@Override public StringBuffer toNHX() { final StringBuffer sb = new StringBuffer(); if ( !isUnassigned() && ( isSpeciationOrDuplication() || isDuplication() || isSpeciation() ) ) { sb.append( ":" ); sb.append( NHXtags.IS_DUPLICATION ); if ( isSpeciationOrDuplication() ) { sb.append( "?" ); } else if ( isDuplication() ) { sb.append( "Y" ); } else if ( isSpeciation() ) { sb.append( "N" ); } } return sb; }
/** * Returns true if this PhylogenyNode represents a _duplication event, false * otherwise. */ final public boolean isDuplication() { return getNodeData().isHasEvent() && getNodeData().getEvent().isDuplication(); }
if ( isDuplication() ) { if ( getNumberOfDuplications() == 1 ) { sb.append( "duplication" );
if ( e1.isDuplication() ) { return false; if ( e2.isDuplication() ) { return false; if ( e3.isDuplication() ) { return false;
.getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) ) || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent() .isDuplication() || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent() .isSpeciationOrDuplication() ) ) ) { if ( event.isDuplication() ) { outline_color = getTreeColorSet().getDuplicationBoxColor();
.isDuplication() ) ) { return false; .isDuplication() ) { return false; .isDuplication() ) { return false; .isDuplication() ) { return false; .isDuplication() ) { return false; if ( !TestGSDI.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) { return false; .getEvent().isDuplication() ) { return false; if ( !TestGSDI.getEvent( g2_14, "b1", "a1_1" ).isDuplication() ) { return false; if ( !TestGSDI.getEvent( g2_15, "b1", "a2" ).isDuplication() ) { return false; if ( !TestGSDI.getEvent( g2_16, "j3", "n2" ).isDuplication() ) { return false;
return false; if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) { return false;