+++ /dev/null
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research
-// 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.sdi;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-
-import org.forester.io.parsers.PhylogenyParser;
-import org.forester.io.parsers.util.ParserUtils;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.util.ForesterUtil;
-
-/*
- * Allows to <ul> <li> <li> <li> </ul>
- *
- * @see SDIse
- *
- * @see SDI
- *
- * @author Christian M. Zmasek
- *
- * @version 1.400 -- last modified: 10/29/2005
- */
-public class ORcount {
-
- private static final String[] group_1 = { "ANOGA", "DROME", "CAEBR", "CAEEL" };
- private static final String[] group_2 = { "CIOIN", "FUGRU", "MOUSE", "RAT",
- "HUMAN" };
- private static final String[] all_species = { "ANOGA", "DROME", "CAEBR", "CAEEL",
- "CIOIN", "FUGRU", "MOUSE", "RAT", "HUMAN" };
- private final Phylogeny[] _trees;
- private HashMap<String, HashMap<Object, Integer>> _species = null;
- private ArrayList<String> _names = null;
- private int _group1_vs_2_counter = 0;
-
- /**
- * Default contructor which
- */
- public ORcount( final Phylogeny[] trees ) {
- _trees = trees;
- } // ORcount( final Phylogeny[] trees )
-
- private void count( final PhylogenyNode node ) {
- final List<PhylogenyNode> external_nodes = node.getAllExternalDescendants();
- for( int i = 1; i < external_nodes.size(); ++i ) {
- for( int j = 0; j < i; ++j ) {
- final PhylogenyNode node_i = external_nodes.get( i );
- final PhylogenyNode node_j = external_nodes.get( j );
- final String si = PhylogenyMethods.getSpecies( node_i );
- final String sj = PhylogenyMethods.getSpecies( node_j );
- count( si, sj, node_i.getName(), node_j.getName() );
- }
- }
- } // count( PhylogenyNode )
-
- private void count( final String a, final String b, final String seq_name_a, final String seq_name_b ) {
- HashMap<Object, Integer> h1 = _species.get( a );
- if ( h1 == null ) {
- throw new RuntimeException( "Unexpected error: Species \"" + a + "\" not present in species matrix." );
- }
- Object h2 = h1.get( b );
- String species_in_h1 = b;
- // We only look at the half matrix, and we do not know/care about the
- // order
- // of the keys (species).
- if ( h2 == null ) {
- h1 = _species.get( b );
- if ( h1 == null ) {
- throw new RuntimeException( "Unexpected error: Species \"" + b + "\" not present in species matrix." );
- }
- h2 = h1.get( a );
- species_in_h1 = a;
- }
- if ( h2 == null ) {
- throw new RuntimeException( "Unexpected error: Species \"" + a + "\" not present in species matrix." );
- }
- h1.put( species_in_h1, new Integer( ( ( Integer ) h2 ).intValue() + 1 ) );
- _names.add( a + "-" + seq_name_a + " = " + b + "-" + seq_name_b );
- } // count( String, String )
-
- public void countSharedAncestralClades( final Phylogeny tree,
- final int bootstrap_threshold,
- final String[] group_1,
- final String[] group_2 ) {
- if ( ( group_1 == null ) || ( group_2 == null ) ) {
- throw new IllegalArgumentException( "String[](s) in arguments to method \"ORcount.countSharedAncestralClades\" is (are) null." );
- }
- if ( !tree.isRooted() ) {
- throw new IllegalArgumentException( "Phylogeny must be rooted in order to count shared ancestral clades." );
- }
- final PhylogenyNodeIterator it = tree.iteratorPostorder();
- tree.setIndicatorsToZero();
- while ( it.hasNext() ) {
- final PhylogenyNode current_node = it.next();
- if ( current_node.getNumberOfDescendants() != 2 ) {
- throw new IllegalArgumentException( "Phylogeny can not contain multifurcations in order to count shared ancestral clades." );
- }
- if ( !current_node.isExternal() ) {
- final PhylogenyNode child1 = current_node.getChildNode1();
- final PhylogenyNode child2 = current_node.getChildNode2();
- if ( ( child1.getIndicator() == 1 ) || ( child2.getIndicator() == 1 ) ) {
- current_node.setIndicator( ( byte ) 1 );
- }
- else {
- final List<PhylogenyNode> external_nodes = current_node.getAllExternalDescendants();
- final String[] external_species = new String[ external_nodes.size() ];
- for( int i = 0; i < external_nodes.size(); ++i ) {
- final PhylogenyNode n = external_nodes.get( i );
