// $Id: TolXmlHandler.java,v 1.10 2010/09/29 23:50:18 cmzmasek Exp $
// 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: cmzmasek@yahoo.com
// WWW: www.phylosoft.org/forester
package org.forester.io.parsers.tol;
import java.util.ArrayList;
import java.util.List;
import org.forester.io.parsers.phyloxml.XmlElement;
import org.forester.io.parsers.util.PhylogenyParserException;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.DefaultHandler;
public final class TolXmlHandler extends DefaultHandler {
private String _current_element_name;
private Phylogeny _current_phylogeny;
private List<Phylogeny> _phylogenies;
private XmlElement _current_xml_element;
private PhylogenyNode _current_node;
private final static StringBuffer _buffer = new StringBuffer();
TolXmlHandler() {
// Constructor.
}
private void addNode() {
final PhylogenyNode new_node = new PhylogenyNode();
getCurrentNode().addAsChild( new_node );
setCurrentNode( new_node );
}
@Override
public void characters( final char[] chars, final int start_index, final int end_index ) {
if ( ( ( getCurrentXmlElement() != null ) && ( getCurrentElementName() != null ) )
&& !getCurrentElementName().equals( TolXmlMapping.CLADE )
&& !getCurrentElementName().equals( TolXmlMapping.PHYLOGENY ) ) {
getCurrentXmlElement().setValue( new String( chars, start_index, end_index ).trim() );
}
}
@Override
public void endElement( final String namespace_uri, final String local_name, final String qualified_name )
throws SAXException {
if ( ForesterUtil.isEmpty( namespace_uri ) || namespace_uri.startsWith( ForesterConstants.PHYLO_XML_LOCATION ) ) {
if ( local_name.equals( TolXmlMapping.CLADE ) ) {
try {
TolXmlHandler.mapElementToPhylogenyNode( getCurrentXmlElement(), getCurrentNode() );
if ( !getCurrentNode().isRoot() ) {
setCurrentNode( getCurrentNode().getParent() );
}
setCurrentXmlElement( getCurrentXmlElement().getParent() );
}
catch ( final PhylogenyParserException ex ) {
throw new SAXException( ex.getMessage() );
}
}
else if ( local_name.equals( TolXmlMapping.PHYLOGENY ) ) {
try {
TolXmlHandler.mapElementToPhylogeny( getCurrentXmlElement(), getCurrentPhylogeny() );
}
catch ( final PhylogenyParserException ex ) {
throw new SAXException( ex.getMessage() );
}
finishPhylogeny();
reset();
}
else if ( ( getCurrentPhylogeny() != null ) && ( getCurrentXmlElement().getParent() != null ) ) {
setCurrentXmlElement( getCurrentXmlElement().getParent() );
}
setCurrentElementName( null );
}
}
private void finishPhylogeny() throws SAXException {
getCurrentPhylogeny().setRooted( true );
getCurrentPhylogeny().recalculateNumberOfExternalDescendants( false );
getPhylogenies().add( getCurrentPhylogeny() );
}
private String getCurrentElementName() {
return _current_element_name;
}
private PhylogenyNode getCurrentNode() {
return _current_node;
}
private Phylogeny getCurrentPhylogeny() {
return _current_phylogeny;
}
private XmlElement getCurrentXmlElement() {
return _current_xml_element;
}
List<Phylogeny> getPhylogenies() {
return _phylogenies;
}
private void init() {
reset();
setPhylogenies( new ArrayList<Phylogeny>() );
}
private void initCurrentNode() {
if ( getCurrentNode() != null ) {
throw new IllegalStateException( "attempt to create new current node when current node already exists" );
}
if ( getCurrentPhylogeny() == null ) {
throw new IllegalStateException( "attempt to create new current node for non-existing phylogeny" );
}
final PhylogenyNode node = new PhylogenyNode();
getCurrentPhylogeny().setRoot( node );
setCurrentNode( getCurrentPhylogeny().getRoot() );
}
private void newClade() {
if ( getCurrentNode() == null ) {
initCurrentNode();
}
else {
addNode();
}
}
private void newPhylogeny() {
setCurrentPhylogeny( new Phylogeny() );
}
private void reset() {
setCurrentPhylogeny( null );
setCurrentNode( null );
setCurrentElementName( null );
setCurrentXmlElement( null );
}
private void setCurrentElementName( final String element_name ) {
_current_element_name = element_name;
}
private void setCurrentNode( final PhylogenyNode current_node ) {
_current_node = current_node;
}
private void setCurrentPhylogeny( final Phylogeny phylogeny ) {
_current_phylogeny = phylogeny;
}
private void setCurrentXmlElement( final XmlElement element ) {
_current_xml_element = element;
}
private void setPhylogenies( final List<Phylogeny> phylogenies ) {
_phylogenies = phylogenies;
}
@Override
public void startDocument() throws SAXException {
init();
}
@Override
public void startElement( final String namespace_uri,
final String local_name,
final String qualified_name,
final Attributes attributes ) throws SAXException {
setCurrentElementName( local_name );
if ( local_name.equals( TolXmlMapping.CLADE ) ) {
final XmlElement element = new XmlElement( namespace_uri, local_name, local_name, attributes );
getCurrentXmlElement().addChildElement( element );
setCurrentXmlElement( element );
newClade();
}
else if ( local_name.equals( TolXmlMapping.PHYLOGENY ) ) {
setCurrentXmlElement( new XmlElement( "", "", "", null ) );
newPhylogeny();
}
else if ( getCurrentPhylogeny() != null ) {
final XmlElement element = new XmlElement( namespace_uri, local_name, local_name, attributes );
getCurrentXmlElement().addChildElement( element );
setCurrentXmlElement( element );
}
}
public static boolean attributeEqualsValue( final XmlElement element,
final String attributeName,
final String attributeValue ) {
final String attr = element.getAttribute( attributeName );
return ( ( attr != null ) && attr.equals( attributeValue ) );
}
public static String getAtttributeValue( final XmlElement element, final String attributeName ) {
final String attr = element.getAttribute( attributeName );
if ( attr != null ) {
return attr;
}
else {
return "";
}
}
private static void mapElementToPhylogeny( final XmlElement xml_element, final Phylogeny phylogeny )
throws PhylogenyParserException {
// Not needed for now.
