ++j ) { - final PhylogenyNode lca = PhylogenyMethods.getInstance().obtainLCA( nodes.get( i ), - nodes.get( j ) ); + final PhylogenyNode lca = PhylogenyMethods.calculateLCA( nodes.get( i ), nodes.get( j ) ); String rank = "unknown"; if ( lca.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) { @@ -409,7 +477,7 @@ public final class SurfacingUtil { out_for_rank_counts.close(); out_for_ancestor_species_counts.close(); if ( !ForesterUtil.isEmpty( outfilename_for_protein_stats ) - && ( ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) { + && ( ( domain_length_stats_by_domain != null ) || ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) { final BufferedWriter w = new BufferedWriter( new FileWriter( outfilename_for_protein_stats ) ); w.write( "Domain Lengths: " ); w.write( "\n" ); @@ -455,12 +523,17 @@ public final class SurfacingUtil { w.write( "\n" ); w.write( "Gained once, domain lengths:" ); w.write( "\n" ); - w.write( gained_once_domain_length_stats.toString() ); + w.write( "N: " + gained_once_domain_length_count ); + w.write( "\n" ); + w.write( "Avg: " + ( ( double ) gained_once_domain_length_sum / gained_once_domain_length_count ) ); w.write( "\n" ); w.write( "\n" ); w.write( "Gained multiple times, domain lengths:" ); w.write( "\n" ); - w.write( gained_multiple_times_domain_length_stats.toString() ); + w.write( "N: " + gained_multiple_times_domain_length_count ); + w.write( "\n" ); + w.write( "Avg: " + + ( ( double ) gained_multiple_times_domain_length_sum / gained_multiple_times_domain_length_count ) ); w.write( "\n" ); w.write( "\n" ); w.write( "\n" ); @@ -624,7 +697,7 @@ public final class SurfacingUtil { public static Map> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file ) throws IOException { - final BasicTable primary_table = BasicTableParser.parse( secondary_features_map_file, "\t" ); + final BasicTable primary_table = BasicTableParser.parse( secondary_features_map_file, '\t' ); final Map> map = new TreeMap>(); for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) { final DomainId domain_id = new DomainId( primary_table.getValue( 0, r ) ); @@ -639,7 +712,7 @@ public final class SurfacingUtil { 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 ); + final Phylogeny phylogeny = nj.execute( ( BasicSymmetricalDistanceMatrix ) distance ); phylogeny.setName( nj_tree_outfile.getName() ); writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() ); return phylogeny; @@ -1181,23 +1254,61 @@ public final class SurfacingUtil { final DomainId domain_id, final Writer out, final String separator, - final String limit_to_species ) throws IOException { + final String limit_to_species, + final double domain_e_cutoff ) throws IOException { + System.out.println( "Per domain E-value: " + domain_e_cutoff ); for( final Species species : protein_lists_per_species.keySet() ) { + System.out.println( species + ":" ); for( final Protein protein : protein_lists_per_species.get( species ) ) { if ( ForesterUtil.isEmpty( limit_to_species ) || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) { final List 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( domain_id.toString() ); + out.write( separator ); + int prev_to = -1; + for( final Domain domain : domains ) { + if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) { + out.write( "/" ); + out.write( domain.getFrom() + "-" + domain.getTo() ); + if ( prev_to >= 0 ) { + final int l = domain.getFrom() - prev_to; + System.out.println( l ); + } + prev_to = domain.getTo(); + } + } + out.write( "/" ); out.write( separator ); + final List domain_list = new ArrayList(); + for( final Domain domain : protein.getProteinDomains() ) { + if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) { + domain_list.add( domain ); + } + } + final Domain domain_ary[] = new Domain[ domain_list.size() ]; + for( int i = 0; i < domain_list.size(); ++i ) { + domain_ary[ i ] = domain_list.get( i ); + } + Arrays.sort( domain_ary, new DomainComparator( true ) ); + out.write( "{" ); + boolean first = true; + for( final Domain domain : domain_ary ) { + if ( first ) { + first = false; + } + else { + out.write( "," ); + } + out.write( domain.getDomainId().toString() ); + out.write( ":" + domain.getFrom() + "-" + domain.getTo() ); + out.write( ":" + domain.getPerDomainEvalue() ); + } + out.write( "}" ); if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription() .equals( SurfacingConstants.NONE ) ) ) { out.write( protein.getDescription() ); @@ -1580,58 +1691,50 @@ public final class SurfacingUtil { + all_pfams_encountered.size() ); ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping : " + pfams_without_mappings_counter + " [" - + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" ); + + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" ); ForesterUtil.programMessage( surfacing.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.PRG_NAME, - "Pfams with a mapping : " + pfams_with_mappings_counter - + " [" - + ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() ) - + "%]" ); + + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping : " + + pfams_with_mappings_counter + " [" + + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" ); ForesterUtil.programMessage( surfacing.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.PRG_NAME, - "Pfams with mapping to biological process: " + biological_process_counter - + " [" - + ( 100 * biological_process_counter / all_pfams_encountered.size() ) - + "%]" ); - ForesterUtil.programMessage( surfacing.PRG_NAME, - "Pfams with mapping to molecular function: " + molecular_function_counter - + " [" - + ( 100 * molecular_function_counter / all_pfams_encountered.size() ) - + "%]" ); - ForesterUtil.programMessage( surfacing.PRG_NAME, - "Pfams with mapping to cellular component: " + cellular_component_counter - + " [" - + ( 100 * cellular_component_counter / all_pfams_encountered.size() ) - + "%]" ); + + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to biological process: " + + biological_process_counter + " [" + + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to molecular function: " + + molecular_function_counter + " [" + + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" ); + ForesterUtil.programMessage( surfacing.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() ) + "%]" ); + + " [" + ( ( 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() ) + "%]" ); + + ( ( 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() ) + "%]" ); + + ( ( 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() ) + "%]" ); + + ( ( 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() ) + "%]" ); + + ( ( 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() ) + "%]" ); + + ( ( 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() ) + "%]" ); + + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" ); summary_writer.write( ForesterUtil.LINE_SEPARATOR ); summary_writer.close(); } @@ -2588,4 +2691,24 @@ public final class SurfacingUtil { e.printStackTrace(); } } + + final static class DomainComparator implements Comparator { + + final private boolean _ascending; + + public DomainComparator( final boolean ascending ) { + _ascending = ascending; + } + + @Override + public final int compare( final Domain d0, final Domain d1 ) { + if ( d0.getFrom() < d1.getFrom() ) { + return _ascending ? -1 : 1; + } + else if ( d0.getFrom() > d1.getFrom() ) { + return _ascending ? 1 : -1; + } + return 0; + } + } }