in progress

[jalview.git] / forester / java / src / org / forester / evoinference / TestPhylogenyReconstruction.java

diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
index 2fe3a4c..f6d3975 100644 (file)
--- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
+++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
@@ -34,6 +34,7 @@ import java.util.Date;
 import java.util.List;
 import java.util.SortedSet;
 
+import org.forester.archaeopteryx.Archaeopteryx;
 import org.forester.evoinference.distance.NeighborJoining;
 import org.forester.evoinference.distance.NeighborJoiningF;
 import org.forester.evoinference.distance.NeighborJoiningR;
@@ -90,7 +91,7 @@ public class TestPhylogenyReconstruction {
         else {
             System.out.println( "  failed." );
         }
-        //timeNeighborJoining();
+       // timeNeighborJoining();
     }
 
     public static boolean test( final File test_dir ) {
@@ -2483,6 +2484,7 @@ public class TestPhylogenyReconstruction {
             final NeighborJoining nj = NeighborJoining.createInstance( true, 6 );
             //nj = NeighborJoining.createInstance( true, 6 );
             final Phylogeny pnj = nj.execute( m );
+            Archaeopteryx.createApplication( pnj );
             //
             m = new BasicSymmetricalDistanceMatrix( 7 );
             m.setIdentifier( 0, "Bovine" );
@@ -2502,7 +2504,7 @@ public class TestPhylogenyReconstruction {
             final NeighborJoiningR nj2 = NeighborJoiningR.createInstance( true, 6 );
             //nj = NeighborJoining.createInstance( true, 6 );
             final Phylogeny p2 = nj2.execute( m );
-            //  Archaeopteryx.createApplication( p2 );
+              Archaeopteryx.createApplication( p2 );
             p2.reRoot( p2.getNode( "Bovine" ) );
             if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.151675 ) ) {
                 return false;