@Override public PhylogenyData copy() { return new Identifier( getValue(), getProvider() ); }
@Override public PhylogenyData parse( final XmlElement element ) throws PhyloXmlDataFormatException { if ( element.isHasAttribute( PhyloXmlMapping.IDENTIFIER_PROVIDER_ATTR ) ) { return new Identifier( element.getValueAsString(), element.getAttribute( PhyloXmlMapping.IDENTIFIER_PROVIDER_ATTR ) ); } else if ( element.isHasAttribute( TYPE ) ) { return new Identifier( element.getValueAsString(), element.getAttribute( TYPE ) ); } else { return new Identifier( element.getValueAsString() ); } }
node_to_annotate.getNodeData().setTaxonomy( new Taxonomy() ); node_to_annotate.getNodeData().getTaxonomy().setIdentifier( new Identifier( s.substring( 2 ) ) );
node.getNodeData() .getTaxonomy() .setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ), new_values.get( TP_TAXONOMY_ID_PROVIDER ) ) ); ForesterUtil.ensurePresenceOfTaxonomy( node ); node.getNodeData().getTaxonomy() .setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ) ) );
phylogenies[ 0 ].setIdentifier( new Identifier( s_ary[ 1 ], s_ary[ 0 ] ) );
phylogeny.setIdentifier( new Identifier( identifier, client.getName() ) ); _main_frame.getJMenuBar().remove( _main_frame.getHelpMenu() ); _main_frame.getMenuBarOfMainFrame().add( _main_frame.getHelpMenu() );
Identifier id = tax.getIdentifier(); if ( id == null ) { id = new Identifier();
final Taxonomy t4 = new Taxonomy(); final Taxonomy t5 = new Taxonomy(); t1.setIdentifier( new Identifier( "ecoli" ) ); t1.setTaxonomyCode( "ECOLI" ); t1.setScientificName( "E. coli" ); return false; t2.setIdentifier( new Identifier( "ecoli" ) ); t2.setTaxonomyCode( "OTHER" ); t2.setScientificName( "what" ); return false; t2.setIdentifier( new Identifier( "nemve" ) ); if ( t1.isEqual( t2 ) ) { return false; final Identifier id0 = new Identifier( "123", "pfam" ); final Identifier id1 = ( Identifier ) id0.copy(); if ( !id1.isEqual( id1 ) ) {
.setIdentifier( new Identifier( id, TolXmlMapping.TOL_TAXONOMY_ID_TYPE ) );
tax.setIdentifier( new Identifier( up_tax.getId(), "uniprot" ) );
tax.setIdentifier( new Identifier( up_tax.getId(), "uniprot" ) );
.setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) ); break; .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) ); break; n.getNodeData().setTaxonomy( new Taxonomy() ); n.getNodeData().getTaxonomy().setIdentifier( new Identifier( name ) ); break;
tax.setIdentifier( new Identifier( db_entry.getTaxonomyIdentifier(), "uniprot" ) );
node.getNodeData().setTaxonomy( new Taxonomy() ); node.getNodeData().getTaxonomy().setIdentifier( new Identifier( id, "uniprot" ) ); return id;
ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() ); if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) { getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( value ) ); getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( value, provider ) ); ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() ); if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) { getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( "", value ) ); getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( v, value ) );
n.getNodeData() .getTaxonomy() .setIdentifier( new Identifier( n.getNodeData().getTaxonomy().getIdentifier().getValue(), "ncbi" ) );