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.SDI;
import org.forester.sdi.SDI.TaxonomyComparisonBase;
import org.forester.sdi.SDIse;
+import org.forester.sdi.SdiException;
import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
public final class gsdi {
private static void execute( final CommandLineArguments cla ) throws IOException {
BASE_ALGORITHM base_algorithm = BASE_ALGORITHM.GSDI;
- boolean strip = false;
+ boolean strip_species_tree = false;
boolean most_parsimonous_duplication_model = false;
boolean species_tree_in_phyloxml = true;
boolean allow_stripping_of_gene_tree = false;
if ( cla.isOptionSet( gsdi.STRIP_OPTION ) ) {
- strip = true;
+ strip_species_tree = true;
}
if ( cla.isOptionSet( gsdi.SDI_OPTION ) ) {
base_algorithm = BASE_ALGORITHM.SDI;
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" );
+ log_writer.write( "User Error: gene tree is not completely binary" );
+ log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.close();
+ ForesterUtil.fatalError( gsdi.PRG_NAME, "gene tree is not completely binary" );
}
if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
if ( !species_tree.isCompletelyBinary() ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree (\"" + species_tree_file
- + "\") is not completely binary, use GSDI instead" );
+ log_writer.write( "User Error: species tree is not completely binary, use GSDI instead" );
+ log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.close();
+ ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree is not completely binary, use GSDI instead" );
}
}
// For timing.
// Helper.randomizeSpecies( 1, 8192, gene_tree );
// Helper.intervalNumberSpecies( gene_tree, 4096 );
// Helper.numberSpeciesInDescOrder( gene_tree );
- log_writer.write( PRG_NAME + " " + PRG_VERSION + " " + PRG_DATE );
+ log_writer.write( PRG_NAME + " - " + PRG_DESC );
+ log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.write( " version : " + PRG_VERSION );
+ log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.write( " date : " + PRG_DATE );
+ log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.write( " forester version: " + ForesterConstants.FORESTER_VERSION );
log_writer.write( ForesterUtil.LINE_SEPARATOR );
- log_writer.write( PRG_DESC );
log_writer.write( ForesterUtil.LINE_SEPARATOR );
- log_writer.write( PRG_DESC );
+ log_writer.write( "Start time: " + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.write( "Gene tree file: " + gene_tree_file.getCanonicalPath() );
log_writer.write( ForesterUtil.LINE_SEPARATOR );
- log_writer.write( new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
+ log_writer.write( "Gene tree name: "
+ + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
+ log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.write( "Species tree file: " + species_tree_file.getCanonicalPath() );
+ log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.write( "Species tree name: "
+ + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
log_writer.write( ForesterUtil.LINE_SEPARATOR );
System.out.println();
- System.out.println( "Strip species tree: " + strip );
- log_writer.write( "Strip species tree: " + strip );
+ System.out.println( "Strip species tree: " + strip_species_tree );
+ log_writer.write( "Strip species tree: " + strip_species_tree );
log_writer.write( ForesterUtil.LINE_SEPARATOR );
SDI sdi = null;
final long start_time = new Date().getTime();
log_writer.write( ForesterUtil.LINE_SEPARATOR );
log_writer.write( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree );
log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.flush();
sdi = new GSDI( gene_tree,
species_tree,
most_parsimonous_duplication_model,
- allow_stripping_of_gene_tree );
+ allow_stripping_of_gene_tree,
+ strip_species_tree );
}
else {
System.out.println();
System.out.println( "Using SDIse algorithm" );
log_writer.write( "Using SDIse algorithm" );
log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.flush();
sdi = new SDIse( gene_tree, species_tree );
}
}
+ catch ( final SdiException e ) {
+ log_writer.write( "User Error: " + e.getLocalizedMessage() );
+ log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.close();
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ catch ( final IOException e ) {
+ log_writer.write( "Error: " + e );
+ log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.close();
+ ForesterUtil.fatalError( PRG_NAME, e.toString() );
+ }
catch ( final Exception e ) {
+ log_writer.write( "Error: " + e );
+ log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.close();
e.printStackTrace();
- ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ System.exit( -1 );
}
System.out.println();
System.out.println( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
System.out.println( "Number of duplications : " + sdi.getDuplicationsSum() );
log_writer.write( "Number of duplications : " + sdi.getDuplicationsSum() );
log_writer.write( ForesterUtil.LINE_SEPARATOR );
- if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) && !most_parsimonous_duplication_model ) {
- final int duplications = ( ( GSDI ) sdi ).getSpeciationOrDuplicationEventsSum();
- System.out.println( "Number of potential duplications: " + duplications );
- log_writer.write( "Number of potential duplications: " + duplications );
- log_writer.write( ForesterUtil.LINE_SEPARATOR );
- }
- if ( base_algorithm == BASE_ALGORITHM.GSDI ) {
- final int spec = ( ( GSDI ) sdi ).getSpeciationsSum();
+ if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
+ final GSDI gsdi = ( GSDI ) sdi;
+ if ( !most_parsimonous_duplication_model ) {
+ final int duplications = gsdi.getSpeciationOrDuplicationEventsSum();
+ System.out.println( "Number of potential duplications: " + duplications );
+ log_writer.write( "Number of potential duplications: " + duplications );
+ log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ }
+ final int spec = gsdi.getSpeciationsSum();
System.out.println( "Number of speciations : " + spec );
log_writer.write( "Number of speciations : " + spec );
log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ for( PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
+ System.out.println( n.toString() );
+ }
}
System.out.println();
+ log_writer.close();
// some stat on gene tree:
// filename, name
// number of external nodes, strppided nodes
import org.forester.sdi.DistanceCalculator;
import org.forester.sdi.RIO;
import org.forester.sdi.SDIR;
+import org.forester.sdi.SdiException;
import org.forester.util.ForesterUtil;
public class rio {
final int warn_no_orthos,
final double warn_one_ortho,
final int bootstraps,
- final double t_orthologs_dc ) throws IOException {
+ final double t_orthologs_dc ) throws IOException, SdiException {
Phylogeny consensus_tree = null;
Phylogeny
// to be a consensus tree.
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.sdi.SDIR;
import org.forester.sdi.SDIse;
+import org.forester.sdi.SdiException;
import org.forester.util.ForesterUtil;
/*
* set to true, then out of the resulting trees with minimal
* mapping cost or minimal number of duplications the tree with
* the minimal height is chosen
+ * @throws SdiException
*/
public static void infer( final File indir,
final File species_tree_file,
final boolean write_trees,
final boolean minimize_mapping_cost,
boolean minimize_sum_of_dup,
- final boolean minimize_height ) throws IOException {
+ final boolean minimize_height ) throws IOException, SdiException {
final int MIN_EXT_NODES = 4; // Minimal size of trees [in ext nodes]
// to be analyzed.
final int MAX_EXT_NODES = 5000; // Maximal size of trees [in ext nodes]
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.sdi.SDIx;
+import org.forester.sdi.SdiException;
import org.forester.util.CommandLineArguments;
import org.forester.util.ForesterUtil;
final static private String PRG_VERSION = "0.001 alpha";
final static private String PRG_DATE = "2009.10.14";
- public static void main( final String args[] ) {
+ public static void main( final String args[] ) throws SdiException {
ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE );
System.out.println();
CommandLineArguments cla = null;
+++ /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/forester
-
-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.util.ParserUtils;
-import org.forester.io.writers.PhylogenyWriter;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.sdi.GSDI;
-import org.forester.sdi.SDI;
-import org.forester.sdi.SDIse;
-import org.forester.util.CommandLineArguments;
-import org.forester.util.ForesterUtil;
-
-public class ta {
-
- final static private String STRIP_OPTION = "s";
- final static private String SDISE_OPTION = "b";
- final static private String MOST_PARSIMONIOUS_OPTION = "m";
- final static private String HELP_OPTION_1 = "help";
- final static private String HELP_OPTION_2 = "h";
- final static private String DEFAULT_OUTFILE = "sdi_out.xml";
- final static private String PRG_NAME = "sdi";
- final static private String PRG_VERSION = "alpha 0.3";
- final static private String PRG_DATE = "2008.03.04";
-
- public static void main( final String args[] ) {
- ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE );
