private static void addAnnotation( final DefaultMutableTreeNode top, final Annotation ann, final String name ) { DefaultMutableTreeNode category; category = new DefaultMutableTreeNode( name ); top.add( category ); addSubelement( category, "Source", ann.getSource() ); addSubelement( category, "Type", ann.getType() ); addSubelement( category, "Evidence", ann.getEvidence() ); if ( ann.getConfidence() != null ) { addSubelement( category, CONFIDENCE, ann.getConfidence().asText().toString() ); } if ( ann.getProperties() != null ) { addProperties( category, ann.getProperties(), PROP ); } }
@Override public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException { if ( ( getConfidence() != null ) || ( getProperties() != null ) || ( ( getUris() != null ) && !getUris().isEmpty() ) || !ForesterUtil.isEmpty( getDesc() ) ) { writer.write( ForesterUtil.LINE_SEPARATOR ); getConfidence().toPhyloXML( writer, level, indentation + PhylogenyWriter.PHYLO_XML_INTENDATION_BASE ); if ( getProperties() != null ) { getProperties().toPhyloXML( writer, level, indentation );
@Override public PhylogenyData copy() { final Annotation ann = new Annotation( getRefSource(), getRefValue() ); if ( getConfidence() != null ) { ann.setConfidence( ( Confidence ) getConfidence().copy() ); } else { ann.setConfidence( null ); } ann.setType( getType() ); ann.setDesc( getDesc() ); ann.setEvidence( getEvidence() ); ann.setSource( new String( getSource() ) ); if ( getProperties() != null ) { ann.setProperties( ( PropertiesMap ) getProperties().copy() ); } else { ann.setProperties( null ); } if ( getUris() != null ) { ann.setUris( new ArrayList<Uri>() ); for( final Uri uri : getUris() ) { if ( uri != null ) { ann.getUris().add( uri ); } } } return ann; }
if ( annotation.getProperties() == null ) { annotation.setProperties( new PropertiesMap() ); annotation.getProperties() .addProperty( ( Property ) PropertyParser.getInstance().parse( child_element ) );
return false; if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) { return false; if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) { return false; if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) { return false; if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) { return false; if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) { return false; if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) { return false;
return false; if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) { return false; if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) { return false; if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) { return false; if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) { return false; if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) { return false; if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) { return false;