true );
}
else if ( base_algorithm == ALGORITHM.GSDIR ) {
- sdi = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, 1 );
+ sdi = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, true );
}
}
else {
package org.forester.application;
import java.io.File;
-import java.io.FileWriter;
import java.io.IOException;
-import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.rio.RIO;
import org.forester.rio.RIOException;
-import org.forester.sdi.SDI;
import org.forester.sdi.SDI.ALGORITHM;
import org.forester.sdi.SDIException;
import org.forester.util.CommandLineArguments;
public class rio {
- final static private String PRG_NAME = "rio";
- final static private String PRG_VERSION = "3.00 beta 4";
- final static private String PRG_DATE = "2012.12.10";
- final static private String E_MAIL = "czmasek@burnham.org";
- final static private String WWW = "www.phylosoft.org/forester/";
- final static private String HELP_OPTION_1 = "help";
- final static private String HELP_OPTION_2 = "h";
- final static private String QUERY_OPTION = "q";
- final static private String SORT_OPTION = "s";
- final static private String ALLOW_NON_BIN_SPECIES_TREE_OPTION = "g";
- final static private String OUTPUT_ULTRA_P_OPTION = "u";
- final static private String CUTOFF_ULTRA_P_OPTION = "cu";
- final static private String CUTOFF_ORTHO_OPTION = "co";
- final static private String TABLE_OUTPUT_OPTION = "t";
+ final static private String PRG_NAME = "rio";
+ final static private String PRG_VERSION = "3.00 beta 4";
+ final static private String PRG_DATE = "2012.12.10";
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "www.phylosoft.org/forester/";
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String USE_SDIR = "b";
public static void main( final String[] args ) {
ForesterUtil.printProgramInformation( PRG_NAME,
printHelp();
}
final List<String> allowed_options = new ArrayList<String>();
- allowed_options.add( QUERY_OPTION );
- allowed_options.add( SORT_OPTION );
- allowed_options.add( CUTOFF_ULTRA_P_OPTION );
- allowed_options.add( CUTOFF_ORTHO_OPTION );
- allowed_options.add( TABLE_OUTPUT_OPTION );
- allowed_options.add( OUTPUT_ULTRA_P_OPTION );
- allowed_options.add( ALLOW_NON_BIN_SPECIES_TREE_OPTION );
+ allowed_options.add( USE_SDIR );
final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
}
final File gene_trees_file = cla.getFile( 0 );
final File species_tree_file = cla.getFile( 1 );
- File outfile = null;
- if ( cla.getNumberOfNames() > 2 ) {
- outfile = cla.getFile( 2 );
+ final File othology_outtable = cla.getFile( 2 );
+ final File logfile;
+ if ( cla.getNumberOfNames() > 3 ) {
+ logfile = cla.getFile( 3 );
+ }
+ else {
+ logfile = null;
}
ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, gene_trees_file );
ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, species_tree_file );
- if ( ( outfile != null ) && outfile.exists() ) {
- ForesterUtil.fatalError( PRG_NAME, "[" + outfile + "] already exists" );
- }
- String query = null;
- if ( cla.isOptionSet( QUERY_OPTION ) ) {
- query = cla.getOptionValue( QUERY_OPTION );
- }
- File table_outfile = null;
- if ( cla.isOptionSet( TABLE_OUTPUT_OPTION ) ) {
- table_outfile = new File( cla.getOptionValue( TABLE_OUTPUT_OPTION ) );
- if ( table_outfile.exists() ) {
- ForesterUtil.fatalError( PRG_NAME, "[" + table_outfile + "] already exists" );
- }
- }
- boolean output_ultraparalogs = false;
- if ( cla.isOptionSet( OUTPUT_ULTRA_P_OPTION ) ) {
- output_ultraparalogs = true;
- }
- boolean gsdir = false;
- if ( cla.isOptionSet( ALLOW_NON_BIN_SPECIES_TREE_OPTION ) ) {
- gsdir = true;
- }
- double cutoff_for_orthologs = 50;
- double cutoff_for_ultra_paralogs = 50;
- int sort = 1;
- try {
- if ( cla.isOptionSet( CUTOFF_ORTHO_OPTION ) ) {
- cutoff_for_orthologs = cla.getOptionValueAsDouble( CUTOFF_ORTHO_OPTION );
- if ( query == null ) {
- ForesterUtil.fatalError( PRG_NAME, "missing query name, type \"rio -h\" for help" );
- }
- if ( outfile == null ) {
- ForesterUtil.fatalError( PRG_NAME, "missing outfile, type \"rio -h\" for help" );
- }
- }
- if ( cla.isOptionSet( CUTOFF_ULTRA_P_OPTION ) ) {
- cutoff_for_ultra_paralogs = cla.getOptionValueAsDouble( CUTOFF_ULTRA_P_OPTION );
- output_ultraparalogs = true;
- }
- if ( cla.isOptionSet( SORT_OPTION ) ) {
- sort = cla.getOptionValueAsInt( SORT_OPTION );
- }
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getLocalizedMessage() );
+ if ( othology_outtable.exists() ) {
+ ForesterUtil.fatalError( PRG_NAME, "\"" + othology_outtable + "\" already exists" );
}
- if ( ( cutoff_for_orthologs < 0 ) || ( cutoff_for_ultra_paralogs < 0 ) || ( sort < 0 ) || ( sort > 2 ) ) {
- ForesterUtil.fatalError( PRG_NAME, "numberical option out of range, type \"rio -h\" for help" );
- }
- if ( ( ( query == null ) && ( ( outfile != null ) || output_ultraparalogs ) ) ) {
- ForesterUtil.fatalError( PRG_NAME, "missing query name, type \"rio -h\" for help" );
- }
- if ( ( output_ultraparalogs && ( outfile == null ) ) || ( ( query != null ) && ( outfile == null ) ) ) {
- ForesterUtil.fatalError( PRG_NAME, "missing outfile, type \"rio -h\" for help" );
+ boolean sdir = false;
+ if ( cla.isOptionSet( USE_SDIR ) ) {
+ sdir = true;
}
long time = 0;
System.out.println( "Gene trees : " + gene_trees_file );
System.out.println( "Species tree : " + species_tree_file );
- if ( gsdir ) {
+ System.out.println( "All vs all orthology table: " + othology_outtable );
+ if ( !sdir ) {
System.out.println( "Non binary species tree : allowed (GSDIR algorithm)" );
}
else {
System.out.println( "Non binary species tree : disallowed (SDIR algorithm)" );
}
- if ( query != null ) {
- System.out.println( "Query : " + query );
- System.out.println( "Outfile : " + outfile );
- System.out.println( "Sort : " + sort );
- System.out.println( "Cutoff for orthologs : " + cutoff_for_orthologs );
- if ( output_ultraparalogs ) {
- System.out.println( "Cutoff for ultra paralogs : " + cutoff_for_ultra_paralogs );
- }
- }
- if ( table_outfile != null ) {
- System.out.println( "Table output : " + table_outfile );
- }
System.out.println();
time = System.currentTimeMillis();
Phylogeny species_tree = null;
if ( !species_tree.isRooted() ) {
ForesterUtil.fatalError( PRG_NAME, "species tree is not rooted" );
}
- final SDI.ALGORITHM algorithm;
- if ( gsdir ) {
- algorithm = ALGORITHM.GSDIR;
+ final ALGORITHM algorithm;
+ if ( sdir ) {
+ algorithm = ALGORITHM.SDIR;
}
else {
- algorithm = ALGORITHM.SDIR;
+ algorithm = ALGORITHM.GSDIR;
}
try {
- final RIO rio;
- if ( ForesterUtil.isEmpty( query ) ) {
- rio = new RIO( gene_trees_file, species_tree, algorithm );
- }
- else {
- rio = new RIO( gene_trees_file, species_tree, query, algorithm );
- }
- if ( outfile != null ) {
- final StringBuilder output = new StringBuilder();
- output.append( rio.inferredOrthologsToString( query, sort, cutoff_for_orthologs ) );
- if ( output_ultraparalogs ) {
- output.append( "\n\nUltra paralogs:\n" );
- output.append( rio.inferredUltraParalogsToString( query, cutoff_for_ultra_paralogs ) );
- }
- output.append( "\n\nSort priority: " + RIO.getOrder( sort ) );
- output.append( "\nExt nodes : " + rio.getExtNodesOfAnalyzedGeneTrees() );
- output.append( "\nSamples : " + rio.getNumberOfSamples() + "\n" );
- final PrintWriter out = new PrintWriter( new FileWriter( outfile ), true );
- out.println( output );
- out.close();
- }
- if ( table_outfile != null ) {
- tableOutput( table_outfile, rio );
- }
+ final RIO rio = new RIO( gene_trees_file, species_tree, algorithm );
+ tableOutput( othology_outtable, rio );
}
catch ( final RIOException e ) {
ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
catch ( final Exception e ) {
ForesterUtil.unexpectedFatalError( PRG_NAME, e );
}
- if ( outfile != null ) {
- ForesterUtil.programMessage( PRG_NAME, "wrote results to \"" + outfile + "\"" );
