final List<Taxonomy> taxonomies_to_keep = new ArrayList<Taxonomy>(); for( final String n : names ) { final Taxonomy t = new Taxonomy(); try { t.setTaxonomyCode( n );
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 ); }
/** * 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 ); }
@Override public Taxonomy parse( final XmlElement element ) throws PhyloXmlDataFormatException { final Taxonomy taxonomy = new Taxonomy(); for( int i = 0; i < element.getNumberOfChildElements(); ++i ) { final XmlElement child_element = element.getChildElement( i );
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() );
@Override public PhylogenyData copy() { final Taxonomy t = new Taxonomy(); try { t.setTaxonomyCode( getTaxonomyCode() );
private void addTaxonomy( final DefaultMutableTreeNode top, Taxonomy tax, final String name ) { if ( tax == null ) { tax = 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() );
final Map<String, String> lineage_to_rank_map = MainPanel.getLineageToRankMap(); 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 )
tax = new Taxonomy(); node.getNodeData().addTaxonomy( tax );
final Taxonomy tax = new Taxonomy(); n.getNodeData().setTaxonomy( tax ); tax.setScientificName( last_common );
seq.setLocation( db_entry.getMap() ); final Taxonomy tax = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy() : new Taxonomy(); if ( !ForesterUtil.isEmpty( db_entry.getTaxonomyScientificName() ) ) { tax.setScientificName( db_entry.getTaxonomyScientificName() );
private void createNodes( final DefaultMutableTreeNode top, final PhylogenyNode phylogeny_node ) { if ( !phylogeny_node.getNodeData().isHasTaxonomy() ) { phylogeny_node.getNodeData().addTaxonomy( new Taxonomy() ); } if ( !phylogeny_node.getNodeData().isHasSequence() ) { phylogeny_node.getNodeData().addSequence( new Sequence() ); } if ( !phylogeny_node.getNodeData().isHasDistribution() ) { phylogeny_node.getNodeData().addDistribution( new Distribution( "" ) ); } if ( !phylogeny_node.getNodeData().isHasReference() ) { phylogeny_node.getNodeData().addReference( new Reference( "" ) ); } addBasics( top, phylogeny_node, NodePanel.BASIC ); addTaxonomy( top, phylogeny_node.getNodeData().getTaxonomy(), NodePanel.TAXONOMY ); addSequence( top, phylogeny_node.getNodeData().getSequence(), NodePanel.SEQUENCE ); if ( !phylogeny_node.isExternal() ) { addEvents( top, phylogeny_node.getNodeData().getEvent(), NodePanel.EVENTS ); } addDate( top, phylogeny_node.getNodeData().getDate(), NodePanel.DATE ); addDistribution( top, phylogeny_node.getNodeData().getDistribution(), NodePanel.DISTRIBUTION ); addReference( top, phylogeny_node.getNodeData().getReference(), NodePanel.LIT_REFERENCE ); // addProperties( top, phylogeny_node.getNodeData().getProperties(), "Properties" ); }
n.getNodeData().addTaxonomy( new Taxonomy() );