+++ /dev/null
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org
-
-package org.forester.application;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-
-import org.forester.io.parsers.PhylogenyParser;
-import org.forester.io.parsers.phyloxml.PhyloXmlParser;
-import org.forester.io.writers.PhylogenyWriter;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.sdi.SDIR;
-import org.forester.util.CommandLineArguments;
-import org.forester.util.ForesterUtil;
-
-public class sdi_r {
-
- final static private String HELP_OPTION_1 = "help";
- final static private String HELP_OPTION_2 = "h";
- final static private String MIN_MAPPING_COST_OPTION = "ml";
- final static private String MIN_DUPS_OPTION = "md";
- final static private String MIN_HEIGHT_OPTION = "mh";
- final static private String PRG_NAME = "sdi_r";
- final static private String PRG_VERSION = "1.11";
- final static private String PRG_DATE = "2009.06.19";
- final static private String E_MAIL = "czmasek@burnham.org";
- final static private String WWW = "www.phylosoft.org";
- // How many resulting trees "main" should return/display.
- private final static int TREES_TO_RETURN = 5;
-
- public static void main( final String args[] ) {
- ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
- CommandLineArguments cla = null;
- try {
- cla = new CommandLineArguments( args );
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
- }
- if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
- printHelp();
- System.exit( 0 );
- }
- if ( ( args.length < 3 ) || ( cla.getNumberOfNames() != 2 ) ) {
- System.out.println();
- System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" );
- System.out.println();
- printHelp();
- System.exit( -1 );
- }
- final List<String> allowed_options = new ArrayList<String>();
- allowed_options.add( MIN_MAPPING_COST_OPTION );
- allowed_options.add( MIN_DUPS_OPTION );
- allowed_options.add( MIN_HEIGHT_OPTION );
- final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
- if ( dissallowed_options.length() > 0 ) {
- ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
- }
- final File outfile = new File( "sdir_outfile.xml" );
- if ( outfile.exists() ) {
- ForesterUtil.fatalError( PRG_NAME, "outfile \"" + outfile + "\" already exists" );
- }
- final File gene_tree_file = cla.getFile( 0 );
- final File species_tree_file = cla.getFile( 1 );
- boolean minimize_cost = false;
- if ( cla.isOptionSet( MIN_MAPPING_COST_OPTION ) ) {
- minimize_cost = true;
- }
- boolean minimize_sum_of_dup = false;
- if ( cla.isOptionSet( MIN_DUPS_OPTION ) ) {
- minimize_sum_of_dup = true;
- }
- boolean minimize_height = false;
- if ( cla.isOptionSet( MIN_HEIGHT_OPTION ) ) {
- minimize_height = true;
- }
- int r = 0;
- Phylogeny[] gene_trees = null;
- Phylogeny species_tree = null;
- if ( minimize_cost && minimize_sum_of_dup ) {
- minimize_sum_of_dup = false;
- }
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- try {
- final PhylogenyParser pp = new PhyloXmlParser();
- species_tree = factory.create( species_tree_file, pp )[ 0 ];
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME,
- "failed to read species tree [" + species_tree_file + "]: "
- + e.getLocalizedMessage() );
- }
- if ( !species_tree.isRooted() ) {
- ForesterUtil.fatalError( PRG_NAME, "species tree [" + species_tree_file + "] is not rooted" );
- }
- try {
- final PhylogenyParser pp = new PhyloXmlParser();
- gene_trees = factory.create( gene_tree_file, pp );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME,
- "failed to read gene trees [" + gene_tree_file + "]: " + e.getLocalizedMessage() );
- }
- // Removes from gene_tree all species not found in species_tree.
