PhylogenyNode.setNodeCount( max + 1 );
}
- /**
- * Arranges the order of childern for each node of this Phylogeny in such a
- * way that either the branch with more children is on top (right) or on
- * bottom (left), dependent on the value of boolean order.
- *
- * @param order
- * decides in which direction to order
- */
- public void orderAppearance( final boolean order ) throws RuntimeException {
- if ( !isTree() ) {
- throw new FailedConditionCheckException( "Attempt to order appearance on phylogeny which is not tree-like." );
- }
- if ( isEmpty() ) {
- return;
- }
- orderAppearanceHelper( getRoot(), order );
- }
-
- // Helper method for "orderAppearance(boolean)".
- // Traverses this Phylogeny recusively.
- private void orderAppearanceHelper( final PhylogenyNode n, final boolean order ) {
- if ( n.isExternal() ) {
- return;
- }
- else {
- PhylogenyNode temp = null;
- // FIXME
- if ( ( n.getNumberOfDescendants() == 2 )
- && ( n.getChildNode1().getNumberOfExternalNodes() != n.getChildNode2().getNumberOfExternalNodes() )
- && ( ( n.getChildNode1().getNumberOfExternalNodes() < n.getChildNode2().getNumberOfExternalNodes() ) == order ) ) {
- temp = n.getChildNode1();
- n.setChild1( n.getChildNode2() );
- n.setChild2( temp );
- }
- for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
- orderAppearanceHelper( n.getChildNode( i ), order );
- }
- }
- }
-
public void preOrderReId() {
if ( isEmpty() ) {
return;
_type = type;
}
- /**
- * Swaps the the two childern of a PhylogenyNode node of this Phylogeny.
- * <p>
- * (Last modified: 06/13/01)
- *
- * @param node
- * a PhylogenyNode of this Phylogeny
- */
- public void swapChildren( final PhylogenyNode node ) throws RuntimeException {
- if ( !isTree() ) {
- throw new FailedConditionCheckException( "Attempt to swap children on phylogeny which is not tree-like." );
- }
- if ( isEmpty() || node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
- return;
- }
- final PhylogenyNode first = node.getFirstChildNode();
- for( int i = 1; i < node.getNumberOfDescendants(); ++i ) {
- node.setChildNode( i - 1, node.getChildNode( i ) );
- }
- node.setChildNode( node.getNumberOfDescendants() - 1, first );
- } // swapChildren( PhylogenyNode )
-
public String toNewHampshire() {
return toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
}
}
}
+ public String toNexus() {
+ return toNexus( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
+ }
+
public String toPhyloXML( final int phyloxml_level ) {
try {
return new PhylogenyWriter().toPhyloXML( this, phyloxml_level ).toString();