X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fgsdi.java;h=f413ff84e79f1be7ef22eea8d83e1c09cf2307b0;hb=eb22dac14771c467104f57362e3a624d0140f897;hp=17dbf7e08f26ded6b6759017b46b0d07f0b03438;hpb=8f8bbd46b51ab6778da479b6fa2a444b46ac3a60;p=jalview.git diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java index 17dbf7e..f413ff8 100644 --- a/forester/java/src/org/forester/application/gsdi.java +++ b/forester/java/src/org/forester/application/gsdi.java @@ -26,9 +26,11 @@ package org.forester.application; import java.io.File; +import java.io.FilenameFilter; import java.io.IOException; import java.text.SimpleDateFormat; import java.util.ArrayList; +import java.util.Arrays; import java.util.Date; import java.util.List; import java.util.SortedMap; @@ -62,18 +64,22 @@ public final class gsdi { final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION = "g"; final static private String GSDIR_OPTION = "r"; final static private String MOST_PARSIMONIOUS_OPTION = "m"; + final static private String SUFFIX_FOR_DIR_OPTION = "s"; final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q"; + final static private String TRANSFER_TAXONOMY_OPTION = "t"; 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 OUTTREE_SUFFIX = "_gsdir.xml"; + final static private String LOGFILE_NAME = "00_gsdi_log.tsv"; 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_VERSION = "1.100"; + final static private String PRG_DATE = "170403"; 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"; + final static private String E_MAIL = "phyloxml@gmail.com"; + final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"; public static void main( final String args[] ) { try { @@ -91,7 +97,7 @@ public final class gsdi { catch ( final Exception e ) { ForesterUtil.fatalError( PRG_NAME, e.getMessage() ); } - if ( cla.isOptionSet( gsdi.HELP_OPTION_1 ) || cla.isOptionSet( gsdi.HELP_OPTION_2 ) ) { + if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) { System.out.println(); gsdi.print_help(); System.exit( 0 ); @@ -104,13 +110,15 @@ public final class gsdi { System.exit( -1 ); } final List allowed_options = new ArrayList(); - 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 ); + allowed_options.add( GSDIR_OPTION ); + allowed_options.add( GUESS_FORMAT_OF_SPECIES_TREE ); + allowed_options.add( MOST_PARSIMONIOUS_OPTION ); + allowed_options.add( ALLOW_STRIPPING_OF_GENE_TREE_OPTION ); + allowed_options.add( TRANSFER_TAXONOMY_OPTION ); + allowed_options.add( SUFFIX_FOR_DIR_OPTION ); final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); if ( dissallowed_options.length() > 0 ) { - ForesterUtil.fatalError( gsdi.PRG_NAME, "unknown option(s): " + dissallowed_options ); + ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options ); } execute( cla ); } @@ -119,41 +127,343 @@ public final class gsdi { } } - private static void execute( final CommandLineArguments cla ) throws IOException { + private final static void execute( final CommandLineArguments cla ) throws IOException { ALGORITHM base_algorithm = ALGORITHM.GSDI; boolean most_parsimonous_duplication_model = false; boolean allow_stripping_of_gene_tree = false; - if ( cla.isOptionSet( gsdi.GSDIR_OPTION ) ) { + if ( cla.isOptionSet( GSDIR_OPTION ) ) { base_algorithm = ALGORITHM.GSDIR; } - if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) { + if ( cla.isOptionSet( MOST_PARSIMONIOUS_OPTION ) ) { if ( base_algorithm == ALGORITHM.SDI ) { - ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" ); + ForesterUtil.fatalError( PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" ); } most_parsimonous_duplication_model = true; } - if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) { + if ( cla.isOptionSet( ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) { if ( base_algorithm == ALGORITHM.SDI ) { - ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot allow stripping of gene tree with SDI" ); + ForesterUtil.fatalError( PRG_NAME, "Cannot allow stripping of gene tree with SDI" ); } allow_stripping_of_gene_tree = true; } - Phylogeny species_tree = null; - Phylogeny gene_tree = null; + boolean transfer_taxonomy = false; + if ( cla.isOptionSet( TRANSFER_TAXONOMY_OPTION ) ) { + transfer_taxonomy = true; + } + boolean use_gene_tree_dir = false; + final String gene_tree_suffix; + if ( cla.isOptionSet( SUFFIX_FOR_DIR_OPTION ) ) { + gene_tree_suffix = cla.getOptionValue( SUFFIX_FOR_DIR_OPTION ); + use_gene_tree_dir = true; + } + else { + gene_tree_suffix = null; + } File gene_tree_file = null; File species_tree_file = null; File out_file = null; File log_file = null; - EasyWriter log_writer = null; + File out_dir = null; try { gene_tree_file = cla.getFile( 0 ); species_tree_file = cla.getFile( 1 ); - out_file = cla.getFile( 2 ); - log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX ); + if ( use_gene_tree_dir ) { + out_dir = cla.getFile( 2 ); + if ( out_dir.exists() ) { + if ( !out_dir.isDirectory() ) { + ForesterUtil + .fatalError( gsdi.PRG_NAME, + "out-directory [" + out_dir + "] already exists but is not a directory" ); + } + } + else { + final boolean success = out_dir.mkdirs(); + if ( !success ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, "could not create out-directory [" + out_dir + "]" ); + } + } + } + else { + 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() ); + ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getMessage() ); + } + if ( use_gene_tree_dir ) { + final File indir = new File( gene_tree_file.toString() ); + if ( !indir.exists() ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, "in-directory [" + indir + "] does not exist" ); + } + if ( !indir.isDirectory() ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, "in-directory [" + indir + "] is not a directory" ); + } + final String species_tree_file_name = species_tree_file.getName(); + final File gene_tree_files[] = indir.listFiles( new FilenameFilter() { + + @Override + public boolean accept( final File dir, final String name ) { + return ( ( name.endsWith( gene_tree_suffix ) ) && !( name.equals( species_tree_file_name ) ) ); + } + } ); + if ( gene_tree_files.length < 1 ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, + "in-directory [" + indir + + "] does not contain any gene tree files with suffix " + + gene_tree_suffix ); + } + executeDir( base_algorithm, + most_parsimonous_duplication_model, + allow_stripping_of_gene_tree, + transfer_taxonomy, + gene_tree_files, + species_tree_file, + out_dir ); + } + else { + execute( base_algorithm, + most_parsimonous_duplication_model, + allow_stripping_of_gene_tree, + transfer_taxonomy, + gene_tree_file, + species_tree_file, + out_file, + log_file ); + } + } + + private final static void executeDir( final ALGORITHM base_algorithm, + final boolean most_parsimonous_duplication_model, + final boolean allow_stripping_of_gene_tree, + final boolean transfer_taxonomy, + final File gene_tree_files[], + final File species_tree_file, + final File outdir ) + throws IOException { + final File log_file = new File( outdir, LOGFILE_NAME ); + if ( ForesterUtil.isWritableFile( log_file ) != null ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) ); } + EasyWriter log_writer = null; + try { + log_writer = ForesterUtil.createEasyWriter( log_file ); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() ); + } + log_writer.println( "# " + PRG_NAME ); + log_writer.println( "# Version\t" + PRG_VERSION ); + log_writer.println( "# Date\t" + PRG_DATE ); + log_writer.println( "# Forester version\t" + ForesterConstants.FORESTER_VERSION ); + log_writer.println( "# Species tree\t" + species_tree_file.getCanonicalPath() ); + if ( base_algorithm == ALGORITHM.GSDI ) { + log_writer.println( "# Algorithm\tGSDI" ); + } + else if ( base_algorithm == ALGORITHM.GSDIR ) { + log_writer.println( "# Algorithm\tGSDIR" ); + } + log_writer.println( "# Use most parsimonous duplication model\t" + most_parsimonous_duplication_model ); + log_writer.println( "# Allow stripping of gene tree nodes\t" + allow_stripping_of_gene_tree ); + log_writer.println( "# Start time\t" + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) ); + log_writer.println(); + log_writer.print( "Gene-tree file\t" ); + log_writer.print( "Gene-tree name/#\t" ); + log_writer.print( "Ext. nodes\t" ); + log_writer.print( "Speciations\t" ); + log_writer.print( "Duplications\t" ); + if ( !most_parsimonous_duplication_model ) { + log_writer.print( "Spec. or Dup.