- external_species[ i ] = PhylogenyMethods.getSpecies( n ).trim().toUpperCase();
- }
- if ( ForesterUtil.isIntersecting( external_species, group_1 )
- && ForesterUtil.isIntersecting( external_species, group_2 ) ) {
- current_node.setIndicator( ( byte ) 1 );
- if ( ( group_1.length == 1 ) && ( group_2.length == 1 ) ) {
- count( group_1[ 0 ], group_2[ 0 ], "name a", "name b" );
- }
- else {
- increaseGroup1Vs2Counter();
- }
- }
- }
- }
- } // while
- } // countSharedAncestralClades( Phylogeny, int )
-
- public void countSharedAncestralClades( final Phylogeny[] trees, final int bootstrap_threshold ) {
- for( int i = 1; i < ORcount.all_species.length; ++i ) {
- for( int j = 0; j < i; ++j ) {
- final String all_i = ORcount.all_species[ i ].trim().toUpperCase();
- final String all_j = ORcount.all_species[ j ].trim().toUpperCase();
- final String[] a = { all_i };
- final String[] b = { all_j };
- for( final Phylogeny tree : trees ) {
- countSharedAncestralClades( tree, bootstrap_threshold, a, b );
- }
- }
- }
- // print();
- if ( ( ORcount.group_1 != null ) && ( ORcount.group_2 != null ) && ( ORcount.group_1.length > 0 )
- && ( ORcount.group_2.length > 0 ) ) {
- setGroup1Vs2Counter( 0 );
- for( final Phylogeny tree : trees ) {
- countSharedAncestralClades( tree, bootstrap_threshold, ORcount.group_1, ORcount.group_2 );
- }
- System.out.println( "\nCount [(" + ForesterUtil.stringArrayToString( ORcount.group_1 ) + ") vs ("
- + ForesterUtil.stringArrayToString( ORcount.group_2 ) + ")] = " + getGroup1Vs2Counter() );
- }
- }
-
- public void countSuperOrthologousRelations( final int bootstrap_threshold ) {
- reset();
- for( final Phylogeny _tree : _trees ) {
- countSuperOrthologousRelations( _tree, bootstrap_threshold );
- }
- }
-
- private void countSuperOrthologousRelations( final Phylogeny tree, final int bootstrap_threshold ) {
- final PhylogenyNodeIterator it = tree.iteratorPostorder();
- if ( !tree.isRooted() ) {
- throw new IllegalArgumentException( "Phylogeny must be rooted in order to count 1:1 orthologous relationships." );
- }
- // The purpose of this is to find all substrees
- // which contain only speciation events on all their nodes.
- // All nodes in these subtrees are "painted" with 0's, wheres
- // the rest od the nodes in painted with 1's.
- tree.setIndicatorsToZero();
- it.reset();
- while ( it.hasNext() ) {
- final PhylogenyNode current_node = it.next();
- if ( current_node.getNumberOfDescendants() != 2 ) {
- throw new IllegalArgumentException( "Phylogeny can not contain multifurcations in order to count 1:1 orthologous relationships." );
- }
- if ( !current_node.isExternal() && !current_node.isHasAssignedEvent() ) {
- throw new IllegalArgumentException( "All nodes must have duplication or speciation assigned in order to count 1:1 orthologous relationships." );
- }
- if ( !current_node.isExternal()
- && ( current_node.isDuplication() || ( current_node.getChildNode1().getIndicator() == 1 ) || ( current_node
- .getChildNode2().getIndicator() == 1 ) ) ) {
- current_node.setIndicator( ( byte ) 1 );
- }
- }
- // These find the largest subtrees containing only speciations
- // and uses their largest nodes to count all possible species
- // combinations
- // in their extant external nodes.
- // ~~~ this could possibly be combined with the first iteration ~~
- // <<<<<<<<<<<~~~~~~~~~~~~~~~<<<<<<<<<<<<<<<
- it.reset();
- while ( it.hasNext() ) {
- final PhylogenyNode current_node = it.next();
- if ( !current_node.isExternal()
- && ( current_node.getIndicator() == 0 )
- && ( current_node.isRoot() || ( current_node.getParent().getIndicator() == 1 ) )
- && ( ( bootstrap_threshold < 1 ) || ( ( PhylogenyMethods.getConfidenceValue( current_node ) >= bootstrap_threshold )
- && ( PhylogenyMethods.getConfidenceValue( current_node.getChildNode1() ) >= bootstrap_threshold ) && ( PhylogenyMethods
- .getConfidenceValue( current_node.getChildNode2() ) >= bootstrap_threshold ) ) ) ) {
- count( current_node );
- }
- }
- } // countOneToOneOrthologs( Phylogeny, int )
-
- // This puts all the species found in Phylogeny array _trees into
- // species HashMap.
