private static String extractBracketedScientificNames( final PhylogenyNode node, final String new_value ) { final int i = new_value.lastIndexOf( "[" ); final String scientific_name = new_value.substring( i + 1, new_value.length() - 1 ); ForesterUtil.ensurePresenceOfTaxonomy( node ); node.getNodeData().getTaxonomy().setScientificName( scientific_name ); return new_value.substring( 0, i - 1 ).trim(); }
final String tc = t.getTaxonomyCode(); if ( tc.equals( "ACRALC" ) ) { t.setScientificName( "Acremonium alcalophilum" ); t.setTaxonomyCode( "AALXX" ); t.setScientificName( "Amphimedon queenslandica" ); t.setTaxonomyCode( "AMPQE" ); t.setScientificName( "Aquifex aeolicus (strain VF5)" ); t.setScientificName( "Asterochloris sp. Cgr/DA1pho" ); t.setTaxonomyCode( "ASCXX" ); t.setScientificName( "Baudoinia compniacensis" ); t.setTaxonomyCode( "BCOXX" ); t.setScientificName( "Capitella sp.1" ); t.setTaxonomyCode( "CTEXX" ); t.setScientificName( "Capsaspora owczarzaki (strain ATCC 30864)" ); t.setTaxonomyCode( "CAPO3" ); t.setScientificName( "Chlorella variabilis" ); t.setTaxonomyCode( "CHLVA" ); t.setScientificName( "Citrus clementina" ); t.setTaxonomyCode( "CCLXX" ); t.setScientificName( "Cladonia grayi" );
public static void setScientificName( final PhylogenyNode node, final String scientific_name ) { if ( !node.getNodeData().isHasTaxonomy() ) { node.getNodeData().setTaxonomy( new Taxonomy() ); } node.getNodeData().getTaxonomy().setScientificName( scientific_name ); }
node_to_annotate.getNodeData().setTaxonomy( new Taxonomy() ); node_to_annotate.getNodeData().getTaxonomy().setScientificName( s.substring( 2 ) );
node.getNodeData().getTaxonomy().setScientificName( new_values.get( TP_TAXONOMY_SN ) );
taxonomy.setScientificName( child_element.getValueAsString() );
public static boolean extractFastaInformation( final Phylogeny phy ) { boolean could_extract = false; for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) { final PhylogenyNode node = iter.next(); if ( !ForesterUtil.isEmpty( node.getName() ) ) { final Matcher name_m = FastaParser.FASTA_DESC_LINE.matcher( node.getName() ); if ( name_m.lookingAt() ) { could_extract = true; final String acc_source = name_m.group( 1 ); final String acc = name_m.group( 2 ); final String seq_name = name_m.group( 3 ); final String tax_sn = name_m.group( 4 ); if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) { ForesterUtil.ensurePresenceOfSequence( node ); node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) ); } if ( !ForesterUtil.isEmpty( seq_name ) ) { ForesterUtil.ensurePresenceOfSequence( node ); node.getNodeData().getSequence( 0 ).setName( seq_name ); } if ( !ForesterUtil.isEmpty( tax_sn ) ) { ForesterUtil.ensurePresenceOfTaxonomy( node ); node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn ); } } } } return could_extract; }
t0.getRoot().getNodeData().getTaxonomy().setScientificName( "metazoa" ); t0.getNode( "b" ).setName( "Bee" ); if ( !t0.toNewHampshireX().equals( "((Bee,d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=metazoa]" ) ) {
e.printStackTrace(); t.setScientificName( getScientificName() ); t.setCommonName( getCommonName() ); t.setAuthority( getAuthority() );
public void init() { setScientificName( "" ); setCommonName( "" ); setIdentifier( null ); try { setRank( "" ); } catch ( final PhyloXmlDataFormatException e ) { e.printStackTrace(); } try { setTaxonomyCode( "" ); } catch ( final PhyloXmlDataFormatException e ) { e.printStackTrace(); } setAuthority( "" ); setSynonyms( null ); setUris( null ); setLineage( null ); }
t1.setIdentifier( new Identifier( "ecoli" ) ); t1.setTaxonomyCode( "ECOLI" ); t1.setScientificName( "E. coli" ); t1.setCommonName( "coli" ); final Taxonomy t0 = ( Taxonomy ) t1.copy(); t2.setScientificName( "what" ); t2.setCommonName( "something" ); if ( !t1.isEqual( t2 ) ) { t3.setScientificName( "what" ); t3.setCommonName( "something" ); if ( !t1.isEqual( t3 ) ) { t4.setScientificName( "E. ColI" ); t4.setCommonName( "something" ); if ( !t1.isEqual( t4 ) ) { return false; t4.setScientificName( "B. subtilis" ); t4.setCommonName( "something" ); if ( t1.isEqual( t4 ) ) { t1.setScientificName( "" ); t5.setCommonName( "COLI" ); if ( !t1.isEqual( t5 ) ) {
node.getNodeData().getTaxonomy().setScientificName( name );
for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) { final Taxonomy temp_tax = new Taxonomy(); temp_tax.setScientificName( lin ); if ( lineage_to_rank_map.containsKey( lin ) && !ForesterUtil.isEmpty( lineage_to_rank_map.get( lin ) )
tax.setScientificName( last_common ); final UniProtTaxonomy up_tax = TaxonomyDataManager.obtainUniProtTaxonomyFromLineage( last_common_lineage ); if ( up_tax != null ) {
if ( ( qt != QUERY_TYPE.SN ) && !ForesterUtil.isEmpty( up_tax.getScientificName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) { tax.setScientificName( up_tax.getScientificName() );
t1.setScientificName( "Nematostella vectensis" ); d1.getNodeData().addTaxonomy( t1 ); final Taxonomy t2 = new Taxonomy(); t2.setScientificName( "Monosiga brevicollis" ); d2.getNodeData().addTaxonomy( t2 );
n.getNodeData().setTaxonomy( new Taxonomy() ); n.getNodeData().getTaxonomy().setScientificName( name ); break; case TAXONOMY_COMMON_NAME:
tax.setScientificName( db_entry.getTaxonomyScientificName() );
node.getNodeData().setTaxonomy( new Taxonomy() ); node.getNodeData().getTaxonomy().setScientificName( sn ); return sn;
t.setScientificName( n.getName() ); n.setName( "" );