X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FMinimalDomainomeCalculator.java;h=0c9ca73ca250da1e43768e892fefa157e9f2c44d;hb=d605114bdf420c6cb680b02bb10ea25f09db769c;hp=9abb02a37f91cfcbadbb243004e37cc8ef8f239e;hpb=2320da44a171273ec44c0adcaf991687a4780b6e;p=jalview.git diff --git a/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java b/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java index 9abb02a..0c9ca73 100644 --- a/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java +++ b/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java @@ -19,6 +19,7 @@ import java.util.TreeSet; import org.forester.application.surfacing; import org.forester.phylogeny.Phylogeny; +import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.protein.Domain; @@ -30,12 +31,14 @@ import org.forester.util.ForesterUtil; public final class MinimalDomainomeCalculator { - static final public void calcOme( final boolean use_domain_architectures, - final Phylogeny tre, - final SortedMap> protein_lists_per_species, - final String separator, - final double ie_cutoff, - final String outfile_base ) + public final static void calc( final boolean use_domain_architectures, + final Phylogeny tre, + final int target_level, + final SortedMap> protein_lists_per_species, + final String separator, + final double ie_cutoff, + final String outfile_base, + final boolean write_protein_files ) throws IOException { final SortedMap> species_to_features_map = new TreeMap>(); if ( protein_lists_per_species == null || tre == null ) { @@ -59,8 +62,20 @@ public final class MinimalDomainomeCalculator { final BufferedWriter out_table = new BufferedWriter( new FileWriter( outfile_table ) ); out.write( "SPECIES\tCOMMON NAME\tCODE\tRANK\t#EXT NODES\tEXT NODE CODES\t#" + x + "\t" + x + "" ); out.write( ForesterUtil.LINE_SEPARATOR ); + /////////// + ////////// + SortedMap> protein_lists_per_quasi_species = null; + if ( target_level >= 1 ) { + protein_lists_per_quasi_species = makeProteinListsPerQuasiSpecies( tre, + target_level, + protein_lists_per_species ); + + } + ///////// + /////////// for( final PhylogenyNodeIterator iter = tre.iteratorPostorder(); iter.hasNext(); ) { final PhylogenyNode node = iter.next(); + final int node_level = PhylogenyMethods.calculateLevel( node ); final String species_name = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy().getScientificName() : node.getName(); final String common = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy().getCommonName() @@ -68,67 +83,126 @@ public final class MinimalDomainomeCalculator { final String tcode = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy().getTaxonomyCode() : ""; final String rank = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy().getRank() : ""; - out.write( species_name ); - if ( !ForesterUtil.isEmpty( common ) ) { - out.write( "\t" + common ); - } - else { - out.write( "\t" ); - } - if ( !ForesterUtil.isEmpty( tcode ) ) { - out.write( "\t" + tcode ); - } - else { - out.write( "\t" ); - } - if ( !ForesterUtil.isEmpty( rank ) ) { - out.write( "\t" + rank ); - } - else { - out.write( "\t" ); - } final List external_descs = node.getAllExternalDescendants(); - if ( node.isInternal() ) { - out.write( "\t" + external_descs.size() + "\t" ); - } - else { - out.write( "\t\t" ); + if ( ( target_level < 1 ) || ( node_level >= target_level ) ) { + out.write( species_name ); + if ( !ForesterUtil.isEmpty( common ) ) { + out.write( "\t" + common ); + } + else { + out.write( "\t" ); + } + if ( !ForesterUtil.isEmpty( tcode ) ) { + out.write( "\t" + tcode ); + } + else { + out.write( "\t" ); + } + if ( !ForesterUtil.isEmpty( rank ) ) { + out.write( "\t" + rank ); + } + else { + out.write( "\t" ); + } + if ( node.isInternal() ) { + out.write( "\t" + external_descs.size() + "\t" ); + } + else { + out.write( "\t\t" ); + } } final List> features_per_genome_list = new ArrayList>(); boolean first = true; - for( final PhylogenyNode external_desc : external_descs ) { - final String code = external_desc.getNodeData().getTaxonomy().getTaxonomyCode(); - if ( node.isInternal() ) { - if ( first ) { - first = false; - } - else { - out.write( ", " ); + if ( target_level >= 1 ) { + //////////// + //////////// + if ( node_level >= target_level ) { + final List given_level_descs = PhylogenyMethods + .getAllDescendantsOfGivenLevel( node, target_level ); + for( final PhylogenyNode given_level_desc : given_level_descs ) { + final String spec_name = given_level_desc.getNodeData().isHasTaxonomy() + ? given_level_desc.getNodeData().getTaxonomy().getScientificName() + : given_level_desc.getName(); + if ( node.isInternal() ) { + if ( first ) { + first = false; + } + else { + out.write( ", " ); + } + out.write( "sp_n=" + spec_name ); + } + final List proteins_per_species = protein_lists_per_quasi_species.get( spec_name ); + if ( proteins_per_species != null ) { + final SortedSet features_per_genome = new TreeSet(); + for( final Protein protein : proteins_per_species ) { + if ( use_domain_architectures ) { + final String da = protein.toDomainArchitectureString( separator, ie_cutoff ); + features_per_genome.add( da ); + } + else { + List domains = protein.getProteinDomains(); + for( final Domain domain : domains ) { + if ( ( ie_cutoff <= -1 ) || ( domain.getPerDomainEvalue() <= ie_cutoff ) ) { + features_per_genome.add( domain.getDomainId() ); + } + } + } + } + System.out.println( ">>>>>>>>>>>>>> features_per_genome.size()=" + features_per_genome.size() ); + if ( features_per_genome.size() > 0 ) { + features_per_genome_list.add( features_per_genome ); + } + else { + System.out.println( "error!" ); + System.exit( -1 ); + } + } + else { + System.out.println( "error!" ); + System.exit( -1 ); + } } - out.write( code ); } - final List proteins_per_species = protein_lists_per_species.get( new BasicSpecies( code ) ); - if ( proteins_per_species != null ) { - final SortedSet features_per_genome = new TreeSet(); - for( final Protein protein : proteins_per_species ) { - if ( use_domain_architectures ) { - final String da = protein.toDomainArchitectureString( separator, ie_cutoff ); - features_per_genome.add( da ); + /////////// + /////////// + } + else { + for( final PhylogenyNode external_desc : external_descs ) { + final String code = external_desc.getNodeData().getTaxonomy().getTaxonomyCode(); + if ( node.isInternal() ) { + if ( first ) { + first = false; } else { - List domains = protein.getProteinDomains(); - for( final Domain domain : domains ) { - if ( ( ie_cutoff <= -1 ) || ( domain.getPerDomainEvalue() <= ie_cutoff ) ) { - features_per_genome.add( domain.getDomainId() ); + out.write( ", " ); + } + out.write( code ); + } + final List proteins_per_species = protein_lists_per_species + .get( new BasicSpecies( code ) ); + if ( proteins_per_species != null ) { + final SortedSet features_per_genome = new TreeSet(); + for( final Protein protein : proteins_per_species ) { + if ( use_domain_architectures ) { + final String da = protein.toDomainArchitectureString( separator, ie_cutoff ); + features_per_genome.add( da ); + } + else { + List domains = protein.getProteinDomains(); + for( final Domain domain : domains ) { + if ( ( ie_cutoff <= -1 ) || ( domain.getPerDomainEvalue() <= ie_cutoff ) ) { + features_per_genome.add( domain.getDomainId() ); + } } } } + if ( features_per_genome.size() > 0 ) { + features_per_genome_list.add( features_per_genome ); + } } - if ( features_per_genome.size() > 0 ) { - features_per_genome_list.add( features_per_genome ); - } - } - } + } // for( final PhylogenyNode external_desc : external_descs ) + } // else if ( features_per_genome_list.size() > 0 ) { SortedSet intersection = calcIntersection( features_per_genome_list ); out.write( "\t" + intersection.size() + "\t" ); @@ -192,26 +266,80 @@ public final class MinimalDomainomeCalculator { out_table.close(); ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote minimal DAome data to : " + outfile ); ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote minimal DAome data to (as table): " + outfile_table ); - for( String f : all_features ) { + if ( write_protein_files ) { + final String protdirname; final String a; + final String b; if ( use_domain_architectures ) { - a = "DA_"; + a = "_DA"; + b = "domain architectures (DAs)"; + protdirname = "_DAS"; } else { - a = "domain_"; + a = "_domain"; + b = "domains"; + protdirname = "_DOMAINS"; + } + final File prot_dir = new File( outfile_base + protdirname ); + final boolean