// $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
*
* @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> _species = null;
private ArrayList _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 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 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 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( int k = 0; k < trees.length; ++k ) {
countSharedAncestralClades( trees[ k ], 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( int k = 0; k < trees.length; ++k ) {
countSharedAncestralClades( trees[ k ], 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( int i = 0; i < _trees.length; ++i ) {
countSuperOrthologousRelations( _trees[ i ], 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>() );
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> 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();
}
private void setGroup1Vs2Counter( final int group1_vs_2_counter ) {
_group1_vs_2_counter = group1_vs_2_counter;
}
private void setSpecies( final HashMap> 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 h = new HashMap();
// 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.
*
* (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.