X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fgsdi.java;h=eab52df09d22bdf1d1ea05a4ec5df41ee039438a;hb=6005bacbd8aecc0d320b70568a24d321a30bc85c;hp=e97b504fb40f85d2a1a26fcbb5d478dfe6a5c0c4;hpb=f95ddfc23b184985166c2838f452c20b1a2c8307;p=jalview.git diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java index e97b504..eab52df 100644 --- a/forester/java/src/org/forester/application/gsdi.java +++ b/forester/java/src/org/forester/application/gsdi.java @@ -27,110 +27,139 @@ package org.forester.application; import java.io.File; import java.io.IOException; +import java.text.SimpleDateFormat; import java.util.ArrayList; import java.util.Date; import java.util.List; - +import java.util.SortedMap; +import java.util.SortedSet; +import java.util.TreeMap; +import java.util.TreeSet; import org.forester.io.parsers.PhylogenyParser; +import org.forester.io.parsers.nhx.NHXParser; +import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException; import org.forester.io.parsers.phyloxml.PhyloXmlParser; import org.forester.io.parsers.util.ParserUtils; 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.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; import org.forester.sdi.GSDI; +import org.forester.sdi.GSDIR; import org.forester.sdi.SDI; +import org.forester.sdi.SDI.TaxonomyComparisonBase; +import org.forester.sdi.SDIException; import org.forester.sdi.SDIse; import org.forester.util.CommandLineArguments; +import org.forester.util.EasyWriter; +import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; public final class gsdi { - final static private String STRIP_OPTION = "s"; - final static private String SDI_OPTION = "b"; - final static private String MOST_PARSIMONIOUS_OPTION = "m"; - final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q"; - final static private String HELP_OPTION_1 = "help"; - final static private String HELP_OPTION_2 = "h"; - final static private String DEFAULT_OUTFILE = "gsdi_out.phylo.xml"; - final static private String PRG_NAME = "gsdi"; - final static private String PRG_VERSION = "0.5"; - final static private String PRG_DATE = "120608"; - final static private String PRG_DESC = "general speciation duplication inference"; - final static private String E_MAIL = "phylosoft@gmail.com"; - final static private String WWW = "www.phylosoft.org/forester"; + private enum BASE_ALGORITHM { + GSDIR, GSDI, SDI + } + final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true; + final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION = "g"; + final static private String SDISE_OPTION = "b"; + final static private String GSDIR_OPTION = "r"; + final static private String MOST_PARSIMONIOUS_OPTION = "m"; + final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q"; + final static private String HELP_OPTION_1 = "help"; + final static private String HELP_OPTION_2 = "h"; + final static private String SUFFIX_FOR_SPECIES_TREE_USED = "_species_tree_used.xml"; + final static private String LOGFILE_SUFFIX = "_gsdi_log.txt"; + final static private String REMAPPED_SUFFIX = "_gsdi_remapped.txt"; + final static private String PRG_NAME = "gsdi"; + final static private String PRG_VERSION = "1.000"; + final static private String PRG_DATE = "120629"; + final static private String PRG_DESC = "general speciation duplication inference"; + final static private String E_MAIL = "phylosoft@gmail.com"; + final static private String WWW = "www.phylosoft.org/forester"; public static void main( final String args[] ) { - ForesterUtil.printProgramInformation( PRG_NAME, - PRG_DESC, - PRG_VERSION, - PRG_DATE, - E_MAIL, - WWW, - ForesterUtil.getForesterLibraryInformation() ); - CommandLineArguments cla = null; try { - cla = new CommandLineArguments( args ); + ForesterUtil.printProgramInformation( PRG_NAME, + PRG_DESC, + PRG_VERSION, + PRG_DATE, + E_MAIL, + WWW, + ForesterUtil.getForesterLibraryInformation() ); + CommandLineArguments cla = null; + try { + cla = new CommandLineArguments( args ); + } + catch ( final Exception e ) { + ForesterUtil.fatalError( PRG_NAME, e.getMessage() ); + } + if ( cla.isOptionSet( gsdi.HELP_OPTION_1 ) || cla.isOptionSet( gsdi.HELP_OPTION_2 ) ) { + System.out.println(); + gsdi.print_help(); + System.exit( 0 ); + } + else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() != 3 ) ) { + System.out.println(); + System.out.println( "Wrong number of arguments." ); + System.out.println(); + gsdi.print_help(); + System.exit( -1 ); + } + final List allowed_options = new ArrayList(); + allowed_options.add( gsdi.SDISE_OPTION ); + allowed_options.add( gsdi.GSDIR_OPTION ); + allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE ); + allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION ); + allowed_options.add( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ); + final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); + if ( dissallowed_options.length() > 0 ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, "unknown option(s): " + dissallowed_options ); + } + execute( cla ); } - catch ( final Exception e ) { - ForesterUtil.fatalError( PRG_NAME, e.getMessage() ); - } - if ( cla.isOptionSet( gsdi.HELP_OPTION_1 ) || cla.isOptionSet( gsdi.HELP_OPTION_2 ) ) { - System.out.println(); - gsdi.print_help(); - System.exit( 0 ); - } - else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() < 2 ) || ( cla.getNumberOfNames() > 3 ) ) { - System.out.println(); - System.out.println( "Wrong number of arguments." ); - System.out.println(); - gsdi.print_help(); - System.exit( -1 ); - } - final List allowed_options = new ArrayList(); - allowed_options.add( gsdi.STRIP_OPTION ); - allowed_options.add( gsdi.SDI_OPTION ); - allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE ); - allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION ); - final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); - if ( dissallowed_options.length() > 0 ) { - ForesterUtil.fatalError( gsdi.PRG_NAME, "unknown option(s): " + dissallowed_options ); - } - boolean use_sdise = false; - boolean strip = false; + catch ( final IOException e ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, e.getMessage() ); + } + } + + private static void execute( final CommandLineArguments cla ) throws IOException { + BASE_ALGORITHM base_algorithm = BASE_ALGORITHM.GSDI; boolean most_parsimonous_duplication_model = false; - boolean species_tree_in_phyloxml = true; - if ( cla.isOptionSet( gsdi.STRIP_OPTION ) ) { - strip = true; + boolean allow_stripping_of_gene_tree = false; + if ( cla.isOptionSet( gsdi.GSDIR_OPTION ) ) { + base_algorithm = BASE_ALGORITHM.GSDIR; } - if ( cla.isOptionSet( gsdi.SDI_OPTION ) ) { - use_sdise = true; + else if ( cla.isOptionSet( gsdi.SDISE_OPTION ) ) { + base_algorithm = BASE_ALGORITHM.SDI; } if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) { - if ( use_sdise ) { - ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only use most parsimonious duplication mode with GSDI" ); + if ( base_algorithm == BASE_ALGORITHM.SDI ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" ); } most_parsimonous_duplication_model = true; } - if ( cla.isOptionSet( gsdi.GUESS_FORMAT_OF_SPECIES_TREE ) ) { - species_tree_in_phyloxml = false; + if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) { + if ( base_algorithm == BASE_ALGORITHM.SDI ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot allow stripping of gene tree with SDI" ); + } + allow_stripping_of_gene_tree = true; } Phylogeny species_tree = null; Phylogeny gene_tree = null; File gene_tree_file = null; File species_tree_file = null; File out_file = null; + File log_file = null; + EasyWriter log_writer = null; try { gene_tree_file = cla.getFile( 0 ); species_tree_file = cla.getFile( 1 ); - if ( cla.getNumberOfNames() == 3 ) { - out_file = cla.getFile( 2 ); - } - else { - out_file = new File( gsdi.DEFAULT_OUTFILE ); - } + out_file = cla.getFile( 2 ); + log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX ); } catch ( final IllegalArgumentException e ) { ForesterUtil.fatalError( gsdi.PRG_NAME, "error in command line: " + e.getMessage() ); @@ -144,125 +173,358 @@ public final class gsdi { if ( ForesterUtil.isWritableFile( out_file ) != null ) { ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) ); } + if ( ForesterUtil.isWritableFile( log_file ) != null ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) ); + } try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - if ( species_tree_in_phyloxml ) { - species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ]; - } - else { - final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true ); - species_tree = factory.create( species_tree_file, p )[ 0 ]; - PhylogenyMethods.transferNodeNameToField( species_tree, - PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME ); - - } + log_writer = ForesterUtil.createEasyWriter( log_file ); } catch ( final IOException e ) { - ForesterUtil.fatalError( gsdi.PRG_NAME, - "Failed to read species tree from [" + gene_tree_file + "]: " + e.getMessage() ); + ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() ); } - try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ]; } catch ( final IOException e ) { - ForesterUtil.fatalError( gsdi.PRG_NAME, - "Failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage() ); + fatalError( "ERROR", + "Failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(), + log_writer ); + } + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true ); + if ( p instanceof PhyloXmlParser ) { + species_tree = factory.create( species_tree_file, p )[ 0 ]; + } + else { + if ( REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE && ( p instanceof NHXParser ) ) { + ( ( NHXParser ) p ).setReplaceUnderscores( true ); + } + species_tree = factory.create( species_tree_file, p )[ 0 ]; + final TaxonomyComparisonBase comp_base = GSDI.determineTaxonomyComparisonBase( gene_tree ); + switch ( comp_base ) { + case SCIENTIFIC_NAME: + try { + PhylogenyMethods + .transferNodeNameToField( species_tree, + PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME, + true ); + } + catch ( final PhyloXmlDataFormatException e ) { + fatalError( "USER ERROR", "Failed to transfer general node name to scientific name, in [" + + species_tree_file + "]: " + e.getMessage(), log_writer ); + } + break; + case CODE: + try { + PhylogenyMethods + .transferNodeNameToField( species_tree, + PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE, + true ); + } + catch ( final PhyloXmlDataFormatException e ) { + fatalError( "USER ERROR", "Failed to transfer general node name to taxonomy code, in [" + + species_tree_file + "]: " + e.getMessage(), log_writer ); + } + break; + case ID: + try { + PhylogenyMethods.transferNodeNameToField( species_tree, + PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID, + true ); + } + catch ( final PhyloXmlDataFormatException e ) { + fatalError( "USER ERROR", "Failed to transfer general node name to taxonomy id, in [" + + species_tree_file + "]: " + e.getMessage(), log_writer ); + } + break; + default: + fatalError( "UNEXPECTED ERROR", "unable to determine comparison base", log_writer ); + } + } + } + catch ( final IOException e ) { + fatalError( "ERROR", + "Failed to read species tree from [" + species_tree_file + "]: " + e.getMessage(), + log_writer ); } gene_tree.setRooted( true ); species_tree.setRooted( true ); if ( !gene_tree.isCompletelyBinary() ) { - ForesterUtil.fatalError( gsdi.PRG_NAME, "gene tree (\"" + gene_tree_file + "\") is not completely binary" ); + fatalError( "user error", "gene tree is not completely binary", log_writer ); } - if ( use_sdise ) { + if ( base_algorithm == BASE_ALGORITHM.SDI ) { if ( !species_tree.isCompletelyBinary() ) { - ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree (\"" + species_tree_file - + "\") is not completely binary" ); + fatalError( "user error", + "species tree is not completely binary, use GSDI or GSDIR instead", + log_writer ); } } - // For timing. - // gene_tree = Helper.createBalancedTree( 10 ); - // species_tree = Helper.createBalancedTree( 13 ); - // species_tree = Helper.createUnbalancedTree( 1024 ); - // gene_tree = Helper.createUnbalancedTree( 8192 ); - // species_tree = gene_tree.copyTree(); - // gene_tree = species_tree.copyTree(); - // Helper.numberSpeciesInOrder( species_tree ); - // Helper.numberSpeciesInOrder( gene_tree ); - // Helper.randomizeSpecies( 1, 8192, gene_tree ); - // Helper.intervalNumberSpecies( gene_tree, 4096 ); - // Helper.numberSpeciesInDescOrder( gene_tree ); - System.out.println(); - System.out.println( "Strip species tree: " + strip ); + log_writer.println( PRG_NAME + " - " + PRG_DESC ); + log_writer.println( " version : " + PRG_VERSION ); + log_writer.println( " date : " + PRG_DATE ); + log_writer.println( " forester version: " + ForesterConstants.FORESTER_VERSION ); + log_writer.println(); + log_writer.println( "Start time : " + + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) ); + System.out.println( "Start time : " + + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) ); + log_writer.println( "Gene tree file : " + gene_tree_file.getCanonicalPath() ); + System.out.println( "Gene tree file : " + gene_tree_file.getCanonicalPath() ); + log_writer.println( "Gene tree name : " + + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) ); + System.out.println( "Gene tree name : " + + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) ); + log_writer.println( "Species tree file : " + species_tree_file.getCanonicalPath() ); + System.out.println( "Species tree file : " + species_tree_file.getCanonicalPath() ); + log_writer.println( "Species tree name : " + + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) ); + System.out.println( "Species tree name : " + + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) ); SDI sdi = null; final long start_time = new Date().getTime(); try { - if ( use_sdise ) { - System.out.println(); - System.out.println( "Using SDIse algorithm" ); - sdi = new SDIse( gene_tree, species_tree ); + if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) || ( base_algorithm == BASE_ALGORITHM.GSDIR ) ) { + if ( base_algorithm == BASE_ALGORITHM.GSDI ) { + System.out.println( "Algorithm : GSDI" ); + log_writer.println( "Algorithm : GSDI" ); + } + else if ( base_algorithm == BASE_ALGORITHM.GSDIR ) { + System.out.println( "Algorithm : GSDIR" ); + log_writer.println( "Algorithm : GSDIR" ); + } + System.out.println( "Use most parsimonous duplication model : " + most_parsimonous_duplication_model ); + System.out.println( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree ); + log_writer.println( "Use most parsimonous duplication model : " + most_parsimonous_duplication_model ); + log_writer.println( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree ); + log_writer.flush(); + if ( base_algorithm == BASE_ALGORITHM.GSDI ) { + sdi = new GSDI( gene_tree, + species_tree, + most_parsimonous_duplication_model, + allow_stripping_of_gene_tree, + true ); + } + else if ( base_algorithm == BASE_ALGORITHM.GSDIR ) { + sdi = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, 1 ); + } } else { System.out.println(); - System.out.println( "Using GSDI algorithm" ); - System.out.println(); - System.out.println( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model ); - sdi = new GSDI( gene_tree, species_tree, most_parsimonous_duplication_model, true ); + System.out.println( "Algorithm : SDI" ); + log_writer.println( "Algorithm : SDI" ); + log_writer.flush(); + sdi = new SDIse( gene_tree, species_tree ); } } + catch ( final SDIException e ) { + fatalError( "user error", e.getLocalizedMessage(), log_writer ); + } + catch ( final IOException e ) { + fatalError( "error", e.toString(), log_writer ); + } catch ( final Exception e ) { - ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); + e.printStackTrace(); + fatalError( "unexpected error", e.toString(), log_writer ); + } + System.out.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time ) + + "ms" ); + log_writer.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time ) + + "ms" ); + if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) { + final GSDI gsdi = ( GSDI ) sdi; + System.out.println( "Mapping based on : " + gsdi.getTaxCompBase() ); + log_writer.println( "Mapping based on : " + gsdi.getTaxCompBase() ); + } + if ( ( base_algorithm == BASE_ALGORITHM.GSDIR ) ) { + final GSDIR gsdir = ( GSDIR ) sdi; + System.out.println( "Mapping based on : " + gsdir.getTaxCompBase() ); + log_writer.println( "Mapping based on : " + gsdir.getTaxCompBase() ); + System.out.println( "Minimal duplications sum : " + gsdir.getMinDuplicationsSum() ); + log_writer.println( "Minimal duplications sum : " + gsdir.getMinDuplicationsSum() ); + System.out.println( "Duplications sum statistics : " + gsdir.getMinDuplicationsSum() ); + log_writer.println( "Duplications sum statistics : " + gsdir.getMinDuplicationsSum() ); } - System.out.println(); - System.out.println( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" ); try { final PhylogenyWriter writer = new PhylogenyWriter(); - writer.toPhyloXML( out_file, gene_tree, 0 ); + if ( base_algorithm == BASE_ALGORITHM.GSDIR ) { + writer.toPhyloXML( out_file, + ( ( GSDIR ) sdi ).getMinDuplicationsSumGeneTrees(), + 0, + ForesterUtil.LINE_SEPARATOR ); + } + else { + writer.toPhyloXML( out_file, gene_tree, 0 ); + } } catch ( final IOException e ) { - ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + out_file + "]: " + e.getMessage() ); + ForesterUtil.fatalError( PRG_NAME, + "Failed to write to [" + out_file.getCanonicalPath() + "]: " + e.getMessage() ); } - System.out.println(); - System.out.println( "Successfully