- 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 ) ) {
- System.out.println();
- 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();
- print_help();
- System.exit( -1 );
- }
- final List<String> allowed_options = new ArrayList<String>();
- allowed_options.add( STRIP_OPTION );
- allowed_options.add( SDISE_OPTION );
- allowed_options.add( MOST_PARSIMONIOUS_OPTION );
- final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
- if ( dissallowed_options.length() > 0 ) {
- ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
- }
- boolean use_sdise = false;
- boolean strip = false;
- boolean most_parsimonous_duplication_model = false;
- if ( cla.isOptionSet( STRIP_OPTION ) ) {
- strip = true;
- }
- if ( cla.isOptionSet( SDISE_OPTION ) ) {
- use_sdise = true;
- }
- if ( cla.isOptionSet( MOST_PARSIMONIOUS_OPTION ) ) {
- if ( use_sdise ) {
- ForesterUtil.fatalError( PRG_NAME, "Can only use most parsimonious duplication mode with GSDI" );
- }
- most_parsimonous_duplication_model = true;
- }
- Phylogeny species_tree = null;
- Phylogeny gene_tree = null;
- File gene_tree_file = null;
- File species_tree_file = null;
- File out_file = 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( DEFAULT_OUTFILE );
- }
- }
- catch ( final IllegalArgumentException e ) {
- ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getMessage() );
- }
- if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
- ForesterUtil.fatalError( PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
- }
- if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
- ForesterUtil.fatalError( PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
- }
- if ( ForesterUtil.isWritableFile( out_file ) != null ) {
- ForesterUtil.fatalError( PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
- }
- try {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
- species_tree = factory.create( species_tree_file, pp )[ 0 ];
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME,
- "Failed to read species tree from \"" + gene_tree_file + "\" [" + e.getMessage()
- + "]" );
- }
- try {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( gene_tree_file, true );
- gene_tree = factory.create( gene_tree_file, pp )[ 0 ];
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME,
- "Failed to read gene tree from \"" + gene_tree_file + "\" [" + e.getMessage()
- + "]" );
- }
- gene_tree.setRooted( true );
- species_tree.setRooted( true );
- if ( !gene_tree.isCompletelyBinary() ) {
- ForesterUtil.fatalError( PRG_NAME, "gene tree is not completely binary." );
- }
- if ( use_sdise ) {
- if ( !species_tree.isCompletelyBinary() ) {
- ForesterUtil.fatalError( PRG_NAME, "species tree is not completely binary." );
- }
- }
- // 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 );
- 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 );
- }
- 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 );
- }
- }
- catch ( final Exception e ) {
- ForesterUtil.unexpectedFatalError( PRG_NAME, e );
- }
- 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, 1 );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME, "Failed to write to \"" + out_file + "\" [" + e.getMessage() + "]" );
- }
- System.out.println();
- System.out.println( "Successfully wrote resulting gene tree to: " + out_file );
- System.out.println();
- // if ( use_sdise ) {
- // computeMappingCostL();
- // System.out.println( "Mapping cost : " + computeMappingCostL() );
- // }
- // System.out.println( "Number of duplications : " + getDuplicationsSum() );
- if ( !use_sdise && !most_parsimonous_duplication_model ) {
- System.out.println( "Number of potential duplications: "
- + ( ( GSDI ) sdi ).getSpeciationOrDuplicationEventsSum() );
- }
- if ( !use_sdise ) {
- System.out.println( "Number speciations : " + ( ( GSDI ) sdi ).getSpeciationsSum() );
- }
- System.out.println();
- } // main( final String args[] )
-
- private static void print_help() {
- System.out.println( "Usage: \"" + PRG_NAME
- + " [-options] <gene tree file name> <species tree file name> [outfile name]\"" );
- System.out.println();
- System.out.println( "Options:" );
- System.out.println( " -" + STRIP_OPTION + ": to strip the species tree prior to duplication inference" );
- System.out.println( " -" + SDISE_OPTION
- + ": to use SDIse algorithm instead of GSDI algorithm (for binary trees only, faster)" );
- 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 unknown because of polytomies in the species tree" );
- System.out.println();
- System.out.println( "Species tree file" );
- System.out.println( " In NHX format, with species names in species name fields unless -n option" );
- System.out.println( " is used." );
- System.out.println();
- System.out.println( "Gene tree file" );
- System.out.println( " In NHX format, with species names in species name fields and sequence names" );
- System.out.println( " in sequence name fields." );
- System.out.println();
- System.out.println( "!! WARNING: GSDI algorithm is under development, please use SDIse (-b) instead !!" );
- System.out.println();
- } // print_help()
-}
customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
_obtain_detailed_taxonomic_information_deleting_jmi
.setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
- _tools_menu
- .add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
+ _tools_menu.add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
customizeJMenuItem( _obtain_uniprot_seq_information_jmi );
_obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information" );
_tools_menu.addSeparator();
GSDI gsdi = null;
int duplications = -1;
try {
- gsdi = new GSDI( gene_tree, _species_tree.copy(), true, true );
+ gsdi = new GSDI( gene_tree, _species_tree.copy(), true, true, false );
duplications = gsdi.getDuplicationsSum();
}
catch ( final Exception e ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
final TaxonomyDataManager t = new TaxonomyDataManager( this,
- _mainpanel.getCurrentTreePanel(),
- phy.copy(), false,true );
+ _mainpanel.getCurrentTreePanel(),
+ phy.copy(),
+ false,
+ true );
new Thread( t ).start();
}
}
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
final TaxonomyDataManager t = new TaxonomyDataManager( this,
- _mainpanel.getCurrentTreePanel(),
- phy.copy(),
- true,true );
+ _mainpanel.getCurrentTreePanel(),
+ phy.copy(),
+ true,
+ true );
new Thread( t ).start();
}
}
final String file_name = f.getName().trim().toLowerCase();
return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
|| file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
- || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
+ || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
|| f.isDirectory();
}
package org.forester.sdi;
+import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
+import java.util.List;
import java.util.Map;
import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeSet;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
private final HashMap<PhylogenyNode, Integer> _transversal_counts;
private final boolean _most_parsimonious_duplication_model;
private final boolean _strip_gene_tree;
+ private final boolean _strip_species_tree;
private int _speciation_or_duplication_events_sum;
private int _speciations_sum;
- private final Set<PhylogenyNode> _stripped_gene_tree_nodes;
+ private final List<PhylogenyNode> _stripped_gene_tree_nodes;
+ private final List<PhylogenyNode> _stripped_species_tree_nodes;
+ private final SortedSet<PhylogenyNode> _mapped_species_tree_nodes;
/**
* Constructor which sets the gene tree and the species tree to be compared.
* set to true to assign nodes as speciations which would
* otherwise be assiged as unknown because of polytomies in the
* species tree.
+ * @throws SdiException
*
*/
public GSDI( final Phylogeny gene_tree,
final Phylogeny species_tree,
final boolean most_parsimonious_duplication_model,
- final boolean strip_gene_tree ) {
+ final boolean strip_gene_tree,
+ final boolean strip_species_tree ) throws SdiException {
super( gene_tree, species_tree );
_speciation_or_duplication_events_sum = 0;
_speciations_sum = 0;
_transversal_counts = new HashMap<PhylogenyNode, Integer>();
_duplications_sum = 0;
_strip_gene_tree = strip_gene_tree;
- _stripped_gene_tree_nodes = new HashSet<PhylogenyNode>();
+ _strip_species_tree = strip_species_tree;
+ _stripped_gene_tree_nodes = new ArrayList<PhylogenyNode>();
+ _stripped_species_tree_nodes = new ArrayList<PhylogenyNode>();
+ _mapped_species_tree_nodes = new TreeSet<PhylogenyNode>();
getSpeciesTree().preOrderReId();
linkNodesOfG();
geneTreePostOrderTraversal( getGeneTree().getRoot() );
}
- public GSDI( final Phylogeny gene_tree,
- final Phylogeny species_tree,
- final boolean most_parsimonious_duplication_model ) {
- this( gene_tree, species_tree, most_parsimonious_duplication_model, false );
+ GSDI( final Phylogeny gene_tree, final Phylogeny species_tree, final boolean most_parsimonious_duplication_model )
+ throws SdiException {
+ this( gene_tree, species_tree, most_parsimonious_duplication_model, false, false );
}
private final Event createDuplicationEvent() {
* Preconditions: Mapping M for external nodes must have been calculated and
* the species tree must be labeled in preorder.
* <p>
- * (Last modified: )
*
* @param g
* starting node of a gene tree - normally the root
}
final PhylogenyNode[] linked_nodes = new PhylogenyNode[ g.getNumberOfDescendants() ];
for( int i = 0; i < linked_nodes.length; ++i ) {
+ if ( g.getChildNode( i ).getLink() == null ) {
+ System.out.println( "link is null for " + g.getChildNode( i ) );
+ System.exit( -1 );
+ }
linked_nodes[ i ] = g.getChildNode( i ).getLink();
}
final int[] min_max = obtainMinMaxIdIndices( linked_nodes );
/**
* This allows for linking of internal nodes of the species tree (as opposed
* to just external nodes, as in the method it overrides.
+ * @throws SdiException
*
*/
@Override
// g.setLink( s );
// }
// }
- final void linkNodesOfG() {
- // final HashMap<Taxonomy, PhylogenyNode> speciestree_ext_nodes = createTaxonomyToNodeMap();
- // if ( _strip_gene_tree ) {
- // stripGeneTree( speciestree_ext_nodes );
- // if ( ( _gene_tree == null ) || ( _gene_tree.getNumberOfExternalNodes() < 2 ) ) {
- // throw new IllegalArgumentException( "species tree does not contain any"
- // + " nodes matching species in the gene tree" );
- // }
- // }
- // // Retrieve the reference to the PhylogenyNode with a matching species.
- // for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
- // final PhylogenyNode g = iter.next();
- // if ( !g.getNodeData().isHasTaxonomy() ) {
- // throw new IllegalArgumentException( "gene tree node " + g + " has no taxonomic data" );
- // }
- // final PhylogenyNode s = speciestree_ext_nodes.get( g.getNodeData().getTaxonomy() );
- // if ( s == null ) {
- // throw new IllegalArgumentException( "species " + g.getNodeData().getTaxonomy()
- // + " not present in species tree" );
- // }
- // g.setLink( s );
- // }
- //////
- final Map<String, PhylogenyNode> speciestree_ext_nodes = new HashMap<String, PhylogenyNode>();
+ final void linkNodesOfG() throws SdiException {
+ final Map<String, PhylogenyNode> species_to_node_map = new HashMap<String, PhylogenyNode>();
+ final Set<PhylogenyNode> species_tree_ext_nodes = new HashSet<PhylogenyNode>();
final TaxonomyComparisonBase tax_comp_base = determineTaxonomyComparisonBase( _gene_tree );
System.out.println( "comp base is: " + tax_comp_base );
- // if ( _strip_gene_tree ) {
- // stripGeneTree2( speciestree_ext_nodes );
- // if ( ( _gene_tree == null ) || ( _gene_tree.getNumberOfExternalNodes() < 2 ) ) {
- // throw new IllegalArgumentException( "species tree does not contain any"
- // + " nodes matching species in the gene tree" );
- // }
- //}
- // Put references to all external nodes of the species tree into a map.
// Stringyfied taxonomy is the key, node is the value.
for( final PhylogenyNodeIterator iter = _species_tree.iteratorExternalForward(); iter.hasNext(); ) {
final PhylogenyNode s = iter.next();
+ species_tree_ext_nodes.add( s );
final String tax_str = taxonomyToString( s, tax_comp_base );
- if ( speciestree_ext_nodes.containsKey( tax_str ) ) {
- throw new IllegalArgumentException( "taxonomy [" + s + "] is not unique in species phylogeny" );
+ if ( !ForesterUtil.isEmpty( tax_str ) ) {
+ if ( species_to_node_map.containsKey( tax_str ) ) {
+ throw new SdiException( "taxonomy \"" + s + "\" is not unique in species tree" );
+ }
+ species_to_node_map.put( tax_str, s );
}
- speciestree_ext_nodes.put( tax_str, s );
}
// Retrieve the reference to the node with a matching stringyfied taxonomy.
for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
if ( !g.getNodeData().isHasTaxonomy() ) {
if ( _strip_gene_tree ) {
_stripped_gene_tree_nodes.add( g );
- continue;
}
else {
- throw new IllegalArgumentException( "gene tree node " + g + " has no taxonomic data" );
+ throw new SdiException( "gene tree node \"" + g + "\" has no taxonomic data" );
}
}
else {
_stripped_gene_tree_nodes.add( g );
}
else {
- throw new IllegalArgumentException( "gene tree node " + g
- + " has no appropriate taxonomic data" );
+ throw new SdiException( "gene tree node \"" + g + "\" has no appropriate taxonomic data" );
}
}
else {
- final PhylogenyNode s = speciestree_ext_nodes.get( tax_str );
- // if ( s == null ) {
- // if ( _strip_gene_tree ) {
- // _stripped_gene_tree_nodes.add( g );
- // }
- // else {
- // throw new IllegalArgumentException( "taxonomy " + g.getNodeData().getTaxonomy()
- // + " not present in species tree" );
- // }
- // }
- // else {
- g.setLink( s );
- System.out.println( "setting link of " + g + " to " + s );
- // }
+ final PhylogenyNode s = species_to_node_map.get( tax_str );
+ if ( s == null ) {
+ if ( _strip_gene_tree ) {
+ _stripped_gene_tree_nodes.add( g );
+ }
+ else {
+ throw new SdiException( "taxonomy \"" + g.getNodeData().getTaxonomy()
+ + "\" not present in species tree" );
+ }
+ }
+ else {
+ g.setLink( s );
+ _mapped_species_tree_nodes.add( s );
+ System.out.println( "setting link of " + g + " to " + s );
+ }
}
}
} // for loop
if ( _strip_gene_tree ) {
- for( final PhylogenyNode n : _stripped_gene_tree_nodes ) {
- // if ( _gene_tree.getNode( n.getId() ) != null ) {
- _gene_tree.deleteSubtree( n, true );
- // }
+ for( final PhylogenyNode g : _stripped_gene_tree_nodes ) {
+ _gene_tree.deleteSubtree( g, true );
}
}
- }
-
- final private HashMap<Taxonomy, PhylogenyNode> createTaxonomyToNodeMap() {
- final HashMap<Taxonomy, PhylogenyNode> speciestree_ext_nodes = new HashMap<Taxonomy, PhylogenyNode>();
- for( final PhylogenyNodeIterator iter = _species_tree.iteratorLevelOrder(); iter.hasNext(); ) {
- final PhylogenyNode n = iter.next();
- if ( n.getNodeData().isHasTaxonomy() ) {
- if ( speciestree_ext_nodes.containsKey( n.getNodeData().getTaxonomy() ) ) {
- throw new IllegalArgumentException( "taxonomy [" + n.getNodeData().getTaxonomy()
- + "] is not unique in species phylogeny" );
+ if ( _strip_species_tree ) {
+ for( final PhylogenyNode s : species_tree_ext_nodes ) {
+ if ( !_mapped_species_tree_nodes.contains( s ) ) {
+ _species_tree.deleteSubtree( s, true );
}
- speciestree_ext_nodes.put( n.getNodeData().getTaxonomy(), n );
- }
- }
- return speciestree_ext_nodes;
- }
-
- private final void stripGeneTree( final HashMap<Taxonomy, PhylogenyNode> speciestree_ext_nodes ) {
- // final Set<PhylogenyNode> to_delete = new HashSet<PhylogenyNode>();
- for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode g = iter.next();
- if ( !g.getNodeData().isHasTaxonomy() ) {
- throw new IllegalArgumentException( "gene tree node " + g + " has no taxonomic data" );
- }
- if ( !speciestree_ext_nodes.containsKey( g.getNodeData().getTaxonomy() ) ) {
- _stripped_gene_tree_nodes.add( g );
}
}
- for( final PhylogenyNode n : _stripped_gene_tree_nodes ) {
- _gene_tree.deleteSubtree( n, true );
- }
}
- private final void stripGeneTree2( final HashMap<Taxonomy, PhylogenyNode> speciestree_ext_nodes ) {
- // final Set<PhylogenyNode> to_delete = new HashSet<PhylogenyNode>();
