From 293498c7e9e58d3ec6e4f99c12ab6561943287af Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Sat, 8 Dec 2012 05:48:20 +0000 Subject: [PATCH] "rio" work --- .../java/src/org/forester/application/sdi_dir.java | 462 -------------------- .../java/src/org/forester/application/sdi_r.java | 2 +- .../org/forester/phylogeny/PhylogenyMethods.java | 7 +- forester/java/src/org/forester/sdi/RIO.java | 27 +- 4 files changed, 25 insertions(+), 473 deletions(-) delete mode 100644 forester/java/src/org/forester/application/sdi_dir.java diff --git a/forester/java/src/org/forester/application/sdi_dir.java b/forester/java/src/org/forester/application/sdi_dir.java deleted file mode 100644 index d1bcbce..0000000 --- a/forester/java/src/org/forester/application/sdi_dir.java +++ /dev/null @@ -1,462 +0,0 @@ -// $Id: -// FORESTER -- software libraries and applications -// for evolutionary biology research and applications. -// -// Copyright (C) 2008-2009 Christian M. Zmasek -// Copyright (C) 2008-2009 Burnham Institute for Medical Research -// Copyright (C) 2000-2001 Washington University School of Medicine -// and Howard Hughes Medical Institute -// All rights reserved -// -// This library is free software; you can redistribute it and/or -// modify it under the terms of the GNU Lesser General Public -// License as published by the Free Software Foundation; either -// version 2.1 of the License, or (at your option) any later version. -// -// This library is distributed in the hope that it will be useful, -// but WITHOUT ANY WARRANTY; without even the implied warranty of -// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -// Lesser General Public License for more details. -// -// You should have received a copy of the GNU Lesser General Public -// License along with this library; if not, write to the Free Software -// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -// -// Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester - -package org.forester.application; - -import java.io.File; -import java.io.FileWriter; -import java.io.IOException; -import java.io.PrintWriter; -import java.util.Arrays; - -import org.forester.io.parsers.phyloxml.PhyloXmlParser; -import org.forester.io.writers.PhylogenyWriter; -import org.forester.phylogeny.Phylogeny; -import org.forester.phylogeny.PhylogenyMethods; -import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; -import org.forester.phylogeny.factories.PhylogenyFactory; -import org.forester.sdi.SDIException; -import org.forester.sdi.SDIR; -import org.forester.sdi.SDIse; -import org.forester.util.ForesterUtil; - -/* - * Allows to infer duplications - speciations on all (rooted or unrooted) gene - * trees in a directory by using method "infer" of class SDIunrooted.

The - * output of this is a (re)rooted tree with speciation - duplication assigned - * for each tree (in "gene tree directory" with suffix "suffix for gene trees"), - * as well as a summary list ("outputfile name").

The summary list contains - * the following. The number in brackets indicates how many external nodes of - * the gene tree had to be removed since the associated species was not found in - * the species tree. "en" indicates the number of external nodes in the - * resulting (analyzed and returned) gene tree. "d" are the number of - * duplications, "L=" the mapping cost, "h=" the height, "d=" the minimal - * difference in tree heights (of the two subtrees at the root; this number is - * 0.0 for a midpoint rooted tree) of the resulting, analyzed and rooted gene - * tree(s).

