// 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;
NODE_NAME,
EVENT,
SEQUENCE_NAME,
+ GENE_NAME,
SEQUENCE_SYMBOL,
SEQUENCE_MOL_SEQ,
+ SEQUENCE_MOL_SEQ_FASTA,
SEQUENCE_ACC,
TAXONOMY_SCIENTIFIC_NAME,
- TAXONOMY_CODE;
+ 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;
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() ) {
return _event;
}
- public Identifier getNodeIdentifier() {
- return _node_identifier;
- }
-
public PropertiesMap getProperties() {
return _properties;
}
@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 getEvent() != null;
}
- public boolean isHasNodeIdentifier() {
- return getNodeIdentifier() != null;
- }
-
public boolean isHasProperties() {
return ( getProperties() != null ) && ( getProperties().size() > 0 );
}
_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() ) {