wrote resulting gene tree to: " + out_file ); - System.out.println(); - if ( use_sdise ) { + System.out.println( "Wrote resulting gene tree to : " + out_file.getCanonicalPath() ); + log_writer.println( "Wrote resulting gene tree to : " + out_file.getCanonicalPath() ); + if ( base_algorithm == BASE_ALGORITHM.SDI ) { sdi.computeMappingCostL(); - System.out.println( "Mapping cost : " + sdi.computeMappingCostL() ); + System.out.println( "Mapping cost : " + sdi.computeMappingCostL() ); + log_writer.println( "Mapping cost : " + sdi.computeMappingCostL() ); } - System.out.println( "Number of duplications : " + sdi.getDuplicationsSum() ); - if ( !use_sdise && !most_parsimonous_duplication_model ) { - System.out.println( "Number of potential duplications: " - + ( ( GSDI ) sdi ).getSpeciationOrDuplicationEventsSum() ); + else if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) || ( base_algorithm == BASE_ALGORITHM.GSDIR ) ) { + final GSDI gsdi = ( GSDI ) sdi; + final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + + SUFFIX_FOR_SPECIES_TREE_USED ); + try { + final PhylogenyWriter writer = new PhylogenyWriter(); + writer.toPhyloXML( species_tree_used_file, gsdi.getSpeciesTree(), 0 ); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + species_tree_used_file.getCanonicalPath() + + "]: " + e.getMessage() ); + } + System.out.println( "Wrote (stripped) species tree to : " + + species_tree_used_file.getCanonicalPath() ); + log_writer.println( "Wrote (stripped) species tree to : " + + species_tree_used_file.getCanonicalPath() ); + if ( ( gsdi.getReMappedScientificNamesFromGeneTree() != null ) + && !gsdi.getReMappedScientificNamesFromGeneTree().isEmpty() ) { + System.out.println( "Number of gene tree species remapped : " + + gsdi.getReMappedScientificNamesFromGeneTree().size() ); + log_writer.println( "Number of gene tree species remapped : " + + gsdi.getReMappedScientificNamesFromGeneTree().size() ); + writeToRemappedFile( out_file, gsdi.getReMappedScientificNamesFromGeneTree(), log_writer ); + } } - if ( !use_sdise ) { - System.out.println( "Number speciations : " + ( ( GSDI ) sdi ).getSpeciationsSum() ); + System.out.println( "Number of external nodes in gene tree : " + gene_tree.getNumberOfExternalNodes() ); + log_writer.println( "Number of external nodes in gene tree : " + gene_tree.getNumberOfExternalNodes() ); + System.out.println( "Number of external nodes in species tree : " + + sdi.getSpeciesTree().getNumberOfExternalNodes() ); + log_writer.println( "Number of external nodes in species tree : " + + sdi.getSpeciesTree().getNumberOfExternalNodes() ); + if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) { + final GSDI gsdi = ( GSDI ) sdi; + final int poly = PhylogenyMethods.countNumberOfPolytomies( gsdi.getSpeciesTree() ); + System.out.println( "Number of polytomies in species tree : " + poly ); + log_writer.println( "Number of polytomies in species tree : " + poly ); + System.out.println( "External nodes stripped from gene tree : " + + gsdi.getStrippedExternalGeneTreeNodes().size() ); + log_writer.println( "External nodes stripped from gene tree : " + + gsdi.getStrippedExternalGeneTreeNodes().size() ); + System.out.println( "External nodes stripped from species tree: " + + gsdi.getStrippedSpeciesTreeNodes().size() ); + log_writer.println( "External nodes stripped from species tree: " + + gsdi.getStrippedSpeciesTreeNodes().size() ); } System.out.println(); + System.out.println( "Number of duplications : " + sdi.getDuplicationsSum() ); + log_writer.println( "Number of duplications : " + sdi.getDuplicationsSum() ); + if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) { + final GSDI gsdi = ( GSDI ) sdi; + if ( !most_parsimonous_duplication_model ) { + final int u = gsdi.getSpeciationOrDuplicationEventsSum(); + System.out.println( "Number of potential duplications : " + u ); + log_writer.println( "Number of potential duplications : " + u ); + } + System.out.println( "Number of speciations : " + gsdi.getSpeciationsSum() ); + log_writer.println( "Number of speciations : " + gsdi.getSpeciationsSum() ); + log_writer.println(); + printMappedNodesToLog( log_writer, gsdi ); + log_writer.println(); + printStrippedGeneTreeNodesToLog( log_writer, gsdi ); + } + System.out.println(); + System.out.println( "Wrote log to : " + log_file.getCanonicalPath() ); + System.out.println(); + log_writer.close(); + } + + private