// 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.util.ArrayList;
import java.util.Date;
import java.util.List;
+import java.util.SortedMap;
+import java.util.SortedSet;
+import java.util.TreeMap;
+import java.util.TreeSet;
-import org.forester.io.parsers.PhylogenyParser;
-import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
-import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.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.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;
public final class gsdi {
- private enum BASE_ALGORITHM {
- GSDI, SDI
- }
- final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true;
- final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION = "g";
- final static private String SDI_OPTION = "b";
- final static private String MOST_PARSIMONIOUS_OPTION = "m";
- final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q";
- final static private String HELP_OPTION_1 = "help";
- final static private String HELP_OPTION_2 = "h";
- final static private String DEFAULT_OUTFILE_SUFFIX = "_gsdi_out.xml";
- final static private String SUFFIX_FOR_LIST_OF_STIPPED_GENE_TREE_NODES = "_stripped_gene_tree_nodes.txt";
- 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 PRG_NAME = "gsdi";
- final static private String PRG_VERSION = "0.901";
- final static private String PRG_DATE = "120608";
- final static private String PRG_DESC = "general speciation duplication inference";
- final static private String E_MAIL = "phylosoft@gmail.com";
- final static private String WWW = "www.phylosoft.org/forester";
+ 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[] ) {
try {
gsdi.print_help();
System.exit( 0 );
}
- else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() < 2 ) || ( cla.getNumberOfNames() > 3 ) ) {
+ else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() != 3 ) ) {
System.out.println();
System.out.println( "Wrong number of arguments." );
System.out.println();
System.exit( -1 );
}
final List<String> allowed_options = new ArrayList<String>();
- allowed_options.add( gsdi.SDI_OPTION );
+ allowed_options.add( gsdi.GSDIR_OPTION );
allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE );
allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION );
allowed_options.add( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION );
}
private static void execute( final CommandLineArguments cla ) throws IOException {
- BASE_ALGORITHM base_algorithm = BASE_ALGORITHM.GSDI;
+ ALGORITHM base_algorithm = ALGORITHM.GSDI;
boolean most_parsimonous_duplication_model = false;
- boolean species_tree_in_phyloxml = true;
boolean allow_stripping_of_gene_tree = false;
- if ( cla.isOptionSet( gsdi.SDI_OPTION ) ) {
- base_algorithm = BASE_ALGORITHM.SDI;
+ if ( cla.isOptionSet( gsdi.GSDIR_OPTION ) ) {
+ base_algorithm = ALGORITHM.GSDIR;
}
if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) {
- if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
- 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.GUESS_FORMAT_OF_SPECIES_TREE ) ) {
- species_tree_in_phyloxml = false;
- }
if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
- if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only allow stripping of gene tree with GSDI" );
+ if ( base_algorithm == ALGORITHM.SDI ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot allow stripping of gene tree with SDI" );
}
allow_stripping_of_gene_tree = true;
}
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( ForesterUtil.removeSuffix( gene_tree_file.toString() ) + DEFAULT_OUTFILE_SUFFIX );
- }
+ out_file = cla.getFile( 2 );
log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX );
}
catch ( final IllegalArgumentException e ) {
gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME,
- "Failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage() );
+ fatalError( "error",
+ "failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(),
+ log_writer );
}
try {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- if ( species_tree_in_phyloxml ) {
- species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
- }
- else {
- final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
- if ( REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE && ( p instanceof NHXParser ) ) {
- ( ( NHXParser ) p ).setReplaceUnderscores( true );
- }
- species_tree = factory.create( species_tree_file, p )[ 0 ];
- final TaxonomyComparisonBase comp_base = GSDI.determineTaxonomyComparisonBase( gene_tree );
- switch ( comp_base ) {
- case SCIENTIFIC_NAME:
- PhylogenyMethods
- .transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
- true );
- break;
- case CODE:
- PhylogenyMethods.transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE,
- true );
- break;
- case ID:
- PhylogenyMethods.transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID,
- true );
- break;
- default:
- ForesterUtil.fatalError( gsdi.PRG_NAME, "unable to determine comparison base" );
- }
- }
+ 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 ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME,
- "Failed to read species tree from [" + gene_tree_file + "]: " + e.getMessage() );
+ 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() ) {
- log_writer.println( "User Error: gene tree is not completely binary" );
- log_writer.close();
- ForesterUtil.fatalError( gsdi.PRG_NAME, "gene tree is not completely binary" );
+ fatalError( "user error", "gene tree is not completely binary", log_writer );
}
- if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
+ if ( base_algorithm == ALGORITHM.SDI ) {
if ( !species_tree.isCompletelyBinary() ) {
- log_writer.println( "User Error: species tree is not completely binary, use GSDI instead" );
- log_writer.close();
- ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree is not completely binary, use GSDI instead" );
+ fatalError( "user error",
+ "species tree is not completely binary, use GSDI or GSDIR instead",
+ log_writer );
}
}
- // For timing.
