public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) { if ( !node.getNodeData().isHasTaxonomy() ) { node.getNodeData().setTaxonomy( new Taxonomy() ); } }
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().setTaxonomy( new Taxonomy() );
/** * Convenience method to set the taxonomy code of a phylogeny node. * * * @param node * @param taxonomy_code * @throws PhyloXmlDataFormatException */ public static void setTaxonomyCode( final PhylogenyNode node, final String taxonomy_code ) throws PhyloXmlDataFormatException { if ( !node.getNodeData().isHasTaxonomy() ) { node.getNodeData().setTaxonomy( new Taxonomy() ); } node.getNodeData().getTaxonomy().setTaxonomyCode( taxonomy_code ); }
final static void collapseSpeciesSpecificSubtrees( final Phylogeny phy ) { boolean inferred = false; for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) { final PhylogenyNode n = it.next(); if ( !n.isExternal() && !n.isCollapse() && ( n.getNumberOfDescendants() > 1 ) ) { final Set<Taxonomy> taxs = TreePanelUtil.obtainDistinctTaxonomies( n ); if ( ( taxs != null ) && ( taxs.size() == 1 ) ) { TreePanelUtil.collapseSubtree( n, true ); if ( !n.getNodeData().isHasTaxonomy() ) { n.getNodeData().setTaxonomy( ( Taxonomy ) n.getAllExternalDescendants().get( 0 ).getNodeData() .getTaxonomy().copy() ); } inferred = true; } else { n.setCollapse( false ); } } } if ( inferred ) { phy.setRerootable( false ); } }
if ( !ForesterUtil.isEmpty( id ) ) { if ( !node.getNodeData().isHasTaxonomy() ) { node.getNodeData().setTaxonomy( new Taxonomy() ); if ( !ForesterUtil.isEmpty( name ) ) { if ( !node.getNodeData().isHasTaxonomy() ) { node.getNodeData().setTaxonomy( new Taxonomy() ); if ( !ForesterUtil.isEmpty( auth ) && !auth.equalsIgnoreCase( "null" ) ) { if ( !node.getNodeData().isHasTaxonomy() ) { node.getNodeData().setTaxonomy( new Taxonomy() ); if ( !ForesterUtil.isEmpty( syn ) && !syn.equalsIgnoreCase( "null" ) ) { if ( !node.getNodeData().isHasTaxonomy() ) { node.getNodeData().setTaxonomy( new Taxonomy() );
if ( !ForesterUtil.isEmpty( id ) ) { if ( !node.getNodeData().isHasTaxonomy() ) { node.getNodeData().setTaxonomy( new Taxonomy() ); if ( !ForesterUtil.isEmpty( sn ) ) { if ( !node.getNodeData().isHasTaxonomy() ) { node.getNodeData().setTaxonomy( new Taxonomy() ); node.getNodeData().setTaxonomy( new Taxonomy() );
n.setName( "" ); if ( !n.getNodeData().isHasTaxonomy() ) { n.getNodeData().setTaxonomy( new Taxonomy() ); n.setName( "" ); if ( !n.getNodeData().isHasTaxonomy() ) { n.getNodeData().setTaxonomy( new Taxonomy() ); case TAXONOMY_ID_UNIPROT_1: { if ( !n.getNodeData().isHasTaxonomy() ) { n.getNodeData().setTaxonomy( new Taxonomy() ); n.getNodeData().setTaxonomy( new Taxonomy() ); n.getNodeData().setTaxonomy( new Taxonomy() );
throw new IllegalArgumentException( "attempt to infer taxonomy from descendants of external node" ); n.getNodeData().setTaxonomy( null ); final List<PhylogenyNode> descs = n.getDescendants(); final List<String[]> lineages = new ArrayList<String[]>(); n.getNodeData().setTaxonomy( tax ); tax.setScientificName( last_common ); final UniProtTaxonomy up_tax = TaxonomyDataManager.obtainUniProtTaxonomyFromLineage( last_common_lineage ); if ( !desc.isExternal() && desc.getNodeData().isHasTaxonomy() && desc.getNodeData().getTaxonomy().isEqual( tax ) ) { desc.getNodeData().setTaxonomy( null );
g.getNodeData().setTaxonomy( s.getNodeData().getTaxonomy() ); if ( g.isInternal() ) { if ( g.getChildNode1().isInternal() && g.getChildNode1().getNodeData().isHasTaxonomy() && ( g.getChildNode1().getNodeData().getTaxonomy() == s.getNodeData().getTaxonomy() ) ) { g.getChildNode1().getNodeData().setTaxonomy( null ); g.getChildNode2().getNodeData().setTaxonomy( null );
tax.setIdentifier( new Identifier( db_entry.getTaxonomyIdentifier(), "uniprot" ) ); node.getNodeData().setTaxonomy( tax ); node.getNodeData().setSequence( seq );