in progress

[jalview.git] / forester / java / src / org / forester / phylogeny / PhylogenyNode.java

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index dd3dba0..7bf60ef 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -27,17 +27,13 @@
 
 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;
@@ -457,10 +453,7 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
         }
         return current_node;
     }
-    
-  
-    
-    
+
     public final NodeData getNodeData() {
         if ( _node_data == null ) {
             _node_data = new NodeData();
@@ -1056,24 +1049,24 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
     }
 
     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 );