public boolean isHasEvent() { return getEvent() != null; }
final public static Event getEventAtLCA( final PhylogenyNode n1, final PhylogenyNode n2 ) { return calculateLCA( n1, n2 ).getNodeData().getEvent(); }
@Override public StringBuffer toNHX() { final StringBuffer sb = new StringBuffer(); if ( isHasTaxonomy() ) { sb.append( getTaxonomy().toNHX() ); } if ( isHasSequence() ) { sb.append( getSequence().toNHX() ); } if ( isHasEvent() ) { sb.append( getEvent().toNHX() ); } return sb; }
/** * Returns true if this PhylogenyNode represents a _duplication event, false * otherwise. */ final public boolean isDuplication() { return getNodeData().isHasEvent() && getNodeData().getEvent().isDuplication(); }
final static boolean isHasAssignedEvent( final PhylogenyNode node ) { if ( !node.getNodeData().isHasEvent() ) { return false; } if ( ( node.getNodeData().getEvent() ).isUnassigned() ) { return false; } return true; }
private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) { return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent(); }
/** * Returns whether a _duplication or speciation event has been assigned for * this PhylogenyNode. */ final public boolean isHasAssignedEvent() { if ( !getNodeData().isHasEvent() ) { return false; } if ( ( getNodeData().getEvent() ).isUnassigned() ) { return false; } return true; }
private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) { return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent(); }
final public boolean isSpeciation() { return getNodeData().isHasEvent() && getNodeData().getEvent().isSpeciation(); }
getEvent().toPhyloXML( writer, level, indentation );
new_data.setEvent( ( Event ) getEvent().copy() );
|| ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT ) || ( node .getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) ) || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent() .isDuplication() || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent() .isSpeciationOrDuplication() ) ) ) { NodeVisualData vis = null; final Event event = node.getNodeData().getEvent(); if ( event.isDuplication() ) { outline_color = getTreeColorSet().getDuplicationBoxColor();
getMyNode().getNodeData().setEvent( new Event() ); getMyNode().getNodeData().getEvent().setDuplications( parsePositiveInt( mtn, value ) ); break; case EVENTS_SPECIATIONS: getMyNode().getNodeData().setEvent( new Event() ); getMyNode().getNodeData().getEvent().setSpeciations( parsePositiveInt( mtn, value ) ); break; case EVENTS_GENE_LOSSES: getMyNode().getNodeData().setEvent( new Event() ); getMyNode().getNodeData().getEvent().setGeneLosses( parsePositiveInt( mtn, value ) ); break; case DATE_DESCRIPTION:
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" ); }
if ( !PhylogenyMethods.calculateLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent() .isSpeciation() ) { return false; if ( !PhylogenyMethods.calculateLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent() .isSpeciationOrDuplication() ) { return false; if ( !( PhylogenyMethods.calculateLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent() .isDuplication() ) ) { return false; if ( !PhylogenyMethods.calculateLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent() .isSpeciation() ) { return false; if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent() .isSpeciation() ) { return false; if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent() .isSpeciation() ) { return false; if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent() .isSpeciationOrDuplication() ) { return false; if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent()
addEvents( top, phylogeny_node.getNodeData().getEvent(), EVENTS );