+ if ( othology_outtable != null ) {
+ ForesterUtil.programMessage( PRG_NAME, "wrote results to \"" + othology_outtable + "\"" );
}
time = System.currentTimeMillis() - time;
ForesterUtil.programMessage( PRG_NAME, "time: " + time + "ms" );
private final static void printHelp() {
System.out.println( "Usage" );
System.out.println();
- System.out.println( PRG_NAME + " [options] <gene trees file> <species tree file> [outfile]" );
+ System.out
+ .println( PRG_NAME
+ + " [options] <gene trees infile> <species tree infile> <all vs all orthology table outfile> [logfile]" );
System.out.println();
System.out.println( " Options" );
- System.out.println( " -" + ALLOW_NON_BIN_SPECIES_TREE_OPTION + " : to allow non-binary species tree" );
- System.out.println( " -" + CUTOFF_ORTHO_OPTION + " : cutoff for ortholog output (default: 50)" );
- System.out.println( " -" + TABLE_OUTPUT_OPTION
- + " : file-name for output table of all vs. all ortholgy support" );
- System.out.println( " -" + QUERY_OPTION
- + " : name for query (sequence/node), if this is used, [outfile] is required as well" );
- System.out.println( " -" + SORT_OPTION + " : sort (default: 1)" );
- System.out.println( " -" + OUTPUT_ULTRA_P_OPTION
- + " : to output ultra-paralogs (species specific expansions/paralogs)" );
- System.out.println( " -" + CUTOFF_ULTRA_P_OPTION + " : cutoff for ultra-paralog output (default: 50)" );
- System.out.println();
- System.out.println( " Note" );
- System.out.println( " Either output of all vs. all ortholgy support with -t=<output table> and/or output for" );
- System.out.println( " one query sequence with -q=<query name> and a [outfile] are required." );
+ System.out.println( " -" + USE_SDIR
+ + " : to use SDIR instead of GSDIR (faster, but non-binary species trees are disallowed)" );
System.out.println();
- System.out.println( " Sort" );
- System.out.println( RIO.getOrderHelp().toString() );
System.out.println( " Formats" );
System.out.println( " The species tree is expected to be in phyloXML format." );
System.out
System.out.println( " (e.g. \"HUMAN\" from \"BCL2_HUMAN\")." );
System.out.println();
System.out.println( " Examples" );
- System.out.println( " \"rio gene_trees.nh species.xml outfile -q=BCL2_HUMAN -t=outtable -u -cu=60 -co=60\"" );
- System.out.println( " \"rio gene_trees.nh species.xml -t=outtable\"" );
+ System.out.println( " \"rio gene_trees.nh species.xml outtable.tsv log.txt\"" );
System.out.println();
System.out.println( " More information: http://code.google.com/p/forester/wiki/RIO" );
System.out.println();
gene_tree.recalculateNumberOfExternalDescendants( false );
GSDIR gsdir = null;
try {
- gsdir = new GSDIR( gene_tree, _species_tree.copy(), true, 1 );
+ gsdir = new GSDIR( gene_tree, _species_tree.copy(), true, true );
}
catch ( final Exception e ) {
JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDIR", JOptionPane.ERROR_MESSAGE );
nodes_to_delete.add( n );
}
}
- for( final PhylogenyNode phylogenyNode : nodes_to_delete ) {
- to_be_stripped.deleteSubtree( phylogenyNode, true );
+ for( final PhylogenyNode n : nodes_to_delete ) {
+ to_be_stripped.deleteSubtree( n, true );
}
to_be_stripped.clearHashIdToNodeMap();
to_be_stripped.externalNodesHaveChanged();
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
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.sdi.GSDIR;
-import org.forester.sdi.SDI;
+import org.forester.sdi.SDI.ALGORITHM;
+import org.forester.sdi.SDI.TaxonomyComparisonBase;
import org.forester.sdi.SDIException;
import org.forester.sdi.SDIR;
import org.forester.util.ForesterUtil;
public final class RIO {
- private final static boolean ROOT_BY_MINIMIZING_SUM_OF_DUPS = true;
- private final static boolean ROOT_BY_MINIMIZING_TREE_HEIGHT = true;
- private Phylogeny[] _analyzed_gene_trees;
- private HashMap<String, HashMap<String, Integer>> _o_maps;
- private HashMap<String, HashMap<String, Integer>> _so_maps;
- private HashMap<String, HashMap<String, Integer>> _up_maps;
- private List<String> _seq_names;
- private List<PhylogenyNode> _removed_gene_tree_nodes;
- private int _samples;
- private int _ext_nodes;
+ private final static boolean ROOT_BY_MINIMIZING_SUM_OF_DUPS = true;
+ private final static boolean ROOT_BY_MINIMIZING_TREE_HEIGHT = true;
+ private Phylogeny[] _analyzed_gene_trees;
+ private List<PhylogenyNode> _removed_gene_tree_nodes;
+ private int _samples;
+ private int _ext_nodes;
+ private TaxonomyComparisonBase _gsdir_tax_comp_base;
- /**
- * Default constructor.
- * @throws SDIException
- * @throws IOException
- * @throws RIOException
- */
- public RIO( final File gene_trees_file,
- final Phylogeny species_tree,
- final String query,
- final SDI.ALGORITHM algorithm ) throws IOException, SDIException, RIOException {
- if ( ForesterUtil.isEmpty( query ) ) {
- throw new IllegalArgumentException( "query is empty" );
- }
- init();
- inferOrthologs( gene_trees_file, species_tree, query, algorithm );
- }
-
- public RIO( final File gene_trees_file, final Phylogeny species_tree, final SDI.ALGORITHM algorithm )
+ public RIO( final File gene_trees_file, final Phylogeny species_tree, final ALGORITHM algorithm )
throws IOException, SDIException, RIOException {
init();
- inferOrthologs( gene_trees_file, species_tree, null, algorithm );
+ inferOrthologs( gene_trees_file, species_tree, algorithm );
}
public final Phylogeny[] getAnalyzedGeneTrees() {
return _ext_nodes;
}
- /**
- * Returns a HashMap containing the inferred "ultra paralogs" of the
- * external gene tree node with the sequence name seq_name. Sequence names
- * are the keys (String), numbers of observations are the values (Int).
- * "ultra paralogs" are to be inferred by method "inferOrthologs". Throws an
- * exception if seq_name is not found.
- *
- * @param seq_name
- * sequence name of a external node of the gene trees
- * @return HashMap containing the inferred ultra paralogs
- * (name(String)->value(Int))
- */
- public final HashMap<String, Integer> getInferredUltraParalogs( final String seq_name ) {
- if ( _up_maps == null ) {
- return null;
- }
- return _up_maps.get( seq_name );
- }
-
public final int getNumberOfSamples() {
return _samples;
}
- /**
- * Returns a String containg the names of orthologs of the PhylogenyNode
- * with seq name query_name. The String also contains how many times a
- * particular ortholog has been observed.
- * <p>
- * <ul>
- * The output order is (per line): Name, Ortholog, Subtree neighbor, Super
- * ortholog, Distance
- * </ul>
- * <p>
- * The sort priority of this is determined by sort in the following manner:
- * <ul>
- * <li>0 : Ortholog
- * <li>1 : Ortholog, Super ortholog
- * <li>2 : Super ortholog, Ortholog
- * </ul>
- * <p>
- * Returns "-" if no putative orthologs have been found (given
- * threshold_orthologs).
- * <p>
- * Orthologs are to be inferred by method "inferOrthologs".
- * <p>
- * (Last modified: 05/08/01)
- *
- * @param query_name
- * sequence name of a external node of the gene trees
- * @param sort
- * order and sort priority
- * @param threshold_orthologs
- * the minimal number of observations for a a sequence to be
- * reported as orthologous, in percents (0.0-100.0%)
- * @param threshold_subtreeneighborings
- * the minimal number of observations for a a sequence to be
- * reported as orthologous, in percents (0.0-100.0%)
- * @return String containing the inferred orthologs, String containing "-"
- * if no orthologs have been found null in case of error
- */
- public final StringBuffer inferredOrthologsToString( final String query_name, int sort, double threshold_orthologs ) {
- HashMap<String, Integer> o_hashmap = null;
- HashMap<String, Integer> s_hashmap = null;
- String name = "";
- double o = 0.0; // Orthologs.
- double s = 0.0; // Super orthologs.
