import java.util.Vector;
import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.BranchData;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Identifier;
* @param remove_us the parent node of the subtree to be deleted
*/
public void deleteSubtree( final PhylogenyNode remove_us, final boolean collapse_resulting_node_with_one_desc ) {
- if ( isEmpty() ) {
+ if ( isEmpty() || ( remove_us.isRoot() && ( getNumberOfExternalNodes() != 1 ) ) ) {
return;
}
- if ( remove_us.isRoot() ) {
+ if ( remove_us.isRoot() && ( getNumberOfExternalNodes() == 1 ) ) {
init();
- return;
}
- if ( !collapse_resulting_node_with_one_desc ) {
+ else if ( !collapse_resulting_node_with_one_desc ) {
remove_us.getParent().removeChildNode( remove_us );
}
else {
}
}
}
- remove_us.setParent( null );
+ remove_us.removeConnections();
setIdHash( null );
externalNodesHaveChanged();
}
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 );
+ return toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
}
- public String toNewHampshire( final boolean simple_nh ) {
+ public String toNewHampshire( final boolean simple_nh,
+ final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style ) {
try {
- return new PhylogenyWriter().toNewHampshire( this, simple_nh, true ).toString();
+ return new PhylogenyWriter().toNewHampshire( this, simple_nh, true, nh_conversion_support_style )
+ .toString();
}
catch ( final IOException e ) {
throw new Error( "this should not have happend: " + e.getMessage() );
}
}
- public String toNexus() {
+ public String toNexus( final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) {
try {
- return new PhylogenyWriter().toNexus( this ).toString();
+ return new PhylogenyWriter().toNexus( this, svs ).toString();
}
catch ( final IOException e ) {
throw new Error( "this should not have happend: " + e.getMessage() );
}
}
+ 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();