}
private static void mapElementToPhylogenyNode( final XmlElement xml_element, final PhylogenyNode node )
throws PhylogenyParserException {
if ( xml_element.isHasAttribute( TolXmlMapping.NODE_ID_ATTR ) ) {
final String id = xml_element.getAttribute( TolXmlMapping.NODE_ID_ATTR );
if ( !ForesterUtil.isEmpty( id ) ) {
if ( !node.getNodeData().isHasTaxonomy() ) {
node.getNodeData().setTaxonomy( new Taxonomy() );
}
node.getNodeData().getTaxonomy()
.setIdentifier( new Identifier( id, TolXmlMapping.TOL_TAXONOMY_ID_TYPE ) );
}
}
boolean put_into_scientific_name = false;
if ( xml_element.isHasAttribute( TolXmlMapping.NODE_ITALICIZENAME_ATTR ) ) {
final String ital = xml_element.getAttribute( TolXmlMapping.NODE_ITALICIZENAME_ATTR );
if ( !ForesterUtil.isEmpty( ital ) && ital.equals( "1" ) ) {
put_into_scientific_name = true;
}
}
for( int i = 0; i < xml_element.getNumberOfChildElements(); ++i ) {
final XmlElement element = xml_element.getChildElement( i );
final String qualified_name = element.getQualifiedName();
if ( qualified_name.equals( TolXmlMapping.TAXONOMY_NAME ) ) {
final String name = element.getValueAsString();
if ( !ForesterUtil.isEmpty( name ) ) {
if ( !node.getNodeData().isHasTaxonomy() ) {
node.getNodeData().setTaxonomy( new Taxonomy() );
}
if ( put_into_scientific_name ) {
node.getNodeData().getTaxonomy().setScientificName( name );
}
else {
node.getNodeData().getTaxonomy().setCommonName( name );
}
}
}
else if ( qualified_name.equals( TolXmlMapping.AUTHORITY ) ) {
String auth = element.getValueAsString();
if ( !ForesterUtil.isEmpty( auth ) && !auth.equalsIgnoreCase( "null" ) ) {
if ( !node.getNodeData().isHasTaxonomy() ) {
node.getNodeData().setTaxonomy( new Taxonomy() );
}
auth = auth.replaceAll( "&", "&" );
node.getNodeData().getTaxonomy().setAuthority( auth );
}
}
else if ( qualified_name.equals( TolXmlMapping.AUTHDATE ) ) {
final String authdate = element.getValueAsString();
if ( !ForesterUtil.isEmpty( authdate ) && !authdate.equalsIgnoreCase( "null" ) ) {
if ( node.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getAuthority() ) ) {
_buffer.setLength( 0 );
_buffer.append( node.getNodeData().getTaxonomy().getAuthority() );
_buffer.append( " " );
_buffer.append( authdate );
node.getNodeData().getTaxonomy().setAuthority( _buffer.toString() );
}
}
}
else if ( qualified_name.equals( TolXmlMapping.OTHERNAMES ) ) {
for( int j = 0; j < element.getNumberOfChildElements(); ++j ) {
final XmlElement element_j = element.getChildElement( j );
if ( element_j.getQualifiedName().equals( TolXmlMapping.OTHERNAME ) ) {
for( int z = 0; z < element_j.getNumberOfChildElements(); ++z ) {
final XmlElement element_z = element_j.getChildElement( z );
if ( element_z.getQualifiedName().equals( TolXmlMapping.OTHERNAME_NAME ) ) {
final String syn = element_z.getValueAsString();
if ( !ForesterUtil.isEmpty( syn ) && !syn.equalsIgnoreCase( "null" ) ) {
if ( !node.getNodeData().isHasTaxonomy() ) {
node.getNodeData().setTaxonomy( new Taxonomy() );
}
node.getNodeData().getTaxonomy().getSynonyms().add( syn );
}
}
}
}
}
}
}
}
}