static void writeToRemappedFile( final File out_file, + final SortedSet remapped, + final EasyWriter log_writer ) throws IOException { + final File file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + REMAPPED_SUFFIX ); + final EasyWriter remapped_writer = ForesterUtil.createEasyWriter( file ); + for( final String s : remapped ) { + remapped_writer.println( s ); + } + remapped_writer.close(); + System.out.println( "Wrote remapped gene tree species to : " + file.getCanonicalPath() ); + log_writer.println( "Wrote remapped gene tree species to : " + file.getCanonicalPath() ); + } + + private static void printMappedNodesToLog( final EasyWriter log_writer, final GSDI gsdi ) throws IOException { + final SortedSet ss = new TreeSet(); + for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) { + ss.add( n.toString() ); + } + log_writer.println( "The following " + ss.size() + " species were used: " ); + for( final String s : ss ) { + log_writer.println( " " + s ); + } + } + + private static void fatalError( final String type, final String msg, final EasyWriter log_writer ) { + try { + log_writer.flush(); + log_writer.println(); + log_writer.print( type.toUpperCase() + ": " ); + log_writer.println( msg ); + log_writer.close(); + } + catch ( final IOException e ) { + e.printStackTrace(); + } + ForesterUtil.fatalError( gsdi.PRG_NAME, msg ); + } + + private static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDI gsdi ) + throws IOException { + final SortedMap sm = new TreeMap(); + for( final PhylogenyNode n : gsdi.getStrippedExternalGeneTreeNodes() ) { + final String s = n.toString(); + if ( sm.containsKey( s ) ) { + sm.put( s, sm.get( s ) + 1 ); + } + else { + sm.put( s, 1 ); + } + } + log_writer.println( "The following " + sm.size() + " nodes were stripped from the gene tree: " ); + for( final String s : sm.keySet() ) { + final int count = sm.get( s ); + if ( count == 1 ) { + log_writer.println( " " + s ); + } + else { + log_writer.println( " " + s + " [" + count + "]" ); + } + } } private static void print_help() { System.out.println( "Usage: " + gsdi.PRG_NAME - + " [-options] [outfile]" ); + + " [-options] " ); System.out.println(); System.out.println( "Options:" ); - System.out.println( " -" + gsdi.STRIP_OPTION + ": to strip the species tree prior to duplication inference" ); - System.out.println( " -" + gsdi.SDI_OPTION + ": to use SDI algorithm instead of GSDI algorithm" ); + System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION + + ": to allow stripping of gene tree nodes without a matching species" ); System.out.println( " -" + gsdi.MOST_PARSIMONIOUS_OPTION + ": use most parimonious duplication model for GSDI: " ); System.out.println( " assign nodes as speciations which would otherwise be assiged" ); - System.out.println( " as unknown because of polytomies in the species tree" ); - System.out.println( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + ": to allow species tree in other formats than" ); - System.out.println( " phyloXML (Newick, NHX, Nexus)" ); - System.out.println(); - System.out.println( "Species tree:" ); - System.out.println( " In phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE - + " is used), with taxonomy data in appropriate fields" ); + System.out.println( " as potential duplications due to polytomies in the species tree" ); + System.out.println( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + + ": to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" ); + System.out.println( " -" + gsdi.SDISE_OPTION + + ": to use SDIse algorithm instead of GSDI algorithm (for binary species trees)" ); + System.out.println( " -" + gsdi.GSDIR_OPTION + + ": to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" ); System.out.println(); System.out.println( "Gene tree:" ); - System.out.println( " In phyloXM format, with taxonomy and sequence data in appropriate fields" ); + System.out.println( " in phyloXM format, with taxonomy and sequence data in appropriate fields" ); + System.out.println(); + System.out.println( "Species tree:" ); + System.out.println( " in phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + " is used)" ); System.out.println(); - System.out.println( "Note -- GSDI algorithm is under development" ); + System.out.println( "Example: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION + + " gene_tree.xml tree_of_life.xml out.xml" ); System.out.println(); } }