- double value1 = 0.0;
- double value2 = 0.0;
- final ArrayList<ResultLine> nv = new ArrayList<ResultLine>();
- if ( ( _o_maps == null ) || ( _so_maps == null ) ) {
- throw new RuntimeException( "orthologs have not been calculated (successfully)" );
- }
- if ( ( sort < 0 ) || ( sort > 2 ) ) {
- sort = 1;
- }
- if ( threshold_orthologs < 0.0 ) {
- threshold_orthologs = 0.0;
- }
- else if ( threshold_orthologs > 100.0 ) {
- threshold_orthologs = 100.0;
- }
- o_hashmap = getInferredOrthologs( query_name );
- s_hashmap = getInferredSuperOrthologs( query_name );
- if ( ( o_hashmap == null ) || ( s_hashmap == null ) ) {
- throw new RuntimeException( "Orthologs for " + query_name + " were not established" );
- }
- final StringBuffer orthologs = new StringBuffer();
- if ( _seq_names.size() > 0 ) {
- I: for( int i = 0; i < _seq_names.size(); ++i ) {
- name = _seq_names.get( i );
- if ( name.equals( query_name ) ) {
- continue I;
- }
- o = getBootstrapValueFromHash( o_hashmap, name );
- if ( o < threshold_orthologs ) {
- continue I;
- }
- s = getBootstrapValueFromHash( s_hashmap, name );
- switch ( sort ) {
- case 0:
- nv.add( new ResultLine( name, o, 5 ) );
- break;
- case 1:
- nv.add( new ResultLine( name, o, s, 5 ) );
- break;
- case 2:
- nv.add( new ResultLine( name, s, o, 5 ) );
- break;
- default:
- nv.add( new ResultLine( name, o, 5 ) );
- }
- } // End of I for loop.
- if ( ( nv != null ) && ( nv.size() > 0 ) ) {
- orthologs.append( "seq name\t\tortho\ts-ortho" + ForesterUtil.LINE_SEPARATOR );
- final ResultLine[] nv_array = new ResultLine[ nv.size() ];
- for( int j = 0; j < nv.size(); ++j ) {
- nv_array[ j ] = nv.get( j );
- }
- Arrays.sort( nv_array );
- for( final ResultLine element : nv_array ) {
- name = element.getKey();
- value1 = element.getValue1();
- value2 = element.getValue2();
- orthologs.append( addNameAndValues( name, value1, value2, sort ) );
- }
- }
- }
- // No orthologs found.
- if ( ( orthologs == null ) || ( orthologs.length() < 1 ) ) {
- orthologs.append( "-" );
- }
- return orthologs;
- }
-
- /**
- * Returns a String containg the names of orthologs of the PhylogenyNode
- * with seq name query_name. The String also contains how many times a
- * particular ortholog has been observed. Returns "-" if no putative
- * orthologs have been found (given threshold_orthologs).
- * <p>
- * Orthologs are to be inferred by method "inferOrthologs".
- *
- * @param query_name
- * sequence name of a external node of the gene trees
- * @param return_dists
- * @param threshold_ultra_paralogs
- * between 1 and 100
- * @return String containing the inferred orthologs, String containing "-"
- * if no orthologs have been found null in case of error
- */
- public final String inferredUltraParalogsToString( final String query_name, double threshold_ultra_paralogs ) {
- HashMap<String, Integer> sp_hashmap = null;
- String name = "", ultra_paralogs = "";
- int sort = 0;
- double sp = 0.0;
- double value1 = 0.0;
- double value2 = 0.0;
- final List<ResultLine> nv = new ArrayList<ResultLine>();
- if ( threshold_ultra_paralogs < 1.0 ) {
- threshold_ultra_paralogs = 1.0;
- }
- else if ( threshold_ultra_paralogs > 100.0 ) {
- threshold_ultra_paralogs = 100.0;
- }
- if ( _up_maps == null ) {
- throw new RuntimeException( "Ultra paralogs have not been calculated (successfully)." );
- }
- sp_hashmap = getInferredUltraParalogs( query_name );
- if ( sp_hashmap == null ) {
- throw new RuntimeException( "Ultra paralogs for " + query_name + " were not established" );
- }
- if ( _seq_names.size() > 0 ) {
- I: for( int i = 0; i < _seq_names.size(); ++i ) {
- name = _seq_names.get( i );
- if ( name.equals( query_name ) ) {
- continue I;
- }
- sp = getBootstrapValueFromHash( sp_hashmap, name );
- if ( sp < threshold_ultra_paralogs ) {
- continue I;
- }
- nv.add( new ResultLine( name, sp, 5 ) );
- } // End of I for loop.
- if ( ( nv != null ) && ( nv.size() > 0 ) ) {
- final ResultLine[] nv_array = new ResultLine[ nv.size() ];
- for( int j = 0; j < nv.size(); ++j ) {
- nv_array[ j ] = nv.get( j );
- }
- Arrays.sort( nv_array );
- sort = 90;
- for( final ResultLine element : nv_array ) {
- name = element.getKey();
- value1 = element.getValue1();
- value2 = element.getValue2();
- ultra_paralogs += addNameAndValues( name, value1, value2, sort );
- }
- }
- }
- // No ultra paralogs found.
- if ( ( ultra_paralogs == null ) || ( ultra_paralogs.length() < 1 ) ) {
- ultra_paralogs = "-";
- }
- return ultra_paralogs;
- }
-
- // Helper method for inferredOrthologsToString.
- // inferredOrthologsToArrayList,
- // and inferredUltraParalogsToString.
- private final double getBootstrapValueFromHash( final HashMap<String, Integer> h, final String name ) {
- if ( !h.containsKey( name ) ) {
- return 0.0;
- }
- final int i = h.get( name );
- return ( ( i * 100.0 ) / getNumberOfSamples() );
- }
-
- /**
- * Returns a HashMap containing the inferred orthologs of the external gene
- * tree node with the sequence name seq_name. Sequence names are the keys
- * (String), numbers of observations are the values (Int). Orthologs are to
- * be inferred by method "inferOrthologs". Throws an exception if seq_name
- * is not found.
- *
- * @param seq_name
- * sequence name of a external node of the gene trees
- * @return HashMap containing the inferred orthologs
- * (name(String)->value(Int))
- */
- private final HashMap<String, Integer> getInferredOrthologs( final String seq_name ) {
- if ( _o_maps == null ) {
- return null;
- }
- return _o_maps.get( seq_name );
- }
-
- /**
- * Returns a HashMap containing the inferred "super orthologs" of the
- * external gene tree node with the sequence name seq_name. Sequence names
- * are the keys (String), numbers of observations are the values (Int).
- * Super orthologs are to be inferred by method "inferOrthologs". Throws an
- * exception if seq_name is not found.
- *
- * @param seq_name
- * sequence name of a external node of the gene trees
- * @return HashMap containing the inferred super orthologs
- * (name(String)->value(Int))
- */
- private final HashMap<String, Integer> getInferredSuperOrthologs( final String seq_name ) {
- if ( _so_maps == null ) {
- return null;
- }
- return _so_maps.get( seq_name );
+ public final List<PhylogenyNode> getRemovedGeneTreeNodes() {
+ return _removed_gene_tree_nodes;
}
- /**
- * Infers the orthologs (as well the "super orthologs", the "subtree
- * neighbors", and the "ultra paralogs") for each external node of the gene
- * Trees in multiple tree File gene_trees_file (=output of PHYLIP NEIGHBOR,
- * for example). Tallies how many times each sequence is (super-)
- * orthologous towards the query. Tallies how many times each sequence is
- * ultra paralogous towards the query. Tallies how many times each sequence
- * is a subtree neighbor of the query. Gene duplications are inferred using
- * SDI. Modifies its argument species_tree. Is a little faster than
- * "inferOrthologs(File,Phylogeny)" since orthologs are only inferred for
- * query.
- * <p>
- * To obtain the results use the methods listed below.
- *
- * @param gene_trees_file
- * a File containing gene Trees in NH format, which is the result
- * of performing a bootstrap analysis in PHYLIP
- * @param species_tree
- * a species Phylogeny, which has species names in its species
- * fields
- * @param query
- * the sequence name of the squence whose orthologs are to be
- * inferred
- * @throws SDIException
- * @throws RIOException
- * @throws IOException
- * @throws FileNotFoundException
- */
private final void inferOrthologs( final File gene_trees_file,
final Phylogeny species_tree,
- final String query,
- final SDI.ALGORITHM algorithm ) throws SDIException, RIOException,
+ final ALGORITHM algorithm ) throws SDIException, RIOException,
FileNotFoundException, IOException {
// Read in first tree to get its sequence names
// and strip species_tree.
