X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2FPhylogenyNode.java;h=a65de7cd83e5e3e6e7f983c87a79362c3a163f0a;hb=89d7b6ec1ddc3a3c1e953cf389c24ba7aae7fbfe;hp=7c272e6d6c4c52a93650b5d5a4674e57c7b9b89f;hpb=2b4d8edabd858f232899cf045ec0124a079ed8ce;p=jalview.git

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index 7c272e6..a65de7c 100644
--- 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;
@@ -923,7 +923,9 @@ 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 boolean write_support_values_in_brackets ) {
         final StringBuilder sb = new StringBuilder();
         String data = "";
         if ( !ForesterUtil.isEmpty( getName() ) ) {
@@ -962,10 +964,16 @@ 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 ( write_support_values_in_brackets && !isExternal()
+                && ( getBranchData().getConfidence( 0 ).getValue() != Confidence.CONFIDENCE_DEFAULT_VALUE ) ) {
+            sb.append( "[" );
+            sb.append( getBranchData().getConfidence( 0 ).getValue() );
+            sb.append( "]" );
+        }
         return sb.toString();
     }
 
@@ -987,7 +995,7 @@ 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() );
         }
@@ -1049,24 +1057,24 @@ 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 );