- // gene_tree = Helper.createBalancedTree( 10 );
- // species_tree = Helper.createBalancedTree( 13 );
- // species_tree = Helper.createUnbalancedTree( 1024 );
- // gene_tree = Helper.createUnbalancedTree( 8192 );
- // species_tree = gene_tree.copyTree();
- // gene_tree = species_tree.copyTree();
- // Helper.numberSpeciesInOrder( species_tree );
- // Helper.numberSpeciesInOrder( gene_tree );
- // Helper.randomizeSpecies( 1, 8192, gene_tree );
- // Helper.intervalNumberSpecies( gene_tree, 4096 );
- // Helper.numberSpeciesInDescOrder( gene_tree );
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( "Start time: " + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
- log_writer.println( "Gene tree file: " + gene_tree_file.getCanonicalPath() );
- log_writer.println( "Gene tree name: "
+ 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() ) );
- log_writer.println( "Species tree file: " + species_tree_file.getCanonicalPath() );
- log_writer.println( "Species tree name: "
+ 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();
- SDI sdi = null;
+ 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 ( base_algorithm == BASE_ALGORITHM.GSDI ) {
- System.out.println();
- 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.write( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree );
- log_writer.flush();
- sdi = new GSDI( gene_tree,
- species_tree,
- most_parsimonous_duplication_model,
- allow_stripping_of_gene_tree,
- true );
+ if ( base_algorithm == ALGORITHM.GSDI ) {
+ System.out.println( "Algorithm : GSDI" );
+ log_writer.println( "Algorithm : GSDI" );
}
- else {
- System.out.println();
- System.out.println( "Using SDIse algorithm" );
- log_writer.println( "Using SDIse algorithm" );
- log_writer.flush();
- sdi = new SDIse( gene_tree, species_tree );
+ 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 ) {
- log_writer.println( "User Error: " + e.getLocalizedMessage() );
- log_writer.close();
- ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ catch ( final SDIException e ) {
+ fatalError( "user error", e.getLocalizedMessage(), log_writer );
}
catch ( final IOException e ) {
- log_writer.println( "Error: " + e );
- log_writer.close();
- ForesterUtil.fatalError( PRG_NAME, e.toString() );
+ fatalError( "error", e.toString(), log_writer );
+ }
+ catch ( final OutOfMemoryError e ) {
+ ForesterUtil.outOfMemoryError( e );
}
catch ( final Exception e ) {
- log_writer.println( "Error: " + e );
- log_writer.close();
e.printStackTrace();
- System.exit( -1 );
+ fatalError( "unexpected error", e.toString(), log_writer );
}
- System.out.println();
- 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( "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() );
+ }
+ try {
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ 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.getCanonicalPath() + "]: " + e.getMessage() );
+ }
+ 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( out_file, gene_tree, 0 );
+ writer.toPhyloXML( species_tree_used_file, species_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 [" + species_tree_used_file.getCanonicalPath()
+ + "]: " + e.getMessage() );
}
+ System.out.println( "Wrote (stripped) species tree to : " + species_tree_used_file.getCanonicalPath() );
+ log_writer.println( "Wrote (stripped) species tree to : " + species_tree_used_file.getCanonicalPath() );
+ if ( ( 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();
- System.out.println( "Wrote resulting gene tree to: " + out_file );
- System.out.println();
- log_writer.println( "Wrote resulting gene tree to: " + out_file );
- if ( base_algorithm == BASE_ALGORITHM.SDI ) {
- sdi.computeMappingCostL();
- System.out.println( "Mapping cost : " + sdi.computeMappingCostL() );
- log_writer.println( "Mapping cost : " + sdi.computeMappingCostL() );
- }
- System.out.println( "Number of duplications : " + sdi.getDuplicationsSum() );
- log_writer.println( "Number of duplications : " + sdi.getDuplicationsSum() );
- if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
- final GSDI gsdi = ( GSDI ) sdi;
- final File species_tree_used_file = new File( out_file + SUFFIX_FOR_SPECIES_TREE_USED );
- try {
- final PhylogenyWriter writer = new PhylogenyWriter();
- writer.toPhyloXML( species_tree_used_file, gsdi.getSpeciesTree(), 0 );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME,
- "Failed to write to [" + species_tree_used_file + "]: " + e.getMessage() );
- }
- System.out.println();
- System.out.println( "Wrote used species tree to: " + species_tree_used_file );
- System.out.println();
- log_writer.println( "Wrote used species tree to: " + species_tree_used_file );
+ 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 duplications = gsdi.getSpeciationOrDuplicationEventsSum();
- System.out.println( "Number of potential duplications: " + duplications );
- log_writer.println( "Number of potential duplications: " + duplications );
- }
- final int spec = gsdi.getSpeciationsSum();
- System.out.println( "Number of speciations : " + spec );
- log_writer.println( "Number of speciations : " + spec );
- for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
- System.out.println( n.toString() );
+ 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();
- // some stat on gene tree:
- // filename, name
- // number of external nodes, strppided nodes
- // some stats on sepcies tree, external nodes,
- // filename, name
- // internal nodes
- // how many of which are polytomies
- //wrote log file to
- // if ( allow_stripping_of_gene_tree ) {
- // stripped x nodes, y external nodes remain
- // }
+ }
+
+ 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]" );
+ + " [-options] <gene tree in phyloXML format> <species tree> <outfile>" );
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 in the species tree (writes list of stripped nodes to " + );
- System.out.println( " -" + gsdi.SDI_OPTION + ": to use SDI algorithm instead of GSDI algorithm" );//TODO gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION not allowed
+ 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( " 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();
- System.out.println( "Species tree:" );
- System.out
- .println( " In phyloXML format (unless option -"
- + gsdi.GUESS_FORMAT_OF_SPECIES_TREE
- + " is used, in which case the species matching between gene tree and species tree must be via scientific name), with taxonomy data in appropriate fields" );
+ 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( "Example:" );
- // System.out.println( "gsdi
- // 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