- int gene_tree_counter = 0;
- final List<Phylogeny> all_result_trees = new ArrayList<Phylogeny>();
- for( final Phylogeny gene_tree : gene_trees ) {
- r = PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gene_tree ).size();
- ForesterUtil.programMessage( PRG_NAME, "Removed " + r + " external nodes from gene tree" );
- final SDIR sdiunrooted = new SDIR();
- final long start_time = new Date().getTime();
- Phylogeny[] result_trees = null;
- try {
- result_trees = sdiunrooted.infer( gene_tree,
- species_tree,
- minimize_cost,
- minimize_sum_of_dup,
- minimize_height,
- true,
- sdi_r.TREES_TO_RETURN );
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
- }
- final long time_req = new Date().getTime() - start_time;
- if ( minimize_cost ) {
- ForesterUtil.programMessage( PRG_NAME, "Rooted by minimizing mapping cost L" );
- if ( minimize_height ) {
- ForesterUtil.programMessage( PRG_NAME,
- "Selected tree(s) with minimal height out of resulting trees" );
- }
- ForesterUtil.programMessage( PRG_NAME, "Number differently rooted trees minimizing criterion : "
- + sdiunrooted.getCount() );
- ForesterUtil.programMessage( PRG_NAME, "Minimal cost : "
- + sdiunrooted.getMinimalMappingCost() );
- ForesterUtil.programMessage( PRG_NAME, "Minimal duplications : "
- + sdiunrooted.getMinimalDuplications() );
- if ( minimize_height ) {
- ForesterUtil.programMessage( PRG_NAME, "Phylogeny height : "
- + ForesterUtil.FORMATTER_06.format( sdiunrooted.getMinimalTreeHeight() ) );
- ForesterUtil.programMessage( PRG_NAME, "Difference in subtree heights : "
- + ForesterUtil.FORMATTER_06.format( sdiunrooted.getMinimalDiffInSubTreeHeights() ) );
- }
- }
- else if ( minimize_sum_of_dup ) {
- ForesterUtil.programMessage( PRG_NAME, "Rooted by minimizing sum of duplications" );
- if ( minimize_height ) {
- ForesterUtil.programMessage( PRG_NAME,
- "Selected tree(s) with minimal height out of resulting trees" );
- }
- ForesterUtil.programMessage( PRG_NAME, "Number differently rooted trees minimizing criterion : "
- + sdiunrooted.getCount() );
- ForesterUtil.programMessage( PRG_NAME, "Minimal duplications : "
- + sdiunrooted.getMinimalDuplications() );
- if ( minimize_height ) {
- ForesterUtil.programMessage( PRG_NAME,
- "Phylogeny height : "
- + ForesterUtil.FORMATTER_06.format( sdiunrooted
- .getMinimalTreeHeight() ) );
- ForesterUtil.programMessage( PRG_NAME,
- "Difference in subtree heights : "
- + ForesterUtil.FORMATTER_06.format( sdiunrooted
- .getMinimalDiffInSubTreeHeights() ) );
- }
- }
- else if ( minimize_height ) {
- ForesterUtil.programMessage( PRG_NAME, "Rooted by minimizing tree height (midpoint rooting)." );
- ForesterUtil.programMessage( PRG_NAME, "Minimal tree height : "
- + ForesterUtil.FORMATTER_06.format( sdiunrooted.getMinimalTreeHeight() ) );
- ForesterUtil.programMessage( PRG_NAME, "Minimal difference in subtree heights: "
- + ForesterUtil.FORMATTER_06.format( sdiunrooted.getMinimalDiffInSubTreeHeights() ) );
- ForesterUtil.programMessage( PRG_NAME,
- "Duplications in midpoint rooted tree : "
- + sdiunrooted.getMinimalDuplications() );
- }
- else {
- ForesterUtil.programMessage( PRG_NAME, "No (re) rooting was performed." );
- ForesterUtil.programMessage( PRG_NAME, "Duplications in tree: " + sdiunrooted.getMinimalDuplications() );
- }
- ForesterUtil.programMessage( PRG_NAME, "Time requirement (minus I/O) : "
- + time_req + "ms" );
- for( int i = 0; i < result_trees.length; ++i ) {
- final String name = result_trees[ i ].getName();
- if ( ForesterUtil.isEmpty( name ) ) {
- result_trees[ i ].setName( "SDIR result [gene tree + " + gene_tree_counter + "]" + " " + i );
- }
- else {
- result_trees[ i ].setName( name + " SDIR result [gene tree + " + gene_tree_counter + "]" + " " + i );
- }
- all_result_trees.add( result_trees[ i ] );
- }
- ++gene_tree_counter;
- } // for( final Phylogeny gene_tree : gene_trees )
- try {
- final PhylogenyWriter w = new PhylogenyWriter();
- w.toPhyloXML( outfile, all_result_trees, 0, ForesterUtil.LINE_SEPARATOR );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME,
- "failure to write output to [" + outfile + "]: " + e.getLocalizedMessage() );
- }
- ForesterUtil.programMessage( PRG_NAME, "Wrote: " + outfile );
- ForesterUtil.programMessage( PRG_NAME, "OK." );
- }
-
- private static void printHelp() {
- System.out.println( "Usage: " + PRG_NAME
- + " <options> <gene tree(s) in phyloXML format> <species tree in phyloXML format>\"" );
- System.out.println( "\nOptions:" );
- System.out.println( " -" + MIN_MAPPING_COST_OPTION
- + " to root by minimizing the mapping cost L (and also the sum of duplications)" );
- System.out.println( " -" + MIN_DUPS_OPTION + " to root by minimizing the sum of duplications" );
- System.out.println( " -" + MIN_HEIGHT_OPTION
- + " to root by minimizing tree height (can be used together with -" + MIN_MAPPING_COST_OPTION + " or -"
- + MIN_DUPS_OPTION + ")" );
- System.out.println( "" );
- }
-}
+++ /dev/null
-// $Id:
-//
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org
-
-package org.forester.application;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-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.io.parsers.nexus.NexusCharactersParser;
-import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
-import org.forester.io.parsers.nexus.PaupLogParser;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.surfacing.DomainParsimonyCalculator;