\t" ); + } + if ( allow_stripping_of_gene_tree ) { + log_writer.print( "Stripped gene-tree ext. nodes\t" ); + } + log_writer.print( "Taxonomy mapping" ); + log_writer.println(); + int counter = 0; + Arrays.sort( gene_tree_files ); + for( final File gene_tree_file : gene_tree_files ) { + String outname = gene_tree_file.getName(); + if ( outname.indexOf( "." ) > 0 ) { + outname = outname.substring( 0, outname.lastIndexOf( "." ) ); + } + outname = outname + OUTTREE_SUFFIX; + counter += executeOneTreeInDir( base_algorithm, + most_parsimonous_duplication_model, + allow_stripping_of_gene_tree, + transfer_taxonomy, + gene_tree_file, + species_tree_file, + new File( outdir, outname ), + log_writer ); + log_writer.flush(); + System.out.print( "\r" + counter ); + } + System.out.print( "\r" ); + log_writer.close(); + System.out.println( "Analyzed " + counter + " gene trees" ); + System.out.println(); + System.out.println( "Wrote log to: " + log_file.getCanonicalPath() ); + System.out.println(); + } + + private final static int executeOneTreeInDir( final ALGORITHM base_algorithm, + final boolean most_parsimonous_duplication_model, + final boolean allow_stripping_of_gene_tree, + final boolean transfer_taxonomy, + final File gene_tree_file, + final File species_tree_file, + final File out_file, + final EasyWriter log_writer ) + throws IOException { + if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) ); + } + if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) ); + } + if ( ForesterUtil.isWritableFile( out_file ) != null ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) ); + } + Phylogeny gene_trees[] = null; + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + gene_trees = factory.create( gene_tree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() ); + } + catch ( final IOException e ) { + fatalError( "error", + "failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(), + log_writer ); + } + int counter = 0; + final List out_trees = new ArrayList(); + for( final Phylogeny gene_tree : gene_trees ) { + if ( !gene_tree.isEmpty() && gene_tree.getNumberOfExternalNodes() > 1 ) { + Phylogeny species_tree = null; + try { + species_tree = SDIutil.parseSpeciesTree( gene_tree, + species_tree_file, + REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE, + true, + TAXONOMY_EXTRACTION.NO ); + } + catch ( final PhyloXmlDataFormatException e ) { + fatalError( "user error", + "failed to transfer general node name, in [" + species_tree_file + "]: " + + e.getMessage(), + log_writer ); + } + catch ( final SDIException e ) { + fatalError( "user error", e.getMessage(), 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() ) { + fatalError( "user error", + "gene tree [" + gene_tree_file + "] is not completely binary", + log_writer ); + } + if ( base_algorithm == ALGORITHM.SDI ) { + if ( !species_tree.isCompletelyBinary() ) { + fatalError( "user error", + "species tree is not completely binary, use GSDI or GSDIR instead", + log_writer ); + } + } + log_writer.print( gene_tree_file.getName() ); + log_writer.print( "\t" ); + log_writer.print( ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) ); + if ( gene_trees.length > 1 ) { + log_writer.print( ( ForesterUtil.isEmpty( gene_tree.getName() ) ? Integer.toString( counter ) + : ( ":" + Integer.toString( counter ) ) ) ); + } + log_writer.print( "\t" ); + GSDII gsdii = null; + try { + if ( base_algorithm == ALGORITHM.GSDI ) { + gsdii = new GSDI( gene_tree, + species_tree, + most_parsimonous_duplication_model, + allow_stripping_of_gene_tree, + true, + transfer_taxonomy ); + } + else if ( base_algorithm == ALGORITHM.GSDIR ) { + gsdii = new GSDIR( gene_tree, + species_tree, + allow_stripping_of_gene_tree, + true, + transfer_taxonomy ); + } + } + catch ( final SDIException e ) { + fatalError( "user error", e.getLocalizedMessage(), log_writer ); + } + catch ( final OutOfMemoryError e ) { + ForesterUtil.outOfMemoryError( e ); + } + catch ( final Exception e ) { + e.printStackTrace(); + fatalError( "unexpected error", e.toString(), log_writer ); + } + if ( base_algorithm == ALGORITHM.GSDIR ) { + final Phylogeny gt = ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTree(); + gt.setRerootable( false ); + out_trees.add( gt ); + } + else { + gene_tree.setRerootable( false ); + out_trees.add( gene_tree ); + } + log_writer.print( gene_tree.getNumberOfExternalNodes() + "\t" ); + log_writer.print( gsdii.getSpeciationsSum() + "\t" ); + if ( ( base_algorithm == ALGORITHM.GSDIR ) ) { + final GSDIR gsdir = ( GSDIR ) gsdii; + log_writer.print( gsdir.getMinDuplicationsSum() + "\t" ); + } + else if ( ( base_algorithm == ALGORITHM.GSDI ) ) { + final GSDI gsdi = ( GSDI ) gsdii; + log_writer.print( gsdi.getDuplicationsSum() + "\t" ); + if ( !most_parsimonous_duplication_model ) { + log_writer.print( gsdi.getSpeciationOrDuplicationEventsSum() + "\t" ); + } + } + if ( allow_stripping_of_gene_tree ) { + log_writer.print( gsdii.getStrippedExternalGeneTreeNodes().size() + "\t" ); + } + log_writer.print( gsdii.getTaxCompBase().toString() ); + log_writer.println(); + ++counter; + } + } + if ( counter > 0 ) { + try { + final PhylogenyWriter writer = new PhylogenyWriter(); + writer.toPhyloXML( out_file, out_trees, 0, ForesterUtil.LINE_SEPARATOR ); + } + catch ( final IOException e ) { + ForesterUtil + .fatalError( PRG_NAME, + "Failed to write to [" + out_file.getCanonicalPath() + "]: " + e.getMessage() ); + } + } + return counter; + } + + private final static void execute( final ALGORITHM base_algorithm, + final boolean most_parsimonous_duplication_model, + final boolean allow_stripping_of_gene_tree, + final boolean transfer_taxonomy, + final File gene_tree_file, + final File species_tree_file, + final File out_file, + final File log_file ) + throws IOException { if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) { ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) ); } @@ -166,15 +476,18 @@ public final class gsdi { if ( ForesterUtil.isWritableFile( log_file ) != null ) { ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) ); } + EasyWriter log_writer = null; try { log_writer = ForesterUtil.createEasyWriter( log_file ); } catch ( final IOException e ) { ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() ); } + Phylogeny species_tree = null; + Phylogeny gene_tree = null; try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ]; + gene_tree = factory.create( gene_tree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ]; } catch ( final IOException e ) { fatalError( "error", @@ -204,7 +517,7 @@ public final class gsdi { gene_tree.setRooted( true ); species_tree.setRooted( true ); if ( !gene_tree.isCompletelyBinary() ) { - fatalError( "user error", "gene tree is not completely binary", log_writer ); + fatalError( "user error", "gene tree [" + gene_tree_file + "] is not completely binary", log_writer ); } if ( base_algorithm == ALGORITHM.SDI ) { if ( !species_tree.isCompletelyBinary() ) { @@ -234,16 +547,17 @@ public final class gsdi { + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) ); System.out.println( "Species tree name : " + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) ); + System.out.println( "Transfer taxonomy : " + transfer_taxonomy ); GSDII gsdii = null; final long start_time = new Date().getTime(); try { if ( base_algorithm == ALGORITHM.GSDI ) { - System.out.println( "Algorithm : GSDI" ); - log_writer.println( "Algorithm : GSDI" ); + System.out.println( "Algorithm : GSDI" ); + log_writer.println( "Algorithm : GSDI" ); } else if ( base_algorithm == ALGORITHM.GSDIR ) { - System.out.println( "Algorithm : GSDIR" ); - log_writer.println( "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 ); @@ -255,10 +569,11 @@ public final class gsdi { species_tree, most_parsimonous_duplication_model, allow_stripping_of_gene_tree, - true ); + true, + transfer_taxonomy ); } else if ( base_algorithm == ALGORITHM.GSDIR ) { - gsdii = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, true ); + gsdii = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, true, transfer_taxonomy ); } } catch ( final SDIException e ) { @@ -280,17 +595,15 @@ public final class gsdi { + "ms" ); System.out.println( "Mapping based on : " + gsdii.getTaxCompBase() ); log_writer.println( "Mapping based on : " + gsdii.getTaxCompBase() ); - if ( ( base_algorithm == ALGORITHM.GSDIR ) ) { - final GSDIR gsdir = ( GSDIR ) gsdii; - System.out.println( "Duplications sum statistics : " + gsdir.getMinDuplicationsSum() ); - log_writer.println( "Duplications sum statistics : " + gsdir.getMinDuplicationsSum() ); - } try { final PhylogenyWriter writer = new PhylogenyWriter(); if ( base_algorithm == ALGORITHM.GSDIR ) { - writer.toPhyloXML( out_file, ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTree(), 0 ); + final Phylogeny gt = ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTree(); + gt.setRerootable( false ); + writer.toPhyloXML( out_file, gt, 0 ); } else { + gene_tree.setRerootable( false ); writer.toPhyloXML( out_file, gene_tree, 0 ); } } @@ -307,8 +620,9 @@ public final class gsdi { writer.toPhyloXML( species_tree_used_file, species_tree, 0 ); } catch ( final IOException e ) { - ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + species_tree_used_file.getCanonicalPath() - + "]: " + e.getMessage() ); + 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() ); @@ -331,8 +645,10 @@ public final class gsdi { + gsdii.getStrippedExternalGeneTreeNodes().size() ); log_writer.println( "External nodes stripped from gene tree : " + gsdii.getStrippedExternalGeneTreeNodes().size() ); - System.out.println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() ); - log_writer.println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() ); + System.out + .println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() ); + log_writer + .println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() ); System.out.println(); System.out.println( "Number of speciations : " + gsdii.getSpeciationsSum() ); log_writer.println( "Number of speciations : " + gsdii.getSpeciationsSum() ); @@ -361,7 +677,7 @@ public final class gsdi { log_writer.close(); } - private static void fatalError( final String type, final String msg, final EasyWriter log_writer ) { + private final static void fatalError( final String type, final String msg, final EasyWriter log_writer ) { try { log_writer.flush(); log_writer.println(); @@ -375,34 +691,45 @@ public final class gsdi { ForesterUtil.fatalError( gsdi.PRG_NAME, msg ); } - private static void print_help() { - System.out.println( "Usage: " + gsdi.PRG_NAME - + " [-options] " ); + private final static void print_help() { + System.out.println( "Usage: " + PRG_NAME + + " [-options] " ); System.out.println(); System.out.println( "Options:" ); - 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 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.GSDIR_OPTION - + ": to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" ); + System.out.println( " -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION + + " : to allow stripping of gene tree nodes without a matching species" ); + System.out.println( " -" + 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 potential duplications due to polytomies in the species tree" ); + System.out.println( " -" + GUESS_FORMAT_OF_SPECIES_TREE + + " : to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" ); + System.out.println( " -" + GSDIR_OPTION + + " : to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" ); + System.out.println( " -" + TRANSFER_TAXONOMY_OPTION + + " : to transfer taxonomic data from species tree to gene tree" ); + System.out.println( " -" + SUFFIX_FOR_DIR_OPTION + + "=: suffix for gene trees for analyzing entire directory of trees" ); + System.out.println(); System.out.println(); - System.out.println( "Gene tree:" ); + System.out.println( "Gene tree(s):" ); 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( " in phyloXML format (unless option -" + GUESS_FORMAT_OF_SPECIES_TREE + " is used)" ); System.out.println(); - System.out.println( "Example: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION + System.out.println( "Examples: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION + " gene_tree.xml tree_of_life.xml out.xml" ); + System.out.println( " gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION + " -" + SUFFIX_FOR_DIR_OPTION + + "=.xml" + " gene_tree_dir tree_of_life.xml out_dir" ); + System.out.println( " gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION + " -" + MOST_PARSIMONIOUS_OPTION + + " -" + GSDIR_OPTION + " -" + TRANSFER_TAXONOMY_OPTION + " -" + SUFFIX_FOR_DIR_OPTION + "=.xml" + + " gene_tree_dir tree_of_life.xml out_dir" ); System.out.println(); } - private static void printMappedNodesToLog( final EasyWriter log_writer, final GSDII gsdi ) throws IOException { + private final static void printMappedNodesToLog( final EasyWriter log_writer, final GSDII gsdi ) + throws IOException { final SortedSet ss = new TreeSet(); for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) { ss.add( n.toString() ); @@ -413,7 +740,7 @@ public final class gsdi { } } - private static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDII gsdi ) + private final static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDII gsdi ) throws IOException { final SortedMap sm = new TreeMap(); for( final PhylogenyNode n : gsdi.getStrippedExternalGeneTreeNodes() ) { @@ -437,9 +764,10 @@ public final class gsdi { } } - private static void writeToRemappedFile( final File out_file, - final SortedSet remapped, - final EasyWriter log_writer ) throws IOException { + private final 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 ) {