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Applications and software libraries for evolutionary biology and comparative genomics research
// $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
// 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.phylogeny.data;
import java.io.IOException;
import java.io.Writer;
import java.util.StringTokenizer;
import org.forester.io.parsers.nhx.NHXFormatException;
import org.forester.io.parsers.nhx.NHXtags;
import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.util.ForesterUtil;
public class Event implements PhylogenyData {
public final static int DEFAULT_VALUE = -1;
private static final String NHX_SEPARATOR = ">";
private int _duplications;
private int _speciations;
private int _gene_losses;
private EventType _event_type;
private Confidence _confidence;
public Event() {
_duplications = DEFAULT_VALUE;
_speciations = DEFAULT_VALUE;
_gene_losses = DEFAULT_VALUE;
_event_type = EventType.unassigned;
}
public Event( final EventType type ) {
_duplications = DEFAULT_VALUE;
_speciations = DEFAULT_VALUE;
_gene_losses = DEFAULT_VALUE;
_event_type = type;
}
public Event( final int duplications, final int speciations, final int gene_losses ) {
_duplications = duplications;
_speciations = speciations;
_gene_losses = gene_losses;
_event_type = EventType.mixed;
}
public Event( final int duplications, final int speciations, final int gene_losses, final String type ) {
_duplications = duplications;
_speciations = speciations;
_gene_losses = gene_losses;
_event_type = EventType.valueOf( type );
}
public Event( final String nhx ) throws NHXFormatException {
if ( ForesterUtil.isEmpty( nhx ) ) {
_duplications = DEFAULT_VALUE;
_speciations = DEFAULT_VALUE;
_gene_losses = DEFAULT_VALUE;
_event_type = EventType.unassigned;
}
else {
final StringTokenizer st = new StringTokenizer( nhx, NHX_SEPARATOR );
if ( st.countTokens() != 4 ) {
throw new NHXFormatException( "malformed NHX format for event [" + nhx + "]" );
}
final String duplications = ( String ) st.nextElement();
final String speciations = ( String ) st.nextElement();
final String losses = ( String ) st.nextElement();
final String event_type = ( String ) st.nextElement();
int d = 0;
int s = 0;
int l = 0;
try {
d = Integer.parseInt( duplications );
s = Integer.parseInt( speciations );
l = Integer.parseInt( losses );
_duplications = d;
_speciations = s;
_gene_losses = l;
_event_type = EventType.valueOf( event_type );
}
catch ( final Exception e ) {
throw new NHXFormatException( "malformed NHX format for event [" + nhx + "]:" + e.getMessage() );
}
}
}
@Override
public StringBuffer asSimpleText() {
final StringBuffer sb = new StringBuffer();
if ( isUnassigned() ) {
}
else if ( isSpeciationOrDuplication() ) {
sb.append( "?" );
}
else if ( isOther() || isRoot() || isTransfer() || isFusion() ) {
sb.append( getEventType().toString() );
}
else {
if ( getNumberOfDuplications() > 0 ) {
if ( getNumberOfDuplications() > 1 ) {
sb.append( getNumberOfDuplications() );
}
sb.append( "D" );
}
if ( getNumberOfSpeciations() > 0 ) {
if ( getNumberOfSpeciations() > 1 ) {
sb.append( getNumberOfSpeciations() );
}
sb.append( "S" );
}
if ( getNumberOfGeneLosses() > 0 ) {
if ( getNumberOfGeneLosses() > 1 ) {
sb.append( getNumberOfGeneLosses() );
}
sb.append( "L" );
}
}
return sb;
}
@Override
public StringBuffer asText() {
final StringBuffer sb = new StringBuffer();
if ( isUnassigned() || isSpeciationOrDuplication() || isOther() || isRoot() || isTransfer() || isFusion() ) {
sb.append( getEventType().toString() );
}
else {
if ( isDuplication() ) {
if ( getNumberOfDuplications() == 1 ) {
sb.append( "duplication" );
}
else {
sb.append( "duplications [" + getNumberOfDuplications() + "]" );
}
}
else if ( isSpeciation() ) {
if ( getNumberOfSpeciations() == 1 ) {
sb.append( "speciation" );
}
else {
sb.append( "speciations [" + getNumberOfSpeciations() + "]" );
}
}
else if ( isGeneLoss() ) {
if ( getNumberOfGeneLosses() == 1 ) {
sb.append( "gene-loss" );
}
else {
sb.append( "gene-losses [" + getNumberOfGeneLosses() + "]" );
}
}
else {
sb.append( "duplications [" + getNumberOfDuplications() + "] " );
sb.append( "speciations [" + getNumberOfSpeciations() + "] " );
sb.append( "gene-losses [" + getNumberOfGeneLosses() + "]" );
}
}
return sb;
}
@Override
public PhylogenyData copy() {
if ( isUnassigned() ) {
return new Event();
}
else if ( _event_type != EventType.mixed ) {
return new Event( _event_type );
}
else {
return new Event( _duplications, _speciations, _gene_losses );
}
}
public Confidence getConfidence() {
return _confidence;
}