The output file ending with "_Sdist" is a file which lists the - * distribution of trees sizes, "_Ddist" lists the distribution of the sums of - * duplications (up to a certain maximal size, set with final variables - * MAX_EXT_NODE_DIST and MAX_DUP_DIST). - * - * @see SDIunrooted - * - * @author Christian M. Zmasek - */ -public class sdi_dir { - - final static private String E_MAIL = "czmasek@burnham.org"; - final static private String WWW = "www.phylosoft.org"; - final static private String PRG_NAME = "sdi_dir"; - final static private String PRG_VERSION = "2.00"; - final static private String PRG_DATE = "2010.04.26"; - - private static void errorInCommandLine() { - System.out.println( "\nsdi_dir: Error in command line.\n" ); - System.out.print( "Usage: % sdi_dir [-options] " ); - System.out.println( " " ); - System.out.println( "\nOptions:" ); - System.out.println( " -l to root by minimizing the mapping cost L (and also the sum of duplications)" ); - System.out.println( " -d to root by minimizing the sum of duplications" ); - System.out.println( " -h to root by minimizing tree height (can be used together with -l or -d)" ); - System.out.println( " -w to write assigned gene trees into output directory" ); - System.out.println( "\nGene tree directory" ); - System.out.println( " The directory from which to read phyloXML formatted gene trees which" ); - System.out.println( " contain taxonomic information in appropriate sub-elements of taxonomy" ); - System.out.println( " (see: www.phyloxml.org)." ); - System.out.println( " The gene trees can either be rooted, in which case no rooting with -l, -d, or -h " ); - System.out.println( " is necessary, or they can be unrooted, in which case rooting is mandatory." ); - System.out.println( "\nSuffix for gene trees" ); - System.out.println( " Suffix of the gene trees to analyze (e.g. \".phyloxml\")." ); - System.out.println( "\nSpecies tree file" ); - System.out.println( " In phyloXML format, taxonomic information in appropriate sub-elements of taxonomy." ); - System.out.println( " (see: www.phyloxml.org)." ); - System.out.println( "\nOutput directory" ); - System.out.println( " The directory into which the assigned gene trees will be written." ); - System.out.println( "\nOutputfile name" ); - System.out.println( " File name for summary output files." ); - System.out.println( "" ); - System.exit( -1 ); - } - - /** - * Runs method "infer" of class SDIunrooted on all gene trees in directory - * indir. - *

- * Trees are rooted by minimizing either the sum of duplications, the - * mapping cost L, or the tree height (or combinations thereof). One - * resulting tree for each (out of possibly many) is stored in outdir and a - * summary outfile is created. The distributions of the tree sizes (name of - * outfile + _Ddist) and the distributions of the sum of duplications per - * tree (name of outfile + _Sdist) are written out as well. - *

- * If both minimize_sum_of_dup and minimize_mapping_cost are true, trees are - * rooted by minimizing by minimizing the mapping cost L. - *

- * If minimize_sum_of_dup, minimize_mapping_cost, and minimize_height are - * false trees are assumed to be alreadty rooted. - *

- * (Last modified: 02/02/01) - * - * @see SDIR#infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) - * @param indir - * a directory containing gene trees in NHX format - * @param species_tree_file - * a species tree file in NHX format - * @param outdir - * a directory where to write trees - * @param outfile - * a file name for the summary file - * @param suffix - * a suffix for the trees to read (e.g. nhx), is case sensitive - * @param write_trees - * set to true to write out one tree with minmal duplications or - * L each - * @param minimize_mapping_cost - * set to true to root by minimizing the mapping cost L - * @param minimize_sum_of_dup - * set to true to root by minimizing the sum of