-import org.forester.surfacing.SurfacingUtil;
-import org.forester.util.CommandLineArguments;
-import org.forester.util.ForesterUtil;
-
-public class surf_paup {
-
- final static private String PRG_VERSION = "0.90";
- final static private String PRG_DATE = "2008.03.28";
- final static private String E_MAIL = "czmasek@burnham.org";
- final static private String WWW = "www.phylosoft.org/forester/applications/surfacing";
- final static private String HELP_OPTION_1 = "help";
- final static private String HELP_OPTION_2 = "h";
- private static final String PRG_NAME = "surf_paup";
-
- public static void main( final String args[] ) {
- ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
- final List<String> allowed_options = new ArrayList<String>();
- allowed_options.add( HELP_OPTION_1 );
- allowed_options.add( HELP_OPTION_2 );
- if ( ( args.length < 2 ) ) {
- printHelp();
- System.exit( -1 );
- }
- CommandLineArguments cla = null;
- try {
- cla = new CommandLineArguments( args );
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
- }
- if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) {
- printHelp();
- System.exit( 0 );
- }
- if ( cla.getNumberOfNames() != 3 ) {
- printHelp();
- System.exit( -1 );
- }
- final File surfacing_nexus_outfile = cla.getFile( 0 );
- final File paup_log_file = cla.getFile( 1 );
- final String outfile_name = cla.getFile( 2 ).toString();
- final NexusCharactersParser nex_char_parser = new NexusCharactersParser();
- try {
- nex_char_parser.setSource( surfacing_nexus_outfile );
- nex_char_parser.parse();
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME, "problem with parsing character labels from ["
- + surfacing_nexus_outfile + "]: " + e.getMessage() );
- e.printStackTrace();
- }
- final String[] labels = nex_char_parser.getCharStateLabels();
- ForesterUtil.programMessage( PRG_NAME, "read in " + labels.length + " character labels" );
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final NexusPhylogeniesParser phylogeny_parser = new NexusPhylogeniesParser();
- Phylogeny[] phylogenies = null;
- try {
- phylogenies = factory.create( surfacing_nexus_outfile, phylogeny_parser );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME,
- "problem with parsing phylogeny [" + surfacing_nexus_outfile + "]: "
- + e.getMessage() );
- e.printStackTrace();
- }
- if ( phylogenies.length != 1 ) {
- ForesterUtil.fatalError( PRG_NAME, "failed to parse one phylogeny from [" + surfacing_nexus_outfile
- + "], got " + phylogenies.length + " instead" );
- }
- final Phylogeny phylogeny = phylogenies[ 0 ];
- if ( !phylogeny.isRooted() ) {
- ForesterUtil.fatalError( PRG_NAME, "phylogeny from [" + surfacing_nexus_outfile + "] is not rooted" );
- }
- postOrderRelabelInternalNodes( phylogeny, phylogeny.getNumberOfExternalNodes() + 1 );
- CharacterStateMatrix<BinaryStates> matrix = null;
- final PaupLogParser paup_log_parser = new PaupLogParser();
- try {
- paup_log_parser.setSource( paup_log_file );
- matrix = paup_log_parser.parse();
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME,
- "failed to parse matrix from [" + paup_log_file + "]: " + e.getMessage() );
- }
- ForesterUtil.programMessage( PRG_NAME,
- "read in character state matrix of size " + matrix.getNumberOfIdentifiers() + "x"
- + matrix.getNumberOfCharacters() );
- final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator.createInstance( phylogeny );
- domain_parsimony.executeOnGivenBinaryStatesMatrix( matrix, labels );
- final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
- SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(),
- outfile_name + "_paup_gl",
- Format.FORESTER );
- SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(),
- outfile_name + "_paup_glc",
- Format.FORESTER );
- SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
- CharacterStateMatrix.GainLossStates.GAIN,
- outfile_name + "_paup_gains",
- sep,
- ForesterUtil.LINE_SEPARATOR,
- null );
- SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
- CharacterStateMatrix.GainLossStates.LOSS,
- outfile_name + "_paup_losses",
- sep,
- ForesterUtil.LINE_SEPARATOR,
- null );
- SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
- + "_paup_present", sep, ForesterUtil.LINE_SEPARATOR, null );
- final String date_time = ForesterUtil.getCurrentDateTime();
- SurfacingUtil.preparePhylogeny( phylogeny, domain_parsimony, date_time, "parsimony (paup)", "paup_"
- + outfile_name, "" );
- SurfacingUtil.writePhylogenyToFile( phylogeny, outfile_name + "_paup.xml" );
- ForesterUtil.programMessage( PRG_NAME, "OK" );
- }
-
- final private static void postOrderRelabelInternalNodes( final Phylogeny phylogeny, final int starting_number ) {
- int i = starting_number;
- for( final PhylogenyNodeIterator it = phylogeny.iteratorPostorder(); it.hasNext(); ) {
- final PhylogenyNode node = it.next();
- if ( !node.isExternal() ) {
- node.setName( String.valueOf( i++ ) );
- }
- }
- }
-
- private static void printHelp() {
- System.out.println();
- System.out.println( "Usage:" );
- System.out.println();
- System.out
- .println( "% java -cp forester.jar org.forester.applications."
- + PRG_NAME
- + " <surfacing nexus outfile with character labels and tree> <paup log file with reconstructed states matrix> <outfile name base>" );
- System.out.println();
- }
-}
\ No newline at end of file
git://source.jalview.org / jalview.git / commitdiff