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[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 7bf60ef..e344279 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -33,7 +33,9 @@ import java.util.List;
 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.Confidence;
 import org.forester.phylogeny.data.NodeData;
+import org.forester.phylogeny.data.PhylogenyDataUtil;
 import org.forester.phylogeny.iterators.ChildNodeIteratorForward;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.phylogeny.iterators.PreorderTreeIterator;
@@ -41,9 +43,7 @@ import org.forester.util.ForesterUtil;
 
 public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode> {
 
-    /** Value of -99.0 is used as default value. */
-    public final static double       DISTANCE_DEFAULT = -1024.0;
-    private static int               _node_count      = 0;
+    private static int               _node_count = 0;
     private byte                     _indicator;
     private int                      _id;
     private int                      _sum_ext_nodes;
@@ -595,7 +595,7 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
         _x = 0;
         _y = 0;
         //_node_name = "";
-        _distance_parent = PhylogenyNode.DISTANCE_DEFAULT;
+        _distance_parent = PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
         _collapse = false;
         _link = null;
         _branch_data = null;
@@ -923,10 +923,18 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
     // ---------------------------------------------------------
     // Writing of Nodes to Strings
     // ---------------------------------------------------------
-    final public String toNewHampshire( final boolean simple_nh, final boolean write_distance_to_parent ) {
+    final public String toNewHampshire( final boolean simple_nh,
+                                        final boolean write_distance_to_parent,
+                                        final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) {
         final StringBuilder sb = new StringBuilder();
         String data = "";
-        if ( !ForesterUtil.isEmpty( getName() ) ) {
+        if ( ( svs == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ) && !isExternal() ) {
+            if ( getBranchData().isHasConfidences()
+                    && ( getBranchData().getConfidence( 0 ).getValue() != Confidence.CONFIDENCE_DEFAULT_VALUE ) ) {
+                data = String.valueOf( getBranchData().getConfidence( 0 ).getValue() );
+            }
+        }
+        else if ( !ForesterUtil.isEmpty( getName() ) ) {
             data = getName();
         }
         else if ( getNodeData().isHasTaxonomy() ) {
@@ -962,10 +970,17 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
                 sb.append( data );
             }
         }
-        if ( ( getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) && write_distance_to_parent ) {
+        if ( write_distance_to_parent && ( getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
             sb.append( ":" );
             sb.append( getDistanceToParent() );
         }
+        if ( ( svs == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) && !isExternal()
+                && getBranchData().isHasConfidences()
+                && ( getBranchData().getConfidence( 0 ).getValue() != Confidence.CONFIDENCE_DEFAULT_VALUE ) ) {
+            sb.append( "[" );
+            sb.append( getBranchData().getConfidence( 0 ).getValue() );
+            sb.append( "]" );
+        }
         return sb.toString();
     }
 
@@ -987,7 +1002,7 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
                 sb.append( name );
             }
         }
-        if ( getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
+        if ( getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
             sb.append( ":" );
             sb.append( getDistanceToParent() );
         }