- for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode g = iter.next();
- if ( !g.getNodeData().isHasTaxonomy() ) {
- _stripped_gene_tree_nodes.add( g );
- }
- else {
- if ( !speciestree_ext_nodes.containsKey( g.getNodeData().getTaxonomy() ) ) {
- _stripped_gene_tree_nodes.add( g );
- }
- }
- }
- for( final PhylogenyNode n : _stripped_gene_tree_nodes ) {
- _gene_tree.deleteSubtree( n, true );
- }
+ public SortedSet<PhylogenyNode> getMappedExternalSpeciesTreeNodes() {
+ return _mapped_species_tree_nodes;
}
+ // final private HashMap<Taxonomy, PhylogenyNode> createTaxonomyToNodeMap() {
+ // final HashMap<Taxonomy, PhylogenyNode> speciestree_ext_nodes = new HashMap<Taxonomy, PhylogenyNode>();
+ // for( final PhylogenyNodeIterator iter = _species_tree.iteratorLevelOrder(); iter.hasNext(); ) {
+ // final PhylogenyNode n = iter.next();
+ // if ( n.getNodeData().isHasTaxonomy() ) {
+ // if ( speciestree_ext_nodes.containsKey( n.getNodeData().getTaxonomy() ) ) {
+ // throw new IllegalArgumentException( "taxonomy [" + n.getNodeData().getTaxonomy()
+ // + "] is not unique in species phylogeny" );
+ // }
+ // speciestree_ext_nodes.put( n.getNodeData().getTaxonomy(), n );
+ // }
+ // }
+ // return speciestree_ext_nodes;
+ // }
+ // private final void stripGeneTree( final HashMap<Taxonomy, PhylogenyNode> speciestree_ext_nodes ) {
+ // // final Set<PhylogenyNode> to_delete = new HashSet<PhylogenyNode>();
+ // for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
+ // final PhylogenyNode g = iter.next();
+ // if ( !g.getNodeData().isHasTaxonomy() ) {
+ // throw new IllegalArgumentException( "gene tree node " + g + " has no taxonomic data" );
+ // }
+ // if ( !speciestree_ext_nodes.containsKey( g.getNodeData().getTaxonomy() ) ) {
+ // _stripped_gene_tree_nodes.add( g );
+ // }
+ // }
+ // for( final PhylogenyNode n : _stripped_gene_tree_nodes ) {
+ // _gene_tree.deleteSubtree( n, true );
+ // }
+ // }
+ // private final void stripGeneTree2( final HashMap<Taxonomy, PhylogenyNode> speciestree_ext_nodes ) {
+ // // final Set<PhylogenyNode> to_delete = new HashSet<PhylogenyNode>();
+ // for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
+ // final PhylogenyNode g = iter.next();
+ // if ( !g.getNodeData().isHasTaxonomy() ) {
+ // _stripped_gene_tree_nodes.add( g );
+ // }
+ // else {
+ // if ( !speciestree_ext_nodes.containsKey( g.getNodeData().getTaxonomy() ) ) {
+ // _stripped_gene_tree_nodes.add( g );
+ // }
+ // }
+ // }
+ // for( final PhylogenyNode n : _stripped_gene_tree_nodes ) {
+ // _gene_tree.deleteSubtree( n, true );
+ // }
+ // }
public static TaxonomyComparisonBase determineTaxonomyComparisonBase( final Phylogeny gene_tree ) {
int with_id_count = 0;
int with_code_count = 0;
}
}
- public Set<PhylogenyNode> getStrippedExternalGeneTreeNodes() {
+ public List<PhylogenyNode> getStrippedExternalGeneTreeNodes() {
return _stripped_gene_tree_nodes;
}
* @param query
* the sequence name of the squence whose orthologs are to be
* inferred
+ * @throws SdiException
*/
public void inferOrthologs( final File gene_trees_file, final Phylogeny species_tree, final String query )
- throws IOException {
+ throws IOException, SdiException {
int bs = 0;
if ( RIO.TIME ) {
_time = System.currentTimeMillis();
// Helper method which performs the actual ortholog inference for
// the external node with seqname query.