success = prot_dir.mkdir(); + if ( !success ) { + throw new IOException( "failed to create dir " + prot_dir ); + } + int total = 0; + final String dir = outfile_base + protdirname + "/"; + for( final String feat : all_features ) { + final File extract_outfile = new File( dir + feat + a + surfacing.SEQ_EXTRACT_SUFFIX ); + SurfacingUtil.checkForOutputFileWriteability( extract_outfile ); + final Writer proteins_file_writer = new BufferedWriter( new FileWriter( extract_outfile ) ); + final int counter = extractProteinFeatures( use_domain_architectures, + protein_lists_per_species, + feat, + proteins_file_writer, + ie_cutoff, + separator ); + if ( counter < 1 ) { + ForesterUtil.printWarningMessage( "surfacing", feat + " not present (in " + b + " extraction)" ); + } + total += counter; + proteins_file_writer.close(); + } + ForesterUtil.programMessage( "surfacing", + "Wrote " + total + " individual " + b + " from a total of " + + all_features.size() + " into: " + dir ); + } + } + + private final static SortedMap> makeProteinListsPerQuasiSpecies( final Phylogeny tre, + final int level, + final SortedMap> protein_lists_per_species ) { + final SortedMap> protein_lists_per_quasi_species = new TreeMap>(); + System.out.println( "---------------------------------" ); + System.out.println( "level=" + level ); + for( final PhylogenyNodeIterator iter = tre.iteratorPostorder(); iter.hasNext(); ) { + final PhylogenyNode node = iter.next(); + final int node_level = PhylogenyMethods.calculateLevel( node ); + if ( node_level == level ) { + System.out.println( "level=" + level ); + final List external_descs = node.getAllExternalDescendants(); + final List protein_list_per_quasi_species = new ArrayList(); + for( final PhylogenyNode external_desc : external_descs ) { + final String code = external_desc.getNodeData().getTaxonomy().getTaxonomyCode(); + final List proteins_per_species = protein_lists_per_species + .get( new BasicSpecies( code ) ); + //System.out.println( code ); + for( Protein protein : proteins_per_species ) { + protein_list_per_quasi_species.add( protein ); + } + } + final String species_name = node.getNodeData().isHasTaxonomy() + ? node.getNodeData().getTaxonomy().getScientificName() : node.getName(); + System.out.println( "species_name=" + species_name ); + protein_lists_per_quasi_species.put( species_name, protein_list_per_quasi_species ); + System.out.println( ">>>>" + protein_list_per_quasi_species.size() ); } - final File prot_dir = new File( outfile_base + "_prot" ); - prot_dir.mkdir(); - final File outt = new File( outfile_base + "_prot/" + a + f + surfacing.SEQ_EXTRACT_SUFFIX ); - final Writer proteins_file_writer = new BufferedWriter( new FileWriter( outt ) ); - extractProteinFeatures( use_domain_architectures, - protein_lists_per_species, - f, - proteins_file_writer, - ie_cutoff, - separator ); - proteins_file_writer.close(); } + + return protein_lists_per_quasi_species; } private final static SortedSet calcIntersection( final List> features_per_genome_list ) { @@ -226,13 +354,14 @@ public final class MinimalDomainomeCalculator { return my_first; } - public static void extractProteinFeatures( final boolean use_domain_architectures, - final SortedMap> protein_lists_per_species, - final String domain_id, - final Writer out, - final double ie_cutoff, - final String domain_separator ) + private final static int extractProteinFeatures( final boolean use_domain_architectures, + final SortedMap> protein_lists_per_species, + final String domain_id, + final Writer out, + final double ie_cutoff, + final String domain_separator ) throws IOException { + int counter = 0; final String separator_for_output = "\t"; for( final Species species : protein_lists_per_species.keySet() ) { final List proteins_per_species = protein_lists_per_species.get( species ); @@ -261,6 +390,7 @@ public final class MinimalDomainomeCalculator { out.write( from + "-" + to ); out.write( "/" ); out.write( SurfacingConstants.NL ); + ++counter; } } else { @@ -315,11 +445,13 @@ public final class MinimalDomainomeCalculator { out.write( protein.getAccession() ); } out.write( SurfacingConstants.NL ); + ++counter; } } } } out.flush(); + return counter; } public static void main( final String[] args ) {