duplications - * @param minimize_height - * set to true to root by minimizing the tree height -- if - * minimize_mapping_cost is set to true or minimize_sum_of_dup is - * set to true, then out of the resulting trees with minimal - * mapping cost or minimal number of duplications the tree with - * the minimal height is chosen - * @throws SDIException - */ - public static void infer( final File indir, - final File species_tree_file, - final File outdir, - final File outfile, - String suffix, - final boolean write_trees, - final boolean minimize_mapping_cost, - boolean minimize_sum_of_dup, - final boolean minimize_height ) throws IOException, SDIException { - final int MIN_EXT_NODES = 4; // Minimal size of trees [in ext nodes] - // to be analyzed. - final int MAX_EXT_NODES = 5000; // Maximal size of trees [in ext nodes] - // to be analyzed. - final int MAX_DUP_DIST = 50; // Max number of dups to output in dup - // distribution ("_Ddist"). - final int MAX_EXT_NODE_DIST = 1000; // Max number of ext nodes to output - // in size - // distribution ("_Sdist"). - int successful = 0, number_of_too_small_trees = 0, number_of_too_large_trees = 0, dups = 0, c = 0, ext_nodes = 0, removed = 0; - final int nodecount0 = 0; - int j = 0; - long total_number_of_d = 0, total_number_of_ext_nodes = 0, sum_costs = 0; - double sum_tree_heights = 0.0, sum_subtree_diff = 0.0; - Phylogeny species_tree = null; - String filename = null; - String[] filenames = null; - Phylogeny[] trees = null; - final int[] duplications = new int[ MAX_EXT_NODES - 1 ], // For dup - // distribution. - sizes = new int[ MAX_EXT_NODES - 1 ]; // For ext nodes dist.of - // successfully assigned trees. - File outtree = null; - PrintWriter out = null, out_ddist = null, out_sdist = null; - final File ddist_outfile = new File( outfile + "_Ddist" ), sdist_outfile = new File( outfile + "_Sdist" ); - final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.0#####" ); - df.setDecimalSeparatorAlwaysShown( true ); - if ( !indir.exists() || !indir.isDirectory() ) { - throw new IllegalArgumentException( indir + " does not exist or is not a directory." ); - } - if ( !outdir.exists() || !outdir.isDirectory() ) { - throw new IllegalArgumentException( outdir + " does not exist or is not a directory." ); - } - if ( outfile.exists() ) { - throw new IllegalArgumentException( outfile + " does already exist." ); - } - if ( ddist_outfile.exists() ) { - throw new IllegalArgumentException( ddist_outfile + " does already exist." ); - } - if ( sdist_outfile.exists() ) { - throw new IllegalArgumentException( sdist_outfile + " does already exist." ); - } - if ( !species_tree_file.exists() || !species_tree_file.isFile() ) { - throw new IllegalArgumentException( species_tree_file + " does not exist or is not a file." ); - } - if ( minimize_mapping_cost && minimize_sum_of_dup ) { - minimize_sum_of_dup = false; - } - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ]; - filenames = indir.list(); - Arrays.sort( filenames ); - suffix = suffix.trim(); - out = new PrintWriter( new FileWriter( outfile ), true ); - //nodecount0 = PhylogenyNode.getNodeCount(); - for( final String filename2 : filenames ) { - filename = filename2; - if ( ( suffix.length() < 1 ) || filename.endsWith( suffix ) ) { - final File gene_tree_file = new File( indir.getPath(), filename ); - if ( gene_tree_file.exists() && gene_tree_file.isFile() ) { - out.print( j + "\t" + filename ); - System.out.println( j + ": " + filename ); - j++; - Phylogeny gene_tree = null; - gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ]; - // Removes from gene_tree all species not found in - // species_tree. - removed = PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gene_tree ); - if ( filename.length() < 8 ) { - out.print( "\t\t\t[-" + removed + "]" ); - } - else if ( filename.length() < 16 ) { - out.print( "\t\t[-" + removed + "]" ); - } - else { - out.print( "\t[-" + removed + "]" ); - } - if ( gene_tree.getNumberOfExternalNodes() < MIN_EXT_NODES ) { - out.print( "\t<" + MIN_EXT_NODES + "en\n" ); - number_of_too_small_trees++; - } - else if ( gene_tree.getNumberOfExternalNodes() > MAX_EXT_NODES ) { - out.print( "\t>" + MAX_EXT_NODES + "en\n" ); - number_of_too_large_trees++; - } - else { - SDIR sdiunrooted = null; - // PhylogenyNode.setNodeCount( nodecount0 ); - sdiunrooted = new SDIR(); - if ( minimize_mapping_cost || minimize_sum_of_dup || minimize_height ) { - trees = sdiunrooted.infer( gene_tree, - species_tree, - minimize_mapping_cost, - minimize_sum_of_dup, - minimize_height, - write_trees, - 1 ); - dups = sdiunrooted.getMinimalDuplications(); - } - else { - final SDIse sdi = new SDIse( gene_tree, species_tree ); - trees = new Phylogeny[ 1 ]; - trees[ 0 ] = gene_tree; - dups = sdi.getDuplicationsSum(); - c = sdi.computeMappingCostL(); - sum_costs += c; - out.print( "\t L=" + c ); - } - successful++; - ext_nodes = gene_tree.getNumberOfExternalNodes(); - total_number_of_ext_nodes += ext_nodes; - sizes[ ext_nodes ]++; - out.print( "\t " + ext_nodes + "en" ); - total_number_of_d += dups; - duplications[ dups ]++; - out.print( "\t " + dups + "d" ); - if ( minimize_mapping_cost ) { - c = sdiunrooted.getMinimalMappingCost(); - sum_costs += c; - out.print( "\t L=" + c ); - } - if ( minimize_height ) { - out.print( "\t h=" + df.format( sdiunrooted.getMinimalTreeHeight() ) ); - out.print( "\t d=" + df.format( sdiunrooted.getMinimalDiffInSubTreeHeights() ) ); - sum_tree_heights += sdiunrooted.getMinimalTreeHeight(); - sum_subtree_diff += sdiunrooted.getMinimalDiffInSubTreeHeights(); - } - out.println(); - if ( write_trees ) { - outtree = new File( outdir, new File( filename2 ).getName() ); - final PhylogenyWriter writer = new PhylogenyWriter(); - writer.toPhyloXML( outtree, trees[ 0 ], 1 ); - } - } - } - } - } - //PhylogenyNode.setNodeCount( nodecount0 ); - if ( minimize_mapping_cost ) { - out.println( "\nRooted by minimizing mapping cost L." ); - System.out.println( "\nRooted by minimizing mapping cost L." ); - if ( minimize_height ) { - out.println( "Selected tree(s) with minimal height out of resulting trees." ); - System.out.println( "Selected tree(s) with minimal height out of resulting trees." ); - } - } - else if ( minimize_sum_of_dup ) { - out.println( "\nRooted by minimizing sum of duplications." ); - System.out.println( "\nRooted by minimizing sum of duplications." ); - if ( minimize_height ) { - out.println( "Selected tree(s) with minimal height out of resulting trees." ); - System.out.println( "Selected tree(s) with minimal height out of resulting trees." ); - } - } - else if ( minimize_height ) { - out.println( "\nRooted by minimizing tree height." ); - System.out.println( "\nRooted by minimizing tree height." ); - } - else { - out.println( "\nNo (re) rooting was performed." ); - System.out.println( "\nNo (re) rooting was performed." ); - } - out.println( "\nTrees directory : " + indir ); - out.println( "Suffix for trees : " + suffix ); - out.println( "Species tree : " + species_tree_file ); - out.println( "Output directory : " + outdir ); - out.println( "Output file : " + outfile ); - out.println( "\nTotal number of attempts (tree files read) : " + j ); - out.println( "Total number of successfully assigned trees : " + successful ); - out.println( "Number of too small trees : " + number_of_too_small_trees ); - out.println( "Number of too large trees : " + number_of_too_large_trees ); - out.println( "\nSum of duplications : " + total_number_of_d ); - if ( minimize_mapping_cost ) { - out.println( "Sum of mapping costs L : " + sum_costs ); - } - if ( minimize_height ) { - out.println( "Sum of tree heights : " + sum_tree_heights ); - out.println( "Sum of differences in subtree heights : " + sum_subtree_diff ); - } - out.println( "Sum of external nodes (in successfully