@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; }
final public boolean isSpeciation() { return getNodeData().isHasEvent() && getNodeData().getEvent().isSpeciation(); }
else if ( isSpeciation() ) { if ( getNumberOfSpeciations() == 1 ) { sb.append( "speciation" );
final public static void deleteNonOrthologousExternalNodes( final Phylogeny phy, final PhylogenyNode n ) { if ( n.isInternal() ) { throw new IllegalArgumentException( "node is not external" ); } final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>(); for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { final PhylogenyNode i = it.next(); if ( !PhylogenyMethods.getEventAtLCA( n, i ).isSpeciation() ) { to_delete.add( i ); } } for( final PhylogenyNode d : to_delete ) { phy.deleteSubtree( d, true ); } phy.clearHashIdToNodeMap(); phy.externalNodesHaveChanged(); }
return false; if ( e3.isSpeciation() ) { return false;
if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) { return false; if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) { return false; if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) { return false; if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) { return false; if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) { return false; if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) { return false; if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) { return false; if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) { return false; if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) { return false; if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) { return false;
.isSpeciation() ) { return false; .isSpeciation() ) { return false; .isSpeciation() ) { return false; .isSpeciation() ) { return false; .isSpeciation() ) { return false; .isSpeciation() ) { return false; .isSpeciation() ) { return false; .isSpeciation() ) { return false; .isSpeciation() ) { return false; .isSpeciation() ) { return false;
|| ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent() .isDuplication() || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent() .isSpeciationOrDuplication() ) ) ) { NodeVisualData vis = null; outline_color = getTreeColorSet().getDuplicationBoxColor(); else if ( event.isSpeciation() ) { outline_color = getTreeColorSet().getSpecBoxColor();