in progress (special coloring is still true)

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

diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java
index 3679cd5..115e885 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/Phylogeny.java
+++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java
@@ -38,6 +38,7 @@ import java.util.Map;
 import java.util.NoSuchElementException;
 import java.util.Vector;
 
+import org.forester.io.parsers.nhx.NHXParser;
 import org.forester.io.writers.PhylogenyWriter;
 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.BranchData;
@@ -47,6 +48,8 @@ import org.forester.phylogeny.data.PhylogenyDataUtil;
 import org.forester.phylogeny.data.Sequence;
 import org.forester.phylogeny.data.SequenceRelation;
 import org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.phylogeny.iterators.ExternalForwardIterator;
 import org.forester.phylogeny.iterators.LevelOrderTreeIterator;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
@@ -304,6 +307,11 @@ public class Phylogeny {
         return _distance_unit;
     }
 
+    public final static Phylogeny createInstanceFromNhxString( final String nhx ) throws IOException {
+        final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+        return factory.create( nhx, new NHXParser() )[ 0 ];
+    }
+
     /**
      * 
      * Warning. The order of the returned nodes is random
@@ -1090,14 +1098,12 @@ public class Phylogeny {
     }
 
     public String toNewHampshire() {
-        return toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
+        return toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
     }
 
-    public String toNewHampshire( final boolean simple_nh,
-                                  final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style ) {
+    public String toNewHampshire( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style ) {
         try {
-            return new PhylogenyWriter().toNewHampshire( this, simple_nh, true, nh_conversion_support_style )
-                    .toString();
+            return new PhylogenyWriter().toNewHampshire( this, true, nh_conversion_support_style ).toString();
         }
         catch ( final IOException e ) {
             throw new Error( "this should not have happend: " + e.getMessage() );