- private void inferOrthologsHelper( final Phylogeny gene_tree, final Phylogeny species_tree, final String query ) {
+ private void inferOrthologsHelper( final Phylogeny gene_tree, final Phylogeny species_tree, final String query )
+ throws SdiException {
Phylogeny assigned_tree = null;
List<PhylogenyNode> nodes = null;
final SDIR sdiunrooted = new SDIR();
GeneralTable<String, Integer> _super_orthologs = null;
GeneralTable<String, Integer> _ultra_paralogs = null;
- private void doInferOrthologs( final Phylogeny gene_tree, final Phylogeny species_tree ) {
+ private void doInferOrthologs( final Phylogeny gene_tree, final Phylogeny species_tree ) throws SdiException {
final SDIR sdiunrooted = new SDIR();
final Phylogeny assigned_tree = sdiunrooted.infer( gene_tree,
species_tree,
* links (sets the field "link" of PhylogenyNode) each external
* PhylogenyNode of gene_tree to the external PhylogenyNode of species_tree
* which has the same species name.
+ * @throws SdiException
*/
- void linkNodesOfG() {
+ void linkNodesOfG() throws SdiException {
final Map<String, PhylogenyNode> speciestree_ext_nodes = new HashMap<String, PhylogenyNode>();
final TaxonomyComparisonBase tax_comp_base = determineTaxonomyComparisonBase();
// Put references to all external nodes of the species tree into a map.
* Array) must be no lower than 1
* @return array of rooted Trees with duplication vs. speciation assigned if
* return_trees is set to true, null otherwise
+ * @throws SdiException
*/
public Phylogeny[] infer( final Phylogeny gene_tree,
final Phylogeny species_tree,
boolean minimize_sum_of_dup,
final boolean minimize_height,
final boolean return_trees,
- int max_trees_to_return ) {
+ int max_trees_to_return ) throws SdiException {
init();
SDIse sdise = null;
final ArrayList<Phylogeny> trees = new ArrayList<Phylogeny>();
* reference to a rooted binary species Phylogeny which might get
* stripped in the process, must have species names in the
* species name fields for all external nodes
+ * @throws SdiException
*/
- public SDIse( final Phylogeny gene_tree, final Phylogeny species_tree ) {
+ public SDIse( final Phylogeny gene_tree, final Phylogeny species_tree ) throws SdiException {
super( gene_tree, species_tree );
_duplications_sum = 0;
getSpeciesTree().preOrderReId();
private void analyze( final Phylogeny gene_tree,
final String gene_tree_file_name,
final Phylogeny[] species_trees,
- final File out_dir ) throws IOException {
+ final File out_dir ) throws IOException, SdiException {
final boolean minimize_cost = true;
final boolean minimize_sum_of_dup = true;
final boolean minimize_height = true;
}
public void method1( final List<File> gene_tree_files, final Phylogeny[] species_trees, final File out_dir )
- throws IOException {
+ throws IOException, SdiException {
checkSpeciesTreesForEqualNumberOfExtNodes( species_trees );
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
for( final File gene_tree_file : gene_tree_files ) {
--- /dev/null
+
+package org.forester.sdi;
+
+public class SdiException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 5154733429066500435L;
+
+ public SdiException() {
+ super();
+ }
+
+ public SdiException( final String message ) {
+ super( message );
+ }
+}
public class TaxonomyAssigner extends SDI {
- public TaxonomyAssigner( final Phylogeny gene_tree, final Phylogeny species_tree ) {
+ public TaxonomyAssigner( final Phylogeny gene_tree, final Phylogeny species_tree ) throws SdiException {
super( gene_tree, species_tree );
getSpeciesTree().preOrderReId();
linkNodesOfG();
}
}
- public static void execute( final Phylogeny gene_tree, final Phylogeny species_tree ) {
+ public static void execute( final Phylogeny gene_tree, final Phylogeny species_tree ) throws SdiException {
new TaxonomyAssigner( gene_tree, species_tree );
}
}
git://source.jalview.org / jalview.git / commitdiff