// 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
// 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
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.phylogeny.data;
public class NodeData implements PhylogenyData {
+ public enum NODE_DATA {
+ NODE_NAME,
+ EVENT,
+ SEQUENCE_NAME,
+ GENE_NAME,
+ SEQUENCE_SYMBOL,
+ SEQUENCE_MOL_SEQ,
+ SEQUENCE_MOL_SEQ_FASTA,
+ SEQUENCE_ACC,
+ TAXONOMY_SCIENTIFIC_NAME,
+ TAXONOMY_COMM0N_NAME,
+ TAXONOMY_CODE,
+ UNKNOWN;
+ }
private String _node_name;
private Event _event;
private List<Sequence> _sequences;
- private Identifier _node_identifier;
private List<Taxonomy> _taxonomies;
private List<Distribution> _distributions;
private Date _date;
private PropertiesMap _properties;
private List<Reference> _references;
private List<Double> _vector;
+ private NodeVisualData _node_visual_data;
public NodeData() {
init();
private void init() {
_node_name = "";
+ _event = null;
+ _sequences = null;
+ _taxonomies = null;
+ _distributions = null;
+ _date = null;
+ _binary_characters = null;
+ _properties = null;
+ _references = null;
+ _vector = null;
+ _node_visual_data = null;
}
public void addDistribution( final Distribution distribution ) {
_taxonomies.add( taxonomy );
}
+ @Override
public StringBuffer asSimpleText() {
throw new UnsupportedOperationException();
}
+ @Override
public StringBuffer asText() {
throw new UnsupportedOperationException();
}
+ @Override
public PhylogenyData copy() {
final NodeData new_data = new NodeData();
new_data.setNodeName( getNodeName() );
if ( isHasEvent() ) {
new_data.setEvent( ( Event ) getEvent().copy() );
}
- if ( isHasNodeIdentifier() ) {
- new_data.setNodeIdentifier( ( Identifier ) getNodeIdentifier().copy() );
- }
if ( ( getTaxonomies() != null ) && ( getTaxonomies().size() > 0 ) ) {
new_data.setTaxonomies( new ArrayList<Taxonomy>() );
for( final Taxonomy t : getTaxonomies() ) {
}
}
}
+ if ( ( getNodeVisualData() != null ) && !getNodeVisualData().isEmpty() ) {
+ new_data.setNodeVisualData( ( NodeVisualData ) getNodeVisualData().copy() );
+ }
if ( isHasDate() ) {
new_data.setDate( ( Date ) getDate().copy() );
}
return _event;
}
- public Identifier getNodeIdentifier() {
- return _node_identifier;
- }
-
public PropertiesMap getProperties() {
return _properties;
}
return _taxonomies.get( index );
}
+ @Override
public boolean isEqual( final PhylogenyData data ) {
- throw new UnsupportedOperationException();
+ throw new NoSuchMethodError();
}
public boolean isHasBinaryCharacters() {
return getBinaryCharacters() != null;
}
+ public boolean isEmpty() {
+ return ( ForesterUtil.isEmpty( _node_name ) && !isHasSequence() && !isHasTaxonomy() && !isHasBinaryCharacters()
+ && !isHasDate() && !isHasDistribution() && !isHasEvent() && !isHasProperties() && !isHasReference() && ( ( _vector == null ) || _vector
+ .isEmpty() ) );
+ }
+
public boolean isHasDate() {
return ( getDate() != null )
&& ( !ForesterUtil.isEmpty( getDate().getDesc() ) || !ForesterUtil.isNull( getDate().getMax() )
|| !ForesterUtil.isNull( getDate().getMin() ) || !ForesterUtil.isNull( getDate().getValue() ) || !ForesterUtil
- .isEmpty( getDate().getUnit() ) );
+ .isEmpty( getDate().getUnit() ) );
}
public boolean isHasDistribution() {
return getEvent() != null;
}
- public boolean isHasNodeIdentifier() {
- return getNodeIdentifier() != null;
- }
-
public boolean isHasProperties() {
- return getProperties() != null;
+ return ( getProperties() != null ) && ( getProperties().size() > 0 );
}
public boolean isHasReference() {
_event = event;
}
- public void setNodeIdentifier( final Identifier node_identifier ) {
- _node_identifier = node_identifier;
- }
-
public void setProperties( final PropertiesMap custom_data ) {
_properties = custom_data;
}
}
}
+ @Override
public StringBuffer toNHX() {
final StringBuffer sb = new StringBuffer();
- if ( isHasNodeIdentifier() ) {
- sb.append( getNodeIdentifier().toNHX() );
- }
if ( isHasTaxonomy() ) {
sb.append( getTaxonomy().toNHX() );
}
if ( isHasEvent() ) {
sb.append( getEvent().toNHX() );
}
- if ( isHasProperties() ) {
- sb.append( getProperties().toNHX() );
- }
return sb;
}
+ @Override
public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
- if ( isHasNodeIdentifier() ) {
- writer.write( ForesterUtil.LINE_SEPARATOR );
- writer.write( indentation );
- // if ( !org.forester.util.ForesterUtil.isEmpty( getNodeIdentifier().getProvider() ) ) {
- // PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.NODE_IDENTIFIER, getNodeIdentifier()
- // .getValue(), PhyloXmlMapping.IDENTIFIER_PROVIDER_ATTR, getNodeIdentifier().getProvider() );
- // }
- // else {
- // PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.NODE_IDENTIFIER, getNodeIdentifier()
- // .getValue() );
- // }
- }
if ( isHasTaxonomy() ) {
for( final Taxonomy t : getTaxonomies() ) {
if ( !t.isEmpty() ) {
if ( isHasProperties() ) {
getProperties().toPhyloXML( writer, level, indentation.substring( 0, indentation.length() - 2 ) );
}
+ if ( ( level == 0 ) && ( getNodeVisualData() != null ) && !getNodeVisualData().isEmpty() ) {
+ getNodeVisualData().toPhyloXML( writer, level, indentation.substring( 0, indentation.length() - 2 ) );
+ }
if ( ( getVector() != null )
&& !getVector().isEmpty()
&& ( ( getProperties() == null ) || getProperties()
public void setNodeName( final String node_name ) {
_node_name = node_name;
}
+
+ public void setNodeVisualData( final NodeVisualData node_visual_data ) {
+ _node_visual_data = node_visual_data;
+ }
+
+ public NodeVisualData getNodeVisualData() {
+ return _node_visual_data;
+ }
}
git://source.jalview.org / jalview.git / blobdiff