- private void getAllSpecies() {
- if ( ( getTrees() == null ) || ( getTrees().length < 1 ) ) {
- throw new RuntimeException( "Phylogeny array in method \"getAllSpecies( HashMap hash )\" is null or empty." );
- }
- setSpecies( new HashMap<String, HashMap<Object, Integer>>() );
- for( int i = 0; i < getTrees().length; ++i ) {
- PhylogenyNode node = getTrees()[ i ].getFirstExternalNode();
- while ( node != null ) {
- getSpecies().put( PhylogenyMethods.getSpecies( node ), null );
- node = node.getNextExternalNode();
- }
- }
- } // void getAllSpecies( HashMap hash )
-
- private int getGroup1Vs2Counter() {
- return _group1_vs_2_counter;
- }
-
- private HashMap<String, HashMap<Object, Integer>> getSpecies() {
- return _species;
- }
-
- private Phylogeny[] getTrees() {
- return _trees;
- }
-
- private void increaseGroup1Vs2Counter() {
- _group1_vs_2_counter++;
- }
-
- private void printCount() {
- if ( ( _species == null ) || ( _species.size() < 2 ) ) {
- throw new RuntimeException( "Species HashMap in method \"setUpCountingMatrix()\" is null or contains less than two species." );
- }
- final Object[] species_array = _species.keySet().toArray();
- final int s = species_array.length;
- for( int i = 0; i < ( s - 1 ); ++i ) {
- final String species = ( String ) species_array[ i ];
- System.out.println();
- System.out.println( species + ":" );
- final HashMap<?, ?> h = _species.get( species );
- // Setting up HashMaps linked to by hash (=_species)
- // Diagonals are ignored, only half the matrix is needed.
- for( int j = 1 + i; j < s; ++j ) {
- final String sp = ( String ) species_array[ j ];
- final int c = ( ( Integer ) h.get( sp ) ).intValue();
- System.out.println( species + "-" + sp + ": " + c );
- }
- }
- }
-
- private void printNames() {
- for( int i = 0; i < _names.size(); ++i ) {
- System.out.println( i + ": " + _names.get( i ) );
- }
- }
-
- public void reset() {
- getAllSpecies();
- setUpCountingMatrix();
- setGroup1Vs2Counter( 0 );
- _names = new ArrayList<String>();
- }
-
- private void setGroup1Vs2Counter( final int group1_vs_2_counter ) {
- _group1_vs_2_counter = group1_vs_2_counter;
- }
-
- private void setSpecies( final HashMap<String, HashMap<Object, Integer>> species ) {
- _species = species;
- }
-
- private void setUpCountingMatrix() {
- if ( ( getSpecies() == null ) || ( getSpecies().size() < 2 ) ) {
- throw new RuntimeException( "Species HashMap in method \"setUpCountingMatrix()\" is null or contains less than two species." );
- }
- final Object[] species_array = getSpecies().keySet().toArray();
- final int s = species_array.length;
- for( int i = 0; i < s; ++i ) {
- final String species = ( String ) species_array[ i ];
- final HashMap<Object, Integer> h = new HashMap<Object, Integer>();
- // Setting up HashMaps linked to by hash (=_species)
- // Diagonals are ignored, only half the matrix is needed.
- for( int j = 1 + i; j < s; ++j ) {
- h.put( species_array[ j ], new Integer( 0 ) );
- }
- getSpecies().put( species, h );
- }
- }
-
- private static void errorInCommandLine() {
- System.out.println( "\nORcount: Error in command line.\n" );
- System.out.println( "Usage: \"\"" );
- System.out.println( "\nOptions:" );
- System.out.println( " -" );
- System.out.println( "" );
- System.exit( -1 );
- } // errorInCommandLine()
-
- /**
- * Main method for this class.
- * <p>
- * (Last modified: 11/26/03)
- *
- * @param args[1or2]
- * gene tree file name (in NHX format with species names in
- * species name fields and sequence names in sequence name
- * fields; unless -n option is used)
- */
- public static void main( final String args[] ) {
- if ( args.length == 0 ) {
- ORcount.errorInCommandLine();
- }
- final Phylogeny[] trees = new Phylogeny[ args.length ];
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- for( int i = 0; i < trees.length; ++i ) {
- try {
- System.out.println( "Reading tree #" + i + " [" + args[ i ] + "]" );
- final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( new File( args[ i ] ), true );
- trees[ i ] = factory.create( new File( args[ i ] ), pp )[ 0 ];
- }
- catch ( final Exception e ) {
- System.out.println( "\nFailed to read \"" + args[ i ] + "\". Terminating.\n" );
- System.exit( -1 );
- }
- }
- System.out.println( "Finished reading in trees.\n\n" );
- final ORcount or_count = new ORcount( trees );
- try {
- System.out.println( "\n\n\n\"1:1 ORTHOLOGOUS GENE PAIRS\":\n" );
- System.out.println( "\n\n\n\"SUPER ORTHOLOGOUS GENE PAIRS\":\n" );
- or_count.countSuperOrthologousRelations( 0 );
- or_count.printNames();
- or_count.printCount();
- // System.out.println( "\n\n\n\"SHARED ANCESTRAL CLADES\":\n");
- // or_count.reset();
- // or_count.countSharedAncestralClades( trees, 0 );
- }
- catch ( final Exception e ) {
- System.out.println( "\nException. Terminating.\n" );
- System.out.println( "\nException is: " + e + "\n" );
- e.printStackTrace();
- System.exit( -1 );
- }
- System.out.println( "\nDone." );
- System.exit( 0 );
- } // main ( String )
-} // End of class ORcount.
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