}
final Phylogeny[] gene_trees = factory.create( gene_trees_file, p );
// Removes from species_tree all species not found in gene_tree.
- final List<PhylogenyNode> _removed_gene_tree_nodes = PhylogenyMethods
+ final List<PhylogenyNode> _removed_species_tree_ext_nodes = PhylogenyMethods
.taxonomyBasedDeletionOfExternalNodes( gene_trees[ 0 ], species_tree );
if ( species_tree.isEmpty() ) {
throw new RIOException( "failed to establish species based mapping between gene and species trees" );
}
- if ( !ForesterUtil.isEmpty( query ) ) {
- PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gene_trees[ 0 ] );
- if ( gene_trees[ 0 ].isEmpty() ) {
- throw new RIOException( "failed to establish species based mapping between gene and species trees" );
- }
- _seq_names = getAllExternalSequenceNames( gene_trees[ 0 ] );
- if ( ( _seq_names == null ) || ( _seq_names.size() < 1 ) ) {
- throw new RIOException( "could not get sequence names" );
- }
- _o_maps = new HashMap<String, HashMap<String, Integer>>();
- _so_maps = new HashMap<String, HashMap<String, Integer>>();
- _up_maps = new HashMap<String, HashMap<String, Integer>>();
- _o_maps.put( query, new HashMap<String, Integer>( _seq_names.size() ) );
- _so_maps.put( query, new HashMap<String, Integer>( _seq_names.size() ) );
- _up_maps.put( query, new HashMap<String, Integer>( _seq_names.size() ) );
- }
_analyzed_gene_trees = new Phylogeny[ gene_trees.length ];
- int c = 0;
+ int i = 0;
int gene_tree_ext_nodes = 0;
for( final Phylogeny gt : gene_trees ) {
- // Removes from gene_tree all species not found in species_tree.
- PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gt );
- if ( gt.isEmpty() ) {
- throw new RIOException( "failed to establish species based mapping between gene and species trees" );
- }
- if ( c == 0 ) {
- gene_tree_ext_nodes = gt.getNumberOfExternalNodes();
- }
- else if ( gene_tree_ext_nodes != gt.getNumberOfExternalNodes() ) {
- throw new RIOException( "(cleaned up) gene tree #" + ( c + 1 )
- + " has a different number of external nodes (" + gt.getNumberOfExternalNodes()
- + ") than those gene trees preceding it (" + gene_tree_ext_nodes + ")" );
+ if ( algorithm == ALGORITHM.SDIR ) {
+ // Removes from gene_tree all species not found in species_tree.
+ PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gt );
+ if ( gt.isEmpty() ) {
+ throw new RIOException( "failed to establish species based mapping between gene and species trees" );
+ }
+ if ( i == 0 ) {
+ gene_tree_ext_nodes = gt.getNumberOfExternalNodes();
+ }
+ else if ( gene_tree_ext_nodes != gt.getNumberOfExternalNodes() ) {
+ throw new RIOException( "(cleaned up) gene tree #" + ( i + 1 )
+ + " has a different number of external nodes (" + gt.getNumberOfExternalNodes()
+ + ") than those gene trees preceding it (" + gene_tree_ext_nodes + ")" );
+ }
}
- _analyzed_gene_trees[ c++ ] = performOrthologInference( gt, species_tree, query, algorithm );
+ _analyzed_gene_trees[ i ] = performOrthologInference( gt, species_tree, algorithm, i );
+ ++i;
}
setNumberOfSamples( gene_trees.length );
}
+ private final void init() {
+ _samples = 1;
+ _ext_nodes = 0;
+ }
+
private final Phylogeny performOrthologInference( final Phylogeny gene_tree,
final Phylogeny species_tree,
- final String query,
- final SDI.ALGORITHM algorithm ) throws SDIException, RIOException {
+ final ALGORITHM algorithm,
+ final int i ) throws SDIException, RIOException {
final Phylogeny assigned_tree;
switch ( algorithm ) {
case SDIR: {
break;
}
case GSDIR: {
- final GSDIR gsdir = new GSDIR( gene_tree, species_tree, true, 1 );
- assigned_tree = gsdir.getMinDuplicationsSumGeneTrees().get( 1 );
+ final GSDIR gsdir = new GSDIR( gene_tree, species_tree, true, i == 0 );
+ assigned_tree = gsdir.getMinDuplicationsSumGeneTrees().get( 0 );
+ _gsdir_tax_comp_base = gsdir.getTaxCompBase();
break;
}
default: {
}
}
setExtNodesOfAnalyzedGeneTrees( assigned_tree.getNumberOfExternalNodes() );
- if ( !ForesterUtil.isEmpty( query ) ) {
- final List<PhylogenyNode> nodes = getNodesViaSequenceName( assigned_tree, query );
- if ( nodes.size() > 1 ) {
- throw new RIOException( "node named [" + query + "] not unique" );
- }
- else if ( nodes.isEmpty() ) {
- throw new RIOException( "no node containing a sequence named [" + query + "] found" );
- }
- final PhylogenyNode query_node = nodes.get( 0 );
- updateCounts( _o_maps, query, PhylogenyMethods.getOrthologousNodes( assigned_tree, query_node ) );
- updateCounts( _so_maps, query, PhylogenyMethods.getSuperOrthologousNodes( query_node ) );
- updateCounts( _up_maps, query, PhylogenyMethods.getUltraParalogousNodes( query_node ) );
- }
return assigned_tree;
}
- private final void init() {
- _o_maps = null;
- _so_maps = null;
- _up_maps = null;
- _seq_names = null;
- _samples = 1;
- _ext_nodes = 0;
- }
-
private final void setExtNodesOfAnalyzedGeneTrees( final int i ) {
_ext_nodes = i;
}
_samples = i;
}
- // Helper for doInferOrthologs( Phylogeny, Phylogeny, String )
- // and doInferOrthologs( Phylogeny, Phylogeny ).
- private final void updateCounts( final HashMap<String, HashMap<String, Integer>> counter_map,
- final String query_seq_name,
- final List<PhylogenyNode> nodes ) {
- final HashMap<String, Integer> hash_map = counter_map.get( query_seq_name );
- if ( hash_map == null ) {
- throw new RuntimeException( "unexpected error in updateCounts" );
- }
- for( int j = 0; j < nodes.size(); ++j ) {
- String seq_name;
- if ( ( nodes.get( j ) ).getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( ( nodes.get( j ) ).getNodeData().getSequence().getName() ) ) {
- seq_name = ( nodes.get( j ) ).getNodeData().getSequence().getName();
- }
- else {
- seq_name = ( nodes.get( j ) ).getName();
- }
- if ( hash_map.containsKey( seq_name ) ) {
- hash_map.put( seq_name, hash_map.get( seq_name ) + 1 );
- }
- else {
- hash_map.put( seq_name, 1 );
- }
- }
- }
-
public final static IntMatrix calculateOrthologTable( final Phylogeny[] analyzed_gene_trees, final boolean sort )
throws RIOException {
final List<String> labels = new ArrayList<String>();
}
return m;
}
-
- /**
- * Returns the order in which ortholog (o), "super ortholog" (s) and
- * distance (d) are returned and sorted (priority of sort always goes from
- * left to right), given sort. For the meaning of sort
- *
- * @see #inferredOrthologsToString(String,int,double,double)
- *
- * @param sort
- * determines order and sort priority
- * @return String indicating the order
- */
- public final static String getOrder( final int sort ) {
- String order = "";
- switch ( sort ) {
- case 0:
- order = "orthologies";
- break;
- case 1:
- order = "orthologies > super orthologies";
- break;
- case 2:
- order = "super orthologies > orthologies";
- break;
- default:
- order = "orthologies";
- break;
- }
- return order;
- }
-
- public final static StringBuffer getOrderHelp() {
- final StringBuffer sb = new StringBuffer();
- sb.append( " 0: orthologies" + ForesterUtil.LINE_SEPARATOR );
- sb.append( " 1: orthologies > super orthologies" + ForesterUtil.LINE_SEPARATOR );
- sb.append( " 2: super orthologies > orthologies" + ForesterUtil.LINE_SEPARATOR );
- return sb;
- }
-
- // Helper method for inferredOrthologsToString
- // and inferredUltraParalogsToString.
- private final static String addNameAndValues( final String name,
- final double value1,
- final double value2,
- final int sort ) {
- final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.#####" );
- df.setDecimalSeparatorAlwaysShown( false );
- String line = "";
- if ( name.length() < 8 ) {
- line += ( name + "\t\t\t" );
- }
- else if ( name.length() < 16 ) {
- line += ( name + "\t\t" );
- }
- else {
- line += ( name + "\t" );
- }
- switch ( sort ) {
- case 0:
- line += addToLine( value1, df );
- line += "-\t";
- break;
- case 1:
- line += addToLine( value1, df );
- line += addToLine( value2, df );
- break;
- case 2:
- line += addToLine( value2, df );
- line += addToLine( value1, df );
- break;
- case 90:
- line += addToLine( value1, df );
- line += "-\t";
- break;
- case 91:
- line += addToLine( value1, df );
- line += addToLine( value2, df );
- break;
- }
- line += ForesterUtil.LINE_SEPARATOR;
- return line;
- }
-
- // Helper for addNameAndValues.