assigned trees): " + total_number_of_ext_nodes ); - out.close(); - System.out.println( "\nTotal number of attempts (tree files read) : " + j ); - System.out.println( "Total number of successfully assigned trees : " + successful ); - System.out.println( "Number of too small trees : " + number_of_too_small_trees ); - System.out.println( "Number of too large trees : " + number_of_too_large_trees ); - System.out.println( "\nSum of duplications : " + total_number_of_d ); - if ( minimize_mapping_cost ) { - System.out.println( "Sum of mapping costs L : " + sum_costs ); - } - if ( minimize_height ) { - System.out.println( "Sum of tree heights : " + sum_tree_heights ); - System.out.println( "Sum of differences in subtree heights : " + sum_subtree_diff ); - } - System.out.println( "Sum of external nodes (in successfully assigned trees): " + total_number_of_ext_nodes ); - out_ddist = new PrintWriter( new FileWriter( ddist_outfile ), true ); - for( int i = 0; ( i < duplications.length ) && ( i <= MAX_DUP_DIST ); ++i ) { - out_ddist.println( i + " " + duplications[ i ] ); - } - out_ddist.close(); - out_sdist = new PrintWriter( new FileWriter( sdist_outfile ), true ); - for( int i = 0; ( i < sizes.length ) && ( i <= MAX_EXT_NODE_DIST ); ++i ) { - out_sdist.println( i + " " + sizes[ i ] ); - } - out_sdist.close(); - } // infer - - /** - * Main method for this class. - *

- * (Last modified: 04/26/10) - * - * @param [args[0] - * -l to root by minimizing mapping cost L] - * @param [args[0] - * -d to root by minimizing sum of duplications] - * @param [args[0] - * -w to write out trees into outdir] - * @param [args[0] - * -h to root by minimizing tree height] - * @param [args[0] - * -n input trees are in New Hampshire format instead of NHX -- - * or gene tree is in NHX, but species information in gene tree - * is only present in the form of SWISS-PROT sequence names] - * @param args[0or1] - * trees directory name - * @param args[1or2] - * suffix for gene trees - * @param args[2or3] - * speciestree file name - * @param args[3or4] - * output directory name - * @param args[4or5] - * output file name - */ - public static void main( final String args[] ) { - ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW ); - // These are the default values. - boolean minimize_mapping_cost = false; - boolean minimize_sum_of_dup = false; - boolean minimize_height = false; - boolean write_trees = false; - File indir = null; - File speciestree_file = null; - File outdir = null; - File outfile = null; - String suffix = null; - if ( args.length == 5 ) { - indir = new File( args[ 0 ] ); - suffix = args[ 1 ]; - speciestree_file = new File( args[ 2 ] ); - outdir = new File( args[ 3 ] ); - outfile = new File( args[ 4 ] ); - } - else if ( args.length == 6 ) { - if ( args[ 0 ].startsWith( "-" ) ) { - minimize_mapping_cost = false; - minimize_sum_of_dup = false; - minimize_height = false; - write_trees = false; - if ( args[ 0 ].toLowerCase().indexOf( "w" ) != -1 ) { - write_trees = true; - } - if ( args[ 0 ].toLowerCase().indexOf( "l" ) != -1 ) { - minimize_mapping_cost = true; - } - if ( args[ 0 ].toLowerCase().indexOf( "d" ) != -1 ) { - minimize_sum_of_dup = true; - } - if ( args[ 0 ].toLowerCase().indexOf( "h" ) != -1 ) { - minimize_height = true; - } - } - else { - sdi_dir.errorInCommandLine(); - } - indir = new File( args[ 1 ] ); - suffix = args[ 2 ]; - speciestree_file = new File( args[ 3 ] ); - outdir = new File( args[ 4 ] ); - outfile = new File( args[ 5 ] ); - } - else { - sdi_dir.errorInCommandLine(); - } - if ( minimize_mapping_cost && minimize_sum_of_dup ) { - minimize_sum_of_dup = false; - } - try { - sdi_dir.infer( indir, - speciestree_file, - outdir, - outfile, - suffix, - write_trees, - minimize_mapping_cost, - minimize_sum_of_dup, - minimize_height ); - } - catch ( final Exception e ) { - ForesterUtil.fatalError( PRG_NAME, "error: " + e.getLocalizedMessage() ); - } - ForesterUtil.programMessage( PRG_NAME, "OK." ); - } -} diff --git a/forester/java/src/org/forester/application/sdi_r.java b/forester/java/src/org/forester/application/sdi_r.java index 0b2475b..026f3f6 100644 --- a/forester/java/src/org/forester/application/sdi_r.java +++ b/forester/java/src/org/forester/application/sdi_r.java @@ -134,7 +134,7 @@ public class sdi_r { int gene_tree_counter = 0; final List all_result_trees = new ArrayList(); for( final Phylogeny gene_tree : gene_trees ) { - r = PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gene_tree ); + r = PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gene_tree ).size(); ForesterUtil.programMessage( PRG_NAME, "Removed " + r + " external nodes from gene tree" ); final SDIR sdiunrooted = new SDIR(); final long start_time = new Date().getTime(); diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java index f839fd6..b89575e 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java @@ -1613,9 +1613,10 @@ public class PhylogenyMethods { * a reference Phylogeny * @param to_be_stripped * Phylogeny to be stripped - * @return number of external nodes removed from to_be_stripped + * @return nodes removed from to_be_stripped */ - public static int taxonomyBasedDeletionOfExternalNodes( final Phylogeny reference, final Phylogeny to_be_stripped ) { + public static List taxonomyBasedDeletionOfExternalNodes( final Phylogeny reference, + final Phylogeny to_be_stripped ) { final Set ref_ext_taxo = new HashSet(); for( final PhylogenyNodeIterator it = reference.iteratorExternalForward(); it.hasNext(); ) { final PhylogenyNode n = it.next(); @@ -1646,7 +1647,7 @@ public class PhylogenyMethods { } to_be_stripped.clearHashIdToNodeMap(); to_be_stripped.externalNodesHaveChanged(); - return nodes_to_delete.size(); + return nodes_to_delete; } /** diff --git a/forester/java/src/org/forester/sdi/RIO.java b/forester/java/src/org/forester/sdi/RIO.java index 31e2fc7..25adc9d 100644 --- a/forester/java/src/org/forester/sdi/RIO.java +++ b/forester/java/src/org/forester/sdi/RIO.java @@ -58,6 +58,7 @@ public final class RIO { private HashMap> _so_maps; private HashMap> _up_maps; private List _seq_names; + private List _removed_gene_tree_nodes; private int _samples; private int _ext_nodes; @@ -392,7 +393,8 @@ public final class RIO { } final Phylogeny[] gene_trees = factory.create( gene_trees_file, p ); // Removes from species_tree all species not found in gene_tree. - PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( gene_trees[ 0 ], species_tree ); + List _removed_gene_tree_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" ); } @@ -414,22 +416,29 @@ public final class RIO { } _analyzed_gene_trees = new Phylogeny[ gene_trees.length ]; int c = 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" ); } - _analyzed_gene_trees[ c++ ] = inferOrthologsHelper( gt, species_tree, query ); + 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 + ")" ); + } + _analyzed_gene_trees[ c++ ] = performOrthologInference( gt, species_tree, query ); } setNumberOfSamples( gene_trees.length ); } - // Helper method which performs the actual ortholog inference for - // the external node with seqname query. - private final Phylogeny inferOrthologsHelper( final Phylogeny gene_tree, - final Phylogeny species_tree, - final String query ) throws SDIException, RIOException { + private final Phylogeny performOrthologInference( final Phylogeny gene_tree, + final Phylogeny species_tree, + final String query ) throws SDIException, RIOException { final SDIR sdiunrooted = new SDIR(); final Phylogeny assigned_tree = sdiunrooted.infer( gene_tree, species_tree, @@ -680,6 +689,10 @@ public final class RIO { return nodes; } + public final List getRemovedGeneTreeNodes() { + return _removed_gene_tree_nodes; + } + private final class ResultLine implements Comparable { public static final int DEFAULT = -999; -- 1.7.10.2