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 e344279..c7a1caf 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -32,6 +32,7 @@ import java.util.List;
 
 import org.forester.io.parsers.nhx.NHXFormatException;
 import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
 import org.forester.phylogeny.data.BranchData;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.NodeData;
@@ -931,7 +932,9 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
         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() );
+                data = Confidence.FORMATTER.format( ForesterUtil
+                        .round( getBranchData().getConfidence( 0 ).getValue(),
+                                PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) );
             }
         }
         else if ( !ForesterUtil.isEmpty( getName() ) ) {
@@ -978,13 +981,32 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
                 && getBranchData().isHasConfidences()
                 && ( getBranchData().getConfidence( 0 ).getValue() != Confidence.CONFIDENCE_DEFAULT_VALUE ) ) {
             sb.append( "[" );
-            sb.append( getBranchData().getConfidence( 0 ).getValue() );
+            sb.append( Confidence.FORMATTER.format( ForesterUtil
+                    .round( getBranchData().getConfidence( 0 ).getValue(),
+                            PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ) );
             sb.append( "]" );
         }
         return sb.toString();
     }
 
     /**
+     * Swaps the the two childern of a PhylogenyNode node of this Phylogeny.
+     */
+    public void swapChildren() throws RuntimeException {
+        if ( isExternal() ) {
+            throw new RuntimeException( "attempt to swap descendants of external node" );
+        }
+        if ( getNumberOfDescendants() != 2 ) {
+            throw new RuntimeException( "attempt to swap descendants of node with " + getNumberOfDescendants()
+                    + " descendants" );
+        }
+        final PhylogenyNode a = getChildNode( 0 );
+        final PhylogenyNode b = getChildNode( 1 );
+        setChildNode( 0, b );
+        setChildNode( 1, a );
+    }
+
+    /**
      * Converts this PhylogenyNode to a New Hampshire X (NHX) String
      * representation.
      */