public class NodeData implements PhylogenyData {
- public enum NODE_DATA {
- NODE_NAME,
- EVENT,
- SEQUENCE_NAME,
- SEQUENCE_SYMBOL,
- SEQUENCE_MOL_SEQ,
- SEQUENCE_MOL_SEQ_FASTA,
- SEQUENCE_ACC,
- TAXONOMY_SCIENTIFIC_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 BinaryCharacters _binary_characters;
- private PropertiesMap _properties;
- private List<Reference> _references;
- private List<Double> _vector;
- private List<NodeVisualization> _node_visualizations;
+ private String _node_name;
+ private Event _event;
+ private List<Sequence> _sequences;
+ private List<Taxonomy> _taxonomies;
+ private List<Distribution> _distributions;
+ private Date _date;
+ private BinaryCharacters _binary_characters;
+ private PropertiesList _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 ) {
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 ( ( getNodeVisualizations() != null ) && ( getNodeVisualizations().size() > 0 ) ) {
- new_data.setNodeVisualizations( new ArrayList<NodeVisualization>() );
- for( final NodeVisualization v : getNodeVisualizations() ) {
- if ( v != null ) {
- new_data.getNodeVisualizations().add( ( NodeVisualization ) v.copy() );
- }
- }
+ if ( ( getNodeVisualData() != null ) && !getNodeVisualData().isEmpty() ) {
+ new_data.setNodeVisualData( ( NodeVisualData ) getNodeVisualData().copy() );
}
if ( isHasDate() ) {
new_data.setDate( ( Date ) getDate().copy() );
}
if ( isHasProperties() ) {
- new_data.setProperties( ( PropertiesMap ) getProperties().copy() );
+ new_data.setProperties( ( PropertiesList ) getProperties().copy() );
}
return new_data;
}
/**
* Convenience method -- always returns the first Distribution.
- *
+ *
* @return Distribution
*/
public Distribution getDistribution() {
}
public Distribution getDistribution( final int index ) {
+ if ( _distributions == null ) {
+ return null;
+ }
return _distributions.get( index );
}
return _event;
}
- public Identifier getNodeIdentifier() {
- return _node_identifier;
- }
-
- public PropertiesMap getProperties() {
+ public PropertiesList getProperties() {
return _properties;
}
/**
* Convenience method -- always returns the first Reference.
- *
+ *
* @return Reference
- *
+ *
*/
public Reference getReference() {
return getReference( 0 );
}
public Reference getReference( final int index ) {
+ if ( _references == null ) {
+ return null;
+ }
return _references.get( index );
}
/**
* Convenience method -- always returns the first Sequence.
- *
+ *
* @return Sequence
*/
public Sequence getSequence() {
}
public Sequence getSequence( final int index ) {
+ if ( _sequences == null ) {
+ return null;
+ }
return _sequences.get( index );
}
/**
* Convenience method -- always returns the first Taxonomy.
- *
+ *
* @return Taxonomy
- *
+ *
*/
public Taxonomy getTaxonomy() {
return getTaxonomy( 0 );
}
public Taxonomy getTaxonomy( final int index ) {
+ if ( _taxonomies == null ) {
+ return null;
+ }
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() )
return ( ( ( getDistributions() != null ) && ( getDistributions().size() > 0 ) ) && ( ( !ForesterUtil
.isEmpty( getDistribution().getDesc() ) )
|| ( ( getDistribution().getPoints() != null ) && ( getDistribution().getPoints().size() > 0 ) ) || ( ( getDistribution()
- .getPolygons() != null ) && ( getDistribution().getPolygons().size() > 0 ) ) ) );
+ .getPolygons() != null ) && ( getDistribution().getPolygons().size() > 0 ) ) ) );
}
public boolean isHasEvent() {
return getEvent() != null;
}
- public boolean isHasNodeIdentifier() {
- return getNodeIdentifier() != null;
- }
-
public boolean isHasProperties() {
return ( getProperties() != null ) && ( getProperties().size() > 0 );
}
public boolean isHasReference() {
return ( ( getReferences() != null ) && ( getReferences().size() > 0 ) )
&& ( !ForesterUtil.isEmpty( getReference().getDoi() ) || !ForesterUtil.isEmpty( getReference()
- .getDescription() ) );
+ .getDescription() ) );
}
public boolean isHasSequence() {
/**
* Convenience method -- always sets the first Distribution.
- *
+ *
*/
public void setDistribution( final Distribution distribution ) {
if ( _distributions == null ) {
_event = event;
}
- public void setNodeIdentifier( final Identifier node_identifier ) {
- _node_identifier = node_identifier;
- }
-
- public void setProperties( final PropertiesMap custom_data ) {
+ public void setProperties( final PropertiesList custom_data ) {
_properties = custom_data;
}
/**
* Convenience method -- always sets the first Reference.
- *
+ *
*/
public void setReference( final Reference reference ) {
if ( _references == null ) {
/**
* Convenience method -- always sets the first Sequence.
- *
+ *
*/
public void setSequence( final Sequence sequence ) {
if ( _sequences == null ) {
/**
* Convenience method -- always sets the first Taxonomy.
- *
+ *
*/
public void setTaxonomy( final Taxonomy taxonomy ) {
if ( _taxonomies == null ) {
@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()
_node_name = node_name;
}
- public void setNodeVisualizations( final List<NodeVisualization> _node_visualizations ) {
- this._node_visualizations = _node_visualizations;
+ public void setNodeVisualData( final NodeVisualData node_visual_data ) {
+ _node_visual_data = node_visual_data;
}
- public List<NodeVisualization> getNodeVisualizations() {
- return _node_visualizations;
+ public NodeVisualData getNodeVisualData() {
+ return _node_visual_data;
}
}
git://source.jalview.org / jalview.git / blobdiff