package org.forester.phylogeny;
-import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
-import org.forester.archaeopteryx.Archaeopteryx;
import org.forester.io.parsers.nhx.NHXFormatException;
import org.forester.io.parsers.nhx.NHXParser;
import org.forester.phylogeny.data.BranchData;
import org.forester.phylogeny.data.NodeData;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.ChildNodeIteratorForward;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.phylogeny.iterators.PreorderTreeIterator;
}
return current_node;
}
-
-
-
-
+
public final NodeData getNodeData() {
if ( _node_data == null ) {
_node_data = new NodeData();
}
public static PhylogenyNode createInstanceFromNhxString( final String nhx ) throws NHXFormatException {
- return new PhylogenyNode( nhx, ForesterUtil.TAXONOMY_EXTRACTION.NO, false );
+ return new PhylogenyNode( nhx, PhylogenyMethods.TAXONOMY_EXTRACTION.NO, false );
}
public static PhylogenyNode createInstanceFromNhxString( final String nhx,
- final ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction )
+ final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction )
throws NHXFormatException {
return new PhylogenyNode( nhx, taxonomy_extraction, false );
}
public static PhylogenyNode createInstanceFromNhxString( final String nhx,
- final ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction,
+ final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction,
final boolean replace_underscores )
throws NHXFormatException {
return new PhylogenyNode( nhx, taxonomy_extraction, replace_underscores );
}
private PhylogenyNode( final String nhx,
- final ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction,
+ final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction,
final boolean replace_underscores ) throws NHXFormatException {
init();
NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores );