in progress

[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 9560dfa..f61a79a 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/Phylogeny.java
+++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java
@@ -39,9 +39,11 @@ import java.util.NoSuchElementException;
 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;
+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;
@@ -111,7 +113,7 @@ public class Phylogeny {
         new_node.setParent( sibling_parent );
         sibling.setParent( new_node );
         sibling_parent.setChildNode( sibling_index, new_node );
-        final double new_dist = sibling.getDistanceToParent() == PhylogenyNode.DISTANCE_DEFAULT ? PhylogenyNode.DISTANCE_DEFAULT
+        final double new_dist = sibling.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ? PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT
                 : sibling.getDistanceToParent() / 2;
         new_node.setDistanceToParent( new_dist );
         sibling.setDistanceToParent( new_dist );
@@ -1108,8 +1110,8 @@ public class Phylogeny {
                 b.setBranchData( ( BranchData ) a.getBranchDataDirectly().copy() );
             }
             // New root is always placed in the middle of the branch:
-            if ( a.getDistanceToParent() == PhylogenyNode.DISTANCE_DEFAULT ) {
-                b.setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
+            if ( a.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
+                b.setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
             }
             else {
                 if ( distance_n_to_parent >= 0.0 ) {
@@ -1142,9 +1144,9 @@ public class Phylogeny {
             if ( c.getNumberOfDescendants() == 2 ) {
                 final PhylogenyNode node = c.getChildNode( 1 - b.getChildNodeIndex( c ) );
                 node.setParent( b );
-                if ( ( c.getDistanceToParent() == PhylogenyNode.DISTANCE_DEFAULT )
-                        && ( node.getDistanceToParent() == PhylogenyNode.DISTANCE_DEFAULT ) ) {
-                    node.setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
+                if ( ( c.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT )
+                        && ( node.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
+                    node.setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
                 }
                 else {
                     node.setDistanceToParent( ( c.getDistanceToParent() >= 0.0 ? c.getDistanceToParent() : 0.0 )
@@ -1277,12 +1279,14 @@ public class Phylogeny {
     } // 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() );
@@ -1298,15 +1302,19 @@ public class Phylogeny {
         }
     }
 
-    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();