- private final static String addToLine( final double value, final java.text.DecimalFormat df ) {
- String s = "";
- if ( value != ResultLine.DEFAULT ) {
- s = df.format( value ) + "\t";
- }
- else {
- s = "-\t";
- }
- return s;
- }
-
- private final static List<String> getAllExternalSequenceNames( final Phylogeny phy ) throws RIOException {
- final List<String> names = new ArrayList<String>();
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode n = iter.next();
- if ( n.getNodeData().isHasSequence() && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
- names.add( n.getNodeData().getSequence().getName() );
- }
- else if ( !ForesterUtil.isEmpty( n.getName() ) ) {
- names.add( n.getName() );
- }
- else {
- throw new RIOException( "node has no (sequence) name: " + n );
- }
- }
- return names;
- }
-
- private final static List<PhylogenyNode> getNodesViaSequenceName( final Phylogeny phy, final String seq_name ) {
- final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode n = iter.next();
- if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getName().equals( seq_name ) ) {
- nodes.add( n );
- }
- if ( !n.getNodeData().isHasSequence() && n.getName().equals( seq_name ) ) {
- nodes.add( n );
- }
- }
- return nodes;
- }
-
- public final List<PhylogenyNode> getRemovedGeneTreeNodes() {
- return _removed_gene_tree_nodes;
- }
-
- private final class ResultLine implements Comparable<ResultLine> {
-
- public static final int DEFAULT = -999;
- private final String _key;
- private final double _value1;
- private final double _value2;
- private int[] _p;
-
- ResultLine( final String name, final double value1, final double value2, final int c ) {
- setSigns();
- _key = name;
- _value1 = value1;
- _value2 = value2;
- if ( ( c >= 0 ) && ( c <= 2 ) ) {
- _p[ c ] = -1;
- }
- }
-
- ResultLine( final String name, final double value1, final int c ) {
- setSigns();
- _key = name;
- _value1 = value1;
- _value2 = ResultLine.DEFAULT;
- if ( c == 0 ) {
- _p[ 0 ] = -1;
- }
- }
-
- @Override
- public int compareTo( final ResultLine n ) {
- if ( ( getValue1() != ResultLine.DEFAULT ) && ( n.getValue1() != ResultLine.DEFAULT ) ) {
- if ( getValue1() < n.getValue1() ) {
- return _p[ 0 ];
- }
- if ( getValue1() > n.getValue1() ) {
- return ( -_p[ 0 ] );
- }
- }
- if ( ( getValue2() != ResultLine.DEFAULT ) && ( n.getValue2() != ResultLine.DEFAULT ) ) {
- if ( getValue2() < n.getValue2() ) {
- return _p[ 1 ];
- }
- if ( getValue2() > n.getValue2() ) {
- return ( -_p[ 1 ] );
- }
- }
- return ( getKey().compareTo( n.getKey() ) );
- }
-
- String getKey() {
- return _key;
- }
-
- double getValue1() {
- return _value1;
- }
-
- double getValue2() {
- return _value2;
- }
-
- private void setSigns() {
- _p = new int[ 2 ];
- _p[ 0 ] = _p[ 1 ] = +1;
- }
- } // ResultLine
}
public class GSDI extends SDI {
private final boolean _most_parsimonious_duplication_model;
- private final boolean _strip_gene_tree;
- private final boolean _strip_species_tree;
protected int _speciation_or_duplication_events_sum;
protected int _speciations_sum;
private final List<PhylogenyNode> _stripped_gene_tree_nodes;
_speciations_sum = 0;
_most_parsimonious_duplication_model = most_parsimonious_duplication_model;
_duplications_sum = 0;
- _strip_gene_tree = strip_gene_tree;
- _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 HashSet<PhylogenyNode>();
_scientific_names_mapped_to_reduced_specificity = new TreeSet<String>();
- linkNodesOfG();
+ linkNodesOfG( null, strip_gene_tree, strip_species_tree );
PhylogenyMethods.preOrderReId( getSpeciesTree() );
geneTreePostOrderTraversal();
}
- GSDI( final Phylogeny gene_tree, final Phylogeny species_tree, final boolean most_parsimonious_duplication_model )
+ // Used by GSDIR
+ protected GSDI( final Phylogeny gene_tree, final Phylogeny species_tree, final boolean strip_gene_tree )
throws SDIException {
- this( gene_tree, species_tree, most_parsimonious_duplication_model, false, false );
- }
-
- public GSDI( final Phylogeny gene_tree,
- final Phylogeny species_tree,
- final boolean most_parsimonious_duplication_model,
- final boolean strip_gene_tree,
- final boolean strip_species_tree,
- final int x ) throws SDIException {
super( gene_tree, species_tree );
- _speciation_or_duplication_events_sum = 0;
+ _speciation_or_duplication_events_sum = -1;
_speciations_sum = 0;
- _most_parsimonious_duplication_model = most_parsimonious_duplication_model;
+ _most_parsimonious_duplication_model = true;
_duplications_sum = 0;
- _strip_gene_tree = strip_gene_tree;
- _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 HashSet<PhylogenyNode>();
/**
* This allows for linking of internal nodes of the species tree (as opposed
* to just external nodes, as in the method it overrides.
+ * If TaxonomyComparisonBase is null, it will try to determine it.
* @throws SDIException
*
*/
- @Override
- final void linkNodesOfG() throws SDIException {
+ final void linkNodesOfG( final TaxonomyComparisonBase tax_comp_base,
+ final boolean strip_gene_tree,
+ final boolean strip_species_tree ) throws SDIException {
final Map<String, PhylogenyNode> species_to_node_map = new HashMap<String, PhylogenyNode>();
final List<PhylogenyNode> species_tree_ext_nodes = new ArrayList<PhylogenyNode>();
- _tax_comp_base = determineTaxonomyComparisonBase( _gene_tree );
+ if ( tax_comp_base == null ) {
+ _tax_comp_base = determineTaxonomyComparisonBase( _gene_tree );
+ }
+ else {
+ _tax_comp_base = tax_comp_base;
+ }
// Stringyfied taxonomy is the key, node is the value.
for( final PhylogenyNodeIterator iter = _species_tree.iteratorExternalForward(); iter.hasNext(); ) {
final PhylogenyNode s = iter.next();
for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
final PhylogenyNode g = iter.next();
if ( !g.getNodeData().isHasTaxonomy() ) {
- if ( _strip_gene_tree ) {
+ if ( strip_gene_tree ) {
_stripped_gene_tree_nodes.add( g );
}
else {
else {
final String tax_str = taxonomyToString( g, _tax_comp_base );
if ( ForesterUtil.isEmpty( tax_str ) ) {
- if ( _strip_gene_tree ) {
+ if ( strip_gene_tree ) {
_stripped_gene_tree_nodes.add( g );
}
else {
s = tryMapByRemovingOverlySpecificData( species_to_node_map, tax_str );
}
if ( s == null ) {
- if ( _strip_gene_tree ) {
+ if ( strip_gene_tree ) {
_stripped_gene_tree_nodes.add( g );
}
else {
}
}
} // for loop
- if ( _strip_gene_tree ) {
+ if ( strip_gene_tree ) {
stripGeneTree();
if ( getGeneTree().isEmpty() || ( getGeneTree().getNumberOfExternalNodes() < 2 ) ) {
throw new SDIException( "species could not be mapped between gene tree and species tree" );
}
}
- if ( _strip_species_tree ) {
+ if ( strip_species_tree ) {
stripSpeciesTree( species_tree_ext_nodes );
}
}
private final BasicDescriptiveStatistics _duplications_sum_stats;\r
private final List<Phylogeny> _min_duplications_sum_gene_trees;\r
\r
- public GSDIR( final Phylogeny gene_tree, final Phylogeny species_tree, final boolean strip_gene_tree, final int x )\r
- throws SDIException {\r
- super( gene_tree.copy(), species_tree, true, strip_gene_tree, true, 1 );\r
- _min_duplications_sum = Integer.MAX_VALUE;\r
- _min_duplications_sum_gene_trees = new ArrayList<Phylogeny>();\r
- _duplications_sum_stats = new BasicDescriptiveStatistics();\r
- linkNodesOfG();\r
+ public GSDIR( final Phylogeny gene_tree,\r
+ final Phylogeny species_tree,\r
+ final boolean strip_gene_tree,\r
+ final boolean strip_species_tree ) throws SDIException {\r
+ super( gene_tree.copy(), species_tree, strip_gene_tree );\r
+ linkNodesOfG( null, strip_gene_tree, strip_species_tree );\r
final List<PhylogenyBranch> gene_tree_branches_post_order = new ArrayList<PhylogenyBranch>();\r
for( final PhylogenyNodeIterator it = _gene_tree.iteratorPostorder(); it.hasNext(); ) {\r
final PhylogenyNode n = it.next();\r
gene_tree_branches_post_order.add( new PhylogenyBranch( n, n.getParent() ) );\r
}\r
}\r
+ _min_duplications_sum = Integer.MAX_VALUE;\r
+ _min_duplications_sum_gene_trees = new ArrayList<Phylogeny>();\r
+ _duplications_sum_stats = new BasicDescriptiveStatistics();\r
for( final PhylogenyBranch branch : gene_tree_branches_post_order ) {\r
_duplications_sum = 0;\r
- _speciation_or_duplication_events_sum = 0;\r
_speciations_sum = 0;\r
_gene_tree.reRoot( branch );\r
PhylogenyMethods.preOrderReId( getSpeciesTree() );\r
final Phylogeny gene_2_1 = factory.create( gene_2_1_str, new NHXParser() )[ 0 ];
multi_species_2.setRooted( true );
gene_2_1.setRooted( true );
- final GSDI sdi = new GSDI( gene_2_1, multi_species_2, false );
+ final GSDI sdi = new GSDI( gene_2_1, multi_species_2, false, false, false );
if ( sdi.getSpeciationOrDuplicationEventsSum() != 0 ) {
return false;
}
s1.setRooted( true );
final Phylogeny g1 = TestGSDI
.createPhylogeny( "((((B[&&NHX:S=B],A1[&&NHX:S=A1]),C[&&NHX:S=C]),A2[&&NHX:S=A2]),D[&&NHX:S=D])" );
- final GSDI sdi1 = new GSDI( g1, s1, false );
+ final GSDI sdi1 = new GSDI( g1, s1, false, false, false );
// Archaeopteryx.createApplication( g1 );
// Archaeopteryx.createApplication( s1 );
if ( sdi1.getDuplicationsSum() != 1 ) {
}
final Phylogeny g2 = TestGSDI
.createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),B[&&NHX:S=B]),C[&&NHX:S=C]),D[&&NHX:S=D])" );
- final GSDI sdi2 = new GSDI( g2, s1, false );
+ final GSDI sdi2 = new GSDI( g2, s1, false, false, false );
if ( sdi2.getDuplicationsSum() != 0 ) {
return false;
}
}
final Phylogeny g3 = TestGSDI
.createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),C[&&NHX:S=C]),B[&&NHX:S=B]),D[&&NHX:S=D])" );
- final GSDI sdi3 = new GSDI( g3, s1, false );
+ final GSDI sdi3 = new GSDI( g3, s1, false, false, false );
if ( sdi3.getDuplicationsSum() != 0 ) {
return false;
}
}
final Phylogeny g4 = TestGSDI
.createPhylogeny( "(((B[&&NHX:S=B],C1[&&NHX:S=C]),C2[&&NHX:S=C]),D[&&NHX:S=D])" );
- final GSDI sdi4 = new GSDI( g4, s1, false );
+ final GSDI sdi4 = new GSDI( g4, s1, false, false, false );
if ( sdi4.getDuplicationsSum() != 1 ) {
return false;
}
}
final Phylogeny g5 = TestGSDI
.createPhylogeny( "(((D1[&&NHX:S=D],A1[&&NHX:S=A1]),B[&&NHX:S=B]),((D2[&&NHX:S=D],D3[&&NHX:S=D]),C[&&NHX:S=C]))" );
- final GSDI sdi5 = new GSDI( g5, s1, false );
+ final GSDI sdi5 = new GSDI( g5, s1, false, false, false );
if ( sdi5.getDuplicationsSum() != 3 ) {
return false;
}
final Phylogeny gene7_2 = TestGSDI
.createPhylogeny( "(((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),j2[&&NHX:S=j2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
gene7_2.setRooted( true );
- final GSDI sdi7_2 = new GSDI( gene7_2, species7, false );
+ final GSDI sdi7_2 = new GSDI( gene7_2, species7, false, false, false );
if ( sdi7_2.getDuplicationsSum() != 1 ) {
return false;
}
return false;
}
final Phylogeny g2_0 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],m3[&&NHX:S=m3])" );
- final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
+ final GSDI sdi2_0 = new GSDI( g2_0, s2, false, false, false );
if ( sdi2_0.getDuplicationsSum() != 0 ) {
return false;
}
return false;
}
final Phylogeny g2_1 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],h2[&&NHX:S=h2])" );
- final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
+ final GSDI sdi2_1 = new GSDI( g2_1, s2, false, false, false );
if ( sdi2_1.getDuplicationsSum() != 0 ) {
return false;
}
return false;
}
final Phylogeny g2_2 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],p4[&&NHX:S=p4])" );
- final GSDI sdi2_2 = new GSDI( g2_2, s2, false );
+ final GSDI sdi2_2 = new GSDI( g2_2, s2, false, false, false );
if ( sdi2_2.getDuplicationsSum() != 0 ) {
return false;
}
return false;
}
final Phylogeny g2_3 = TestGSDI.createPhylogeny( "(e2a[&&NHX:S=e2],e2b[&&NHX:S=e2])" );
- final GSDI sdi2_3 = new GSDI( g2_3, s2, false );
+ final GSDI sdi2_3 = new GSDI( g2_3, s2, false, false, false );
if ( sdi2_3.getDuplicationsSum() != 1 ) {
return false;
}
return false;
}
final Phylogeny g2_4 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),i3[&&NHX:S=i3])" );
- final GSDI sdi2_4 = new GSDI( g2_4, s2, false );
+ final GSDI sdi2_4 = new GSDI( g2_4, s2, false, false, false );
if ( sdi2_4.getDuplicationsSum() != 0 ) {
return false;
}
return false;
}
final Phylogeny g2_5 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),f3[&&NHX:S=f3])" );
- final GSDI sdi2_5 = new GSDI( g2_5, s2, false );
+ final GSDI sdi2_5 = new GSDI( g2_5, s2, false, false, false );
if ( sdi2_5.getDuplicationsSum() != 0 ) {
return false;
}
return false;
}
final Phylogeny g2_6 = TestGSDI.createPhylogeny( "((j3[&&NHX:S=j3],i4[&&NHX:S=i4]),f3[&&NHX:S=f3])" );
- final GSDI sdi2_6 = new GSDI( g2_6, s2, false );
+ final GSDI sdi2_6 = new GSDI( g2_6, s2, false, false, false );
if ( sdi2_6.getDuplicationsSum() != 0 ) {
return false;
}
return false;
}
final Phylogeny g2_7 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k1[&&NHX:S=k1]),i1[&&NHX:S=i1])" );