public EventType getEventType() {
return _event_type;
}
public int getNumberOfDuplications() {
return _duplications;
}
public int getNumberOfGeneLosses() {
return _gene_losses;
}
public int getNumberOfSpeciations() {
return _speciations;
}
/**
* Returns true if this event contains one or more duplications events only
*
* @return true if this event contains one or more duplications events only
*/
public boolean isDuplication() {
return ( _duplications > 0 ) && ( _gene_losses < 1 ) && ( _speciations < 1 );
}
@Override
public boolean isEqual( final PhylogenyData event ) {
if ( ( event == null ) || !( event instanceof Event ) ) {
return false;
}
final Event e = ( Event ) event;
if ( getEventType().compareTo( e.getEventType() ) != 0 ) {
return false;
}
if ( getNumberOfDuplications() != e.getNumberOfDuplications() ) {
return false;
}
if ( getNumberOfSpeciations() != e.getNumberOfSpeciations() ) {
return false;
}
if ( getNumberOfGeneLosses() != e.getNumberOfGeneLosses() ) {
return false;
}
return true;
}
public boolean isFusion() {
return _event_type == EventType.fusion;
}
/**
* Returns true if this event contains one or more gene loss events only
*
* @return true if this event contains one or more gene loss events only
*/
public boolean isGeneLoss() {
return ( _duplications < 1 ) && ( _gene_losses > 0 ) && ( _speciations < 1 );
}
public boolean isOther() {
return _event_type == EventType.other;
}
public boolean isRoot() {
return _event_type == EventType.root;
}
/**
* Returns true if this event contains one or more speciation events only
*
* @return true if this event contains one or more speciation events only
*/
public boolean isSpeciation() {
return ( _duplications < 1 ) && ( _gene_losses < 1 ) && ( _speciations > 0 );
}
public boolean isSpeciationOrDuplication() {
return _event_type == EventType.speciation_or_duplication;
}
public boolean isTransfer() {
return _event_type == EventType.transfer;
}
public boolean isUnassigned() {
return ( _duplications == DEFAULT_VALUE ) && ( _event_type == EventType.unassigned );
}
public void setConfidence( final Confidence confidence ) {
_confidence = confidence;
}
public void setDuplications( final int duplications ) {
_duplications = duplications;
_event_type = EventType.mixed;
}
public void setGeneLosses( final int gene_losses ) {
_gene_losses = gene_losses;
_event_type = EventType.mixed;
}
public void setSpeciations( final int speciations ) {
_speciations = speciations;
_event_type = EventType.mixed;
}
@Override
public StringBuffer toNHX() {
final StringBuffer sb = new StringBuffer();
if ( !isUnassigned() && ( isSpeciationOrDuplication() || isDuplication() || isSpeciation() ) ) {
sb.append( ":" );
sb.append( NHXtags.IS_DUPLICATION );
if ( isSpeciationOrDuplication() ) {
sb.append( "?" );
}
else if ( isDuplication() ) {
sb.append( "Y" );
}
else if ( isSpeciation() ) {
sb.append( "N" );
}
}
return sb;
}
@Override
public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
writer.write( ForesterUtil.LINE_SEPARATOR );
writer.write( indentation );
PhylogenyDataUtil.appendOpen( writer, PhyloXmlMapping.EVENTS );
if ( ( getEventType() != EventType.unassigned ) && ( getEventType() != EventType.mixed ) ) {
PhylogenyDataUtil
.appendElement( writer, PhyloXmlMapping.EVENT_TYPE, getEventType().toString(), indentation );
}
if ( getNumberOfDuplications() > 0 ) {
PhylogenyDataUtil.appendElement( writer,
PhyloXmlMapping.EVENT_DUPLICATIONS,
getNumberOfDuplications() + "",
indentation );
}
if ( getNumberOfSpeciations() > 0 ) {
PhylogenyDataUtil.appendElement( writer,
PhyloXmlMapping.EVENT_SPECIATIONS,
getNumberOfSpeciations() + "",
indentation );
}
if ( getNumberOfGeneLosses() > 0 ) {
PhylogenyDataUtil.appendElement( writer,
PhyloXmlMapping.EVENT_LOSSES,
getNumberOfGeneLosses() + "",
indentation );
}
if ( getConfidence() != null ) {
getConfidence().toPhyloXML( writer, level, indentation + PhylogenyWriter.PHYLO_XML_INTENDATION_BASE );
}
writer.write( ForesterUtil.LINE_SEPARATOR );
writer.write( indentation );
PhylogenyDataUtil.appendClose( writer, PhyloXmlMapping.EVENTS );
}
@Override
public String toString() {
return asText().toString();
}
public static Event createSingleDuplicationEvent() {
return new Event( 1, 0, 0 );
}
public static Event createSingleSpeciationEvent() {
return new Event( 0, 1, 0 );
}
public static Event createSingleSpeciationOrDuplicationEvent() {
return new Event( EventType.speciation_or_duplication );
}
public static enum EventType {
transfer, fusion, root, speciation_or_duplication, other, mixed, unassigned
}
}
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