// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
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.nhx.NHXParser.TAXONOMY_EXTRACTION;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
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.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.SDIse;
+import org.forester.sdi.GSDII;
+import org.forester.sdi.GSDIR;
+import org.forester.sdi.SDIException;
+import org.forester.sdi.SDIutil;
+import org.forester.sdi.SDIutil.ALGORITHM;
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 GSDI_OPTION = "g";
- 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 = "gsdi";
- final static private String PRG_VERSION = "0.4";
- final static private String PRG_DATE = "120607";
- 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 public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true;
+ 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 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<String> allowed_options = new ArrayList<String>();
+ 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<String> allowed_options = new ArrayList<String>();
- allowed_options.add( gsdi.STRIP_OPTION );
- allowed_options.add( gsdi.GSDI_OPTION );
- 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 = true;
- boolean strip = false;
- boolean most_parsimonous_duplication_model = false;
- if ( cla.isOptionSet( gsdi.STRIP_OPTION ) ) {
- strip = true;
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME, e.getMessage() );
}
- if ( cla.isOptionSet( gsdi.GSDI_OPTION ) ) {
- use_sdise = false;
+ }
+
+ private 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 ) ) {
+ base_algorithm = ALGORITHM.GSDIR;
}
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 == ALGORITHM.SDI ) {
+ ForesterUtil.fatalError( gsdi.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 ( base_algorithm == 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() );
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();
- species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
+ 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 {
+ 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() ) {
- 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 == ALGORITHM.SDI ) {
if ( !species_tree.isCompletelyBinary() ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree (\"" + species_tree_file
- + "\") 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;
+ fatalError( "user error",
+ "species tree is not completely binary, use GSDI or GSDIR instead",
+ log_writer );
+ }
+ }
+ 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() ) );
+ GSDII gsdii = 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 == ALGORITHM.GSDI ) {
+ System.out.println( "Algorithm : GSDI" );
+ log_writer.println( "Algorithm : GSDI" );
}
- 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 );
+ else if ( base_algorithm == 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 == ALGORITHM.GSDI ) {
+ gsdii = new GSDI( gene_tree,
+ species_tree,
+ most_parsimonous_duplication_model,
+ allow_stripping_of_gene_tree,
+ true );
}
+ else if ( base_algorithm == ALGORITHM.GSDIR ) {
+ gsdii = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, true );
+ }
+ }
+ catch ( final SDIException e ) {
+ fatalError( "user error", e.getLocalizedMessage(), log_writer );
+ }
+ catch ( final IOException e ) {
+ fatalError( "error", e.toString(), log_writer );
+ }
+ catch ( final OutOfMemoryError e ) {
+ ForesterUtil.outOfMemoryError( e );
}
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" );
+ 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() );
}
- 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 );
+ if ( base_algorithm == ALGORITHM.GSDIR ) {
+ writer.toPhyloXML( out_file, ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTree(), 0 );
+ }
+ 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 ) {
- sdi.computeMappingCostL();
- System.out.println( "Mapping cost : " + sdi.computeMappingCostL() );
+ System.out.println( "Wrote resulting gene tree to : " + out_file.getCanonicalPath() );
+ log_writer.println( "Wrote resulting gene tree to : " + out_file.getCanonicalPath() );
+ 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, species_tree, 0 );
}
- 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() );
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + species_tree_used_file.getCanonicalPath()
+ + "]: " + e.getMessage() );
}
- if ( !use_sdise ) {
- System.out.println( "Number speciations : " + ( ( GSDI ) sdi ).getSpeciationsSum() );
+ 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 ( ( gsdii.getReMappedScientificNamesFromGeneTree() != null )
+ && !gsdii.getReMappedScientificNamesFromGeneTree().isEmpty() ) {
+ System.out.println( "Number of gene tree species remapped : "
+ + gsdii.getReMappedScientificNamesFromGeneTree().size() );
+ log_writer.println( "Number of gene tree species remapped : "
+ + gsdii.getReMappedScientificNamesFromGeneTree().size() );
+ writeToRemappedFile( out_file, gsdii.getReMappedScientificNamesFromGeneTree(), log_writer );
}
+ 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 : " + species_tree.getNumberOfExternalNodes() );
+ log_writer.println( "Number of external nodes in species tree : " + species_tree.getNumberOfExternalNodes() );
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
+ 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 : "
+ + 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();
- } // main( final String args[] )
+ System.out.println( "Number of speciations : " + gsdii.getSpeciationsSum() );
+ log_writer.println( "Number of speciations : " + gsdii.getSpeciationsSum() );
+ if ( ( base_algorithm == ALGORITHM.GSDIR ) ) {
+ final GSDIR gsdir = ( GSDIR ) gsdii;
+ System.out.println( "Minimal number of duplications : " + gsdir.getMinDuplicationsSum() );
+ log_writer.println( "Minimal number of duplications : " + gsdir.getMinDuplicationsSum() );
+ }
+ else if ( ( base_algorithm == ALGORITHM.GSDI ) ) {
+ final GSDI gsdi = ( GSDI ) gsdii;
+ System.out.println( "Number of duplications : " + gsdi.getDuplicationsSum() );
+ log_writer.println( "Number of duplications : " + gsdi.getDuplicationsSum() );
+ 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 );
+ }
+ }
+ log_writer.println();
+ printMappedNodesToLog( log_writer, gsdii );
+ log_writer.println();
+ printStrippedGeneTreeNodesToLog( log_writer, gsdii );
+ System.out.println();
+ System.out.println( "Wrote log to : " + log_file.getCanonicalPath() );
+ System.out.println();
+ log_writer.close();
+ }
+
+ 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 print_help() {
- System.out.println( "Usage: \"" + gsdi.PRG_NAME
- + " [-options] <gene tree in phyloXML format> <species tree in phyloXML format> [outfile]\"" );
+ System.out.println( "Usage: " + gsdi.PRG_NAME
+ + " [-options] <gene tree in phyloXML format> <species tree> <outfile>" );
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.GSDI_OPTION
- + ": to use GSDI algorithm instead of SDIse algorithm (under development, not recommended)" );
- System.out
- .println( " -" + gsdi.MOST_PARSIMONIOUS_OPTION + ": use most parimonious duplication model for GSDI: " );
+ 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();
- System.out.println( "Species tree:" );
- System.out.println( " In phyloXML format, 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.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();
}
+
+ private static void printMappedNodesToLog( final EasyWriter log_writer, final GSDII gsdi ) throws IOException {
+ final SortedSet<String> ss = new TreeSet<String>();
+ 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 printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDII gsdi )
+ throws IOException {
+ final SortedMap<String, Integer> sm = new TreeMap<String, Integer>();
+ 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 writeToRemappedFile( final File out_file,
+ final SortedSet<String> 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() );
+ }
}
git://source.jalview.org / jalview.git / blobdiff