- final GSDI sdi2_7 = new GSDI( g2_7, s2, false );
+ final GSDI sdi2_7 = new GSDI( g2_7, s2, false, false, false );
if ( sdi2_7.getDuplicationsSum() != 0 ) {
return false;
}
return false;
}
final Phylogeny g2_8 = TestGSDI.createPhylogeny( "(j1[&&NHX:S=j1],(k1[&&NHX:S=k1],i1[&&NHX:S=i1]))" );
- final GSDI sdi2_8 = new GSDI( g2_8, s2, false );
+ final GSDI sdi2_8 = new GSDI( g2_8, s2, false, false, false );
if ( sdi2_8.getDuplicationsSum() != 0 ) {
return false;
}
return false;
}
final Phylogeny g2_9 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
- final GSDI sdi2_9 = new GSDI( g2_9, s2, false );
+ final GSDI sdi2_9 = new GSDI( g2_9, s2, false, false, false );
if ( sdi2_9.getDuplicationsSum() != 0 ) {
return false;
}
return false;
}
final Phylogeny g2_10 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
- final GSDI sdi2_10 = new GSDI( g2_10, s2, false );
+ final GSDI sdi2_10 = new GSDI( g2_10, s2, false, false, false );
if ( sdi2_10.getDuplicationsSum() != 0 ) {
return false;
}
return false;
}
final Phylogeny g2_11 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),x[&&NHX:S=x])" );
- final GSDI sdi2_11 = new GSDI( g2_11, s2, false );
+ final GSDI sdi2_11 = new GSDI( g2_11, s2, false, false, false );
if ( sdi2_11.getDuplicationsSum() != 0 ) {
return false;
}
return false;
}
final Phylogeny g2_12 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],(k4[&&NHX:S=k4],x[&&NHX:S=x]))" );
- final GSDI sdi2_12 = new GSDI( g2_12, s2, false );
+ final GSDI sdi2_12 = new GSDI( g2_12, s2, false, false, false );
if ( sdi2_12.getDuplicationsSum() != 0 ) {
return false;
}
return false;
}
final Phylogeny g2_13 = TestGSDI.createPhylogeny( "(x[&&NHX:S=x],(y[&&NHX:S=y],z[&&NHX:S=z]))" );
- final GSDI sdi2_13 = new GSDI( g2_13, s2, false );
+ final GSDI sdi2_13 = new GSDI( g2_13, s2, false, false, false );
if ( sdi2_13.getDuplicationsSum() != 0 ) {
return false;
}
return false;
}
final Phylogeny g2_14 = TestGSDI.createPhylogeny( "(a1_1[&&NHX:S=a1],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
- final GSDI sdi2_14 = new GSDI( g2_14, s2, false );
+ final GSDI sdi2_14 = new GSDI( g2_14, s2, false, false, false );
if ( sdi2_14.getDuplicationsSum() != 1 ) {
return false;
}
return false;
}
final Phylogeny g2_15 = TestGSDI.createPhylogeny( "(a2[&&NHX:S=a2],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
- final GSDI sdi2_15 = new GSDI( g2_15, s2, false );
+ final GSDI sdi2_15 = new GSDI( g2_15, s2, false, false, false );
if ( sdi2_15.getDuplicationsSum() != 1 ) {
return false;
}
return false;
}
final Phylogeny g2_16 = TestGSDI.createPhylogeny( "(n2[&&NHX:S=n2],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
- final GSDI sdi2_16 = new GSDI( g2_16, s2, false );
+ final GSDI sdi2_16 = new GSDI( g2_16, s2, false, false, false );
if ( sdi2_16.getDuplicationsSum() != 1 ) {
return false;
}
return false;
}
final Phylogeny g2_17 = TestGSDI.createPhylogeny( "(p4[&&NHX:S=p4],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
- final GSDI sdi2_17 = new GSDI( g2_17, s2, false );
+ final GSDI sdi2_17 = new GSDI( g2_17, s2, false, false, false );
if ( sdi2_17.getDuplicationsSum() != 1 ) {
return false;
}
}
final Phylogeny g2_18 = TestGSDI
.createPhylogeny( "((n11[&&NHX:S=n1],n12[&&NHX:S=n1]),(n13[&&NHX:S=n1],n14[&&NHX:S=n1]))" );
- final GSDI sdi2_18 = new GSDI( g2_18, s2, false );
+ final GSDI sdi2_18 = new GSDI( g2_18, s2, false, false, false );
if ( sdi2_18.getDuplicationsSum() != 3 ) {
return false;
}
}
final Phylogeny g2_19 = TestGSDI
.createPhylogeny( "((n11[&&NHX:S=n1],n21[&&NHX:S=n2]),(n12[&&NHX:S=n1],n22[&&NHX:S=n2]))" );
- final GSDI sdi2_19 = new GSDI( g2_19, s2, false );
+ final GSDI sdi2_19 = new GSDI( g2_19, s2, false, false, false );
if ( sdi2_19.getDuplicationsSum() != 1 ) {
return false;
}
}
final Phylogeny g2_20 = TestGSDI
.createPhylogeny( "((n11[&&NHX:S=n1],n2[&&NHX:S=n2]),(n12[&&NHX:S=n1],n3[&&NHX:S=n3]))" );
- final GSDI sdi2_20 = new GSDI( g2_20, s2, false );
+ final GSDI sdi2_20 = new GSDI( g2_20, s2, false, false, false );
if ( sdi2_20.getDuplicationsSum() != 1 ) {
return false;
}
}
final Phylogeny g2_21 = TestGSDI
.createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],a1[&&NHX:S=a1]))" );
- final GSDI sdi2_21 = new GSDI( g2_21, s2, false );
+ final GSDI sdi2_21 = new GSDI( g2_21, s2, false, false, false );
if ( sdi2_21.getDuplicationsSum() != 1 ) {
return false;
}
}
final Phylogeny g2_22 = TestGSDI
.createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],n4[&&NHX:S=n4]))" );
- final GSDI sdi2_22 = new GSDI( g2_22, s2, false );
+ final GSDI sdi2_22 = new GSDI( g2_22, s2, false, false, false );
//Archaeopteryx.createApplication( g2_22 );
//Archaeopteryx.createApplication( s2 );
if ( sdi2_22.getDuplicationsSum() != 0 ) {
}
final Phylogeny g2_23 = TestGSDI
.createPhylogeny( "((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),(c1[&&NHX:S=c1],d1[&&NHX:S=d1]))" );
- final GSDI sdi2_23 = new GSDI( g2_23, s2, false );
+ final GSDI sdi2_23 = new GSDI( g2_23, s2, false, false, false );
if ( sdi2_23.getDuplicationsSum() != 0 ) {
return false;
}
}
final Phylogeny g2_24 = TestGSDI
.createPhylogeny( "((a1[&&NHX:S=a1],e1[&&NHX:S=e1]),(i1[&&NHX:S=i1],m1[&&NHX:S=m1]))" );
- final GSDI sdi2_24 = new GSDI( g2_24, s2, false );
+ final GSDI sdi2_24 = new GSDI( g2_24, s2, false, false, false );
if ( sdi2_24.getDuplicationsSum() != 0 ) {
return false;
}
}
final Phylogeny g2_25 = TestGSDI
.createPhylogeny( "((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),(b1[&&NHX:S=b1],c1[&&NHX:S=c1]))" );
- final GSDI sdi2_25 = new GSDI( g2_25, s2, false );
+ final GSDI sdi2_25 = new GSDI( g2_25, s2, false, false, false );
if ( sdi2_25.getDuplicationsSum() != 0 ) {
return false;
}
}
final Phylogeny g2_26 = TestGSDI
.createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),e1[&&NHX:S=e1])" );
- final GSDI sdi2_26 = new GSDI( g2_26, s2, false );
+ final GSDI sdi2_26 = new GSDI( g2_26, s2, false, false, false );
if ( sdi2_26.getDuplicationsSum() != 0 ) {
return false;
}
}
final Phylogeny g2_27 = TestGSDI
.createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1])" );
- final GSDI sdi2_27 = new GSDI( g2_27, s2, false );
+ final GSDI sdi2_27 = new GSDI( g2_27, s2, false, false, false );
if ( sdi2_27.getDuplicationsSum() != 0 ) {
return false;
}
}
final Phylogeny g2_28 = TestGSDI
.createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),e1[&&NHX:S=e1])" );
- final GSDI sdi2_28 = new GSDI( g2_28, s2, false );
+ final GSDI sdi2_28 = new GSDI( g2_28, s2, false, false, false );
if ( sdi2_28.getDuplicationsSum() != 0 ) {
return false;
}
}
final Phylogeny g2_29 = TestGSDI
.createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1])" );
- final GSDI sdi2_29 = new GSDI( g2_29, s2, false );
+ final GSDI sdi2_29 = new GSDI( g2_29, s2, false, false, false );
if ( sdi2_29.getDuplicationsSum() != 0 ) {
return false;
}
}
final Phylogeny g2_30 = TestGSDI
.createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),a2[&&NHX:S=a2])" );
- final GSDI sdi2_30 = new GSDI( g2_30, s2, false );
+ final GSDI sdi2_30 = new GSDI( g2_30, s2, false, false, false );
if ( sdi2_30.getDuplicationsSum() != 1 ) {
return false;
}
}
final Phylogeny g2_31 = TestGSDI
.createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),c2[&&NHX:S=c2])" );
- final GSDI sdi2_31 = new GSDI( g2_31, s2, false );
+ final GSDI sdi2_31 = new GSDI( g2_31, s2, false, false, false );
if ( sdi2_31.getDuplicationsSum() != 1 ) {
return false;
}
}
final Phylogeny g2_32 = TestGSDI
.createPhylogeny( "((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1]),x[&&NHX:S=x]),p1[&&NHX:S=p1]),i1[&&NHX:S=i1]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
- final GSDI sdi2_32 = new GSDI( g2_32, s2, false );
+ final GSDI sdi2_32 = new GSDI( g2_32, s2, false, false, false );
if ( sdi2_32.getDuplicationsSum() != 0 ) {
return false;
}
}
final Phylogeny g2_33 = TestGSDI
.createPhylogeny( "(((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1]),x[&&NHX:S=x]),p1[&&NHX:S=p1]),i1[&&NHX:S=i1]),k2[&&NHX:S=k2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
- final GSDI sdi2_33 = new GSDI( g2_33, s2, false );
+ final GSDI sdi2_33 = new GSDI( g2_33, s2, false, false, false );
if ( sdi2_33.getDuplicationsSum() != 1 ) {
return false;
}
}
final Phylogeny g2_33_d = TestGSDI
.createPhylogeny( "((((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2])[&&NHX:D=N],b1[&&NHX:S=b1])[&&NHX:D=N],c1[&&NHX:S=c1])[&&NHX:D=?],d1[&&NHX:S=d1])[&&NHX:D=?],x[&&NHX:S=x])[&&NHX:D=N],p1[&&NHX:S=p1])[&&NHX:D=?],i1[&&NHX:S=i1])[&&NHX:D=?],k2[&&NHX:S=k2])[&&NHX:D=Y],e1[&&NHX:S=e1])[&&NHX:D=Y],y[&&NHX:S=y])[&&NHX:D=Y],z[&&NHX:S=z])[&&NHX:D=?],(((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2])[&&NHX:D=N],b1[&&NHX:S=b1])[&&NHX:D=N],c1[&&NHX:S=c1])[&&NHX:D=?],d1[&&NHX:S=d1])[&&NHX:D=?],x[&&NHX:S=x])[&&NHX:D=N],p1[&&NHX:S=p1])[&&NHX:D=?],i1[&&NHX:S=i1])[&&NHX:D=?],k2[&&NHX:S=k2])[&&NHX:D=Y],e1[&&NHX:S=e1])[&&NHX:D=Y],y[&&NHX:S=y])[&&NHX:D=Y],z[&&NHX:S=z])[&&NHX:D=?])" );
- final GSDI sdi2_33_d = new GSDI( g2_33_d, s2, false );
+ final GSDI sdi2_33_d = new GSDI( g2_33_d, s2, false, false, false );
if ( sdi2_33_d.getDuplicationsSum() != 3 ) {
return false;
}
}
final Phylogeny g2_34 = TestGSDI
.createPhylogeny( "(((n1_0[&&NHX:S=n1],n2_0[&&NHX:S=n2]),(n1_1[&&NHX:S=n1],n3_0[&&NHX:S=n3])),n4_0[&&NHX:S=n4])" );
- final GSDI sdi2_34 = new GSDI( g2_34, s2, false );
+ final GSDI sdi2_34 = new GSDI( g2_34, s2, false, false, false );
if ( sdi2_34.getDuplicationsSum() != 1 ) {
return false;
}
}
final Phylogeny g2_35 = TestGSDI
.createPhylogeny( "((((n1_0[&&NHX:S=n1],n2_0[&&NHX:S=n2]),(n1_1[&&NHX:S=n1],n3_0[&&NHX:S=n3])),n4_0[&&NHX:S=n4]),a1_0[&&NHX:S=a1])" );
- final GSDI sdi2_35 = new GSDI( g2_35, s2, false );
+ final GSDI sdi2_35 = new GSDI( g2_35, s2, false, false, false );
if ( sdi2_35.getDuplicationsSum() != 1 ) {
return false;
}
}
final Phylogeny g2_36 = TestGSDI
.createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a1_1[&&NHX:S=a1],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" );
- final GSDI sdi2_36 = new GSDI( g2_36, s2, false );
+ final GSDI sdi2_36 = new GSDI( g2_36, s2, false, false, false );
if ( sdi2_36.getDuplicationsSum() != 1 ) {
return false;
}
}
final Phylogeny g2_37 = TestGSDI
.createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a2_0[&&NHX:S=a2],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" );
- final GSDI sdi2_37 = new GSDI( g2_37, s2, false );
+ final GSDI sdi2_37 = new GSDI( g2_37, s2, false, false, false );
if ( sdi2_37.getDuplicationsSum() != 1 ) {
return false;
}
}
final Phylogeny g2_38 = TestGSDI
.createPhylogeny( "(((([&&NHX:S=n1],[&&NHX:S=n1]),([&&NHX:S=n1],[&&NHX:S=n1])),[&&NHX:S=n1]),[&&NHX:S=n1])" );
- final GSDI sdi2_38 = new GSDI( g2_38, s2, false );
+ final GSDI sdi2_38 = new GSDI( g2_38, s2, false, false, false );
if ( sdi2_38.getDuplicationsSum() != 5 ) {
return false;
}
}
final Phylogeny g2_100 = TestGSDI
.createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],h2[&&NHX:S=h2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],b1[&&NHX:S=b1])))" );
- final GSDI sdi2_100 = new GSDI( g2_100, s2, false );
+ final GSDI sdi2_100 = new GSDI( g2_100, s2, false, false, false );
if ( sdi2_100.getDuplicationsSum() != 4 ) {
return false;
}
}
final Phylogeny g2_101 = TestGSDI
.createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],b2[&&NHX:S=b2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],j1[&&NHX:S=j1])))" );
- final GSDI sdi2_101 = new GSDI( g2_101, s2, false );
+ final GSDI sdi2_101 = new GSDI( g2_101, s2, false, false, false );
if ( sdi2_101.getDuplicationsSum() != 2 ) {
return false;
}
+ "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
+ "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
+ "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])" );
- final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false );
+ final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false, false, false );
if ( sdi7_4_1.getDuplicationsSum() != 54 ) {
return false;
}
+ "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
+ "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65]),"
+ "66[&&NHX:S=66]),257[&&NHX:S=257]),258[&&NHX:S=258]),513[&&NHX:S=513]),514[&&NHX:S=514]),769[&&NHX:S=769]),770[&&NHX:S=770])" );
- final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false );
+ final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false, false, false );
if ( sdi7_4_2.getDuplicationsSum() != 58 ) {
return false;
}
final String g2_0_ = "(([&&NHX:S=a1],[&&NHX:S=a2]),([&&NHX:S=o2],[&&NHX:S=o4]))";
final Phylogeny g2_0p = TestGSDI.createPhylogeny( g2_0_ );
g2_0.setRooted( true );
- final GSDI sdi2_0p = new GSDI( g2_0p, s2, false );
+ final GSDI sdi2_0p = new GSDI( g2_0p, s2, false, false, false );
if ( sdi2_0p.getDuplicationsSum() != 0 ) {
return false;
}
// Archaeopteryx.createApplication( s1.copy() );
final Phylogeny g1 = TestGSDI
.createPhylogeny( "(HUMAN[&&NHX:S=HUMAN],(RAT[&&NHX:S=RAT],(CAEEL[&&NHX:T=:S=CAEEL],YEAST[&&NHX:S=YEAST])))" );
- final GSDIR sdi1 = new GSDIR( g1.copy(), s1.copy(), false, 1 );
+ final GSDIR sdi1 = new GSDIR( g1.copy(), s1.copy(), false, false );
if ( sdi1.getMinDuplicationsSum() != 0 ) {
return false;
}
//
final Phylogeny g2 = TestGSDI
.createPhylogeny( "(((HUMAN[&&NHX:S=HUMAN],RAT[&&NHX:S=RAT]),CAEEL[&&NHX:T=:S=CAEEL]),YEAST[&&NHX:S=YEAST])" );
- final GSDIR sdi2 = new GSDIR( g2.copy(), s1.copy(), false, 1 );
+ final GSDIR sdi2 = new GSDIR( g2.copy(), s1.copy(), false, false );
if ( sdi2.getMinDuplicationsSum() != 0 ) {
return false;
}
final Phylogeny g3 = TestGSDI
.createPhylogeny( "(RAT[&&NHX:S=RAT],HUMAN[&&NHX:S=HUMAN],(YEAST[&&NHX:S=YEAST],CAEEL[&&NHX:T=:S=CAEEL]))" );
// Archaeopteryx.createApplication( g3 );
- final GSDIR sdi3 = new GSDIR( g3.copy(), s1.copy(), false, 1 );
+ final GSDIR sdi3 = new GSDIR( g3.copy(), s1.copy(), false, false );
if ( sdi3.getMinDuplicationsSum() != 0 ) {
return false;
}
final Phylogeny g4 = TestGSDI
.createPhylogeny( "(((((MOUSE[&&NHX:S=MOUSE],[&&NHX:S=RAT]),[&&NHX:S=HUMAN]),([&&NHX:S=ARATH],[&&NHX:S=YEAST])),[&&NHX:S=CAEEL]),[&&NHX:S=CAEBR])" );
Archaeopteryx.createApplication( g4 );
- final GSDIR sdi4 = new GSDIR( g4.copy(), s1.copy(), false, 1 );
+ final GSDIR sdi4 = new GSDIR( g4.copy(), s1.copy(), false, false );
if ( sdi4.getMinDuplicationsSum() != 0 ) {
return false;
}
git://source.jalview.org / jalview.git / commitdiff