in progress

diff --git a/forester/java/src/org/forester/application/decorator.java b/forester/java/src/org/forester/application/decorator.java
index 2b711a0..241ddaf 100644 (file)
--- a/forester/java/src/org/forester/application/decorator.java
+++ b/forester/java/src/org/forester/application/decorator.java
@@ -369,7 +369,7 @@ public final class decorator {
             ForesterUtil.unexpectedFatalError( decorator.PRG_NAME, e );
         }
         catch ( final Exception e ) {
-            ForesterUtil.fatalError( decorator.PRG_NAME, "failed to map [" + e + "]" );
+            ForesterUtil.fatalError( decorator.PRG_NAME, e.getLocalizedMessage()  );
         }
         try {
             final PhylogenyWriter w = new PhylogenyWriter();

diff --git a/forester/java/src/org/forester/pccx/ModelingUtils.java b/forester/java/src/org/forester/pccx/ModelingUtils.java
index 1614ca6..8d10e01 100644 (file)
--- a/forester/java/src/org/forester/pccx/ModelingUtils.java
+++ b/forester/java/src/org/forester/pccx/ModelingUtils.java
@@ -39,7 +39,7 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 public final class ModelingUtils {
 
     static double calculateBranchLengthSum( final PhylogenyNode n1, final PhylogenyNode n2 ) {
-        final PhylogenyNode lca = PhylogenyMethods.getInstance().obtainLCA( n1, n2 );
+        final PhylogenyNode lca = PhylogenyMethods.obtainLCA( n1, n2 );
         return ModelingUtils.calculateBranchLengthSumHelper( n1, lca )
                 + ModelingUtils.calculateBranchLengthSumHelper( n2, lca );
     }
@@ -57,7 +57,7 @@ public final class ModelingUtils {
     }
 
     static int calculateBranchSum( final PhylogenyNode n1, final PhylogenyNode n2 ) {
-        final PhylogenyNode lca = PhylogenyMethods.getInstance().obtainLCA( n1, n2 );
+        final PhylogenyNode lca = PhylogenyMethods.obtainLCA( n1, n2 );
         return ModelingUtils.calculateBranchSumHelper( n1, lca ) + ModelingUtils.calculateBranchSumHelper( n2, lca );
     }
 

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index b154b48..313848b 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -47,6 +47,7 @@ import org.forester.phylogeny.data.BranchColor;
 import org.forester.phylogeny.data.BranchWidth;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.DomainArchitecture;
+import org.forester.phylogeny.data.Event;
 import org.forester.phylogeny.data.Identifier;
 import org.forester.phylogeny.data.PhylogenyDataUtil;
 import org.forester.phylogeny.data.Sequence;
@@ -62,7 +63,7 @@ import org.forester.util.ForesterUtil;
 public class PhylogenyMethods {
 
     private static PhylogenyMethods _instance      = null;
-    private final Set<Integer>      _temp_hash_set = new HashSet<Integer>();
+
     private PhylogenyNode           _farthest_1    = null;
     private PhylogenyNode           _farthest_2    = null;
 
@@ -70,6 +71,10 @@ public class PhylogenyMethods {
         // Hidden constructor.
     }
 
+    
+    
+    
+    
     /**
      * Calculates the distance between PhylogenyNodes node1 and node2.
      * 
@@ -114,6 +119,13 @@ public class PhylogenyMethods {
         return farthest_d;
     }
 
+    final public static Event getEventAtLCA( PhylogenyNode n1,
+                                             PhylogenyNode n2 ) {
+        return obtainLCA( n1, n2 ).getNodeData().getEvent();
+    }
+    
+    
+    
     @Override
     public Object clone() throws CloneNotSupportedException {
         throw new CloneNotSupportedException();
@@ -127,6 +139,29 @@ public class PhylogenyMethods {
         return _farthest_2;
     }
 
+    final public static void deleteNonOrthologousExternalNodes( final Phylogeny phy,
+                                                                final PhylogenyNode n) {
+        if ( n.isInternal() ) {
+            throw new IllegalArgumentException( "node is not external" );
+        }
+        
+        final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
+        for ( PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+            final PhylogenyNode i = it.next();
+            if ( !PhylogenyMethods.getEventAtLCA( n, i ).isSpeciation() ) {
+                to_delete.add( i ); 
+            }
+        }
+        for( PhylogenyNode d : to_delete ) {
+            phy.deleteSubtree( d, true );
+        }
+        phy.clearHashIdToNodeMap();
+        phy.externalNodesHaveChanged();
+        
+    }
+    
+    
+    
     /**
      * Returns the LCA of PhylogenyNodes node1 and node2.
      * 
@@ -135,19 +170,19 @@ public class PhylogenyMethods {
      * @param node2
      * @return LCA of node1 and node2
      */
-    public PhylogenyNode obtainLCA( final PhylogenyNode node1, final PhylogenyNode node2 ) {
-        _temp_hash_set.clear();
+    public final static PhylogenyNode obtainLCA( final PhylogenyNode node1, final PhylogenyNode node2 ) {
+        final HashSet<Integer> ids_set = new HashSet<Integer>();
         PhylogenyNode n1 = node1;
         PhylogenyNode n2 = node2;
-        _temp_hash_set.add( n1.getId() );
+        ids_set.add( n1.getId() );
         while ( !n1.isRoot() ) {
             n1 = n1.getParent();
-            _temp_hash_set.add( n1.getId() );
+            ids_set.add( n1.getId() );
         }
-        while ( !_temp_hash_set.contains( n2.getId() ) && !n2.isRoot() ) {
+        while ( !ids_set.contains( n2.getId() ) && !n2.isRoot() ) {
             n2 = n2.getParent();
         }
-        if ( !_temp_hash_set.contains( n2.getId() ) ) {
+        if ( !ids_set.contains( n2.getId() ) ) {
             throw new IllegalArgumentException( "attempt to get LCA of two nodes which do not share a common root" );
         }
         return n2;

diff --git a/forester/java/src/org/forester/sdi/RIOn.java b/forester/java/src/org/forester/sdi/RIOn.java
index 932030a..e7b7c89 100644 (file)
--- a/forester/java/src/org/forester/sdi/RIOn.java
+++ b/forester/java/src/org/forester/sdi/RIOn.java
@@ -64,7 +64,7 @@ public class RIOn {
                 if ( i != j ) {
                     final PhylogenyNode node_i = external_nodes.get( i );
                     final PhylogenyNode node_j = external_nodes.get( j );
-                    final PhylogenyNode lca = methods.obtainLCA( node_i, node_j );
+                    final PhylogenyNode lca = PhylogenyMethods.obtainLCA( node_i, node_j );
                     final Event event = lca.getNodeData().getEvent();
                     final String node_i_name = node_i.getNodeData().getSequence().getName();
                     final String node_j_name = node_j.getNodeData().getSequence().getName();

diff --git a/forester/java/src/org/forester/sdi/TestGSDI.java b/forester/java/src/org/forester/sdi/TestGSDI.java
index 91ac13a..045eebb 100644 (file)
--- a/forester/java/src/org/forester/sdi/TestGSDI.java
+++ b/forester/java/src/org/forester/sdi/TestGSDI.java
@@ -50,7 +50,7 @@ public final class TestGSDI {
     }
 
     private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
-        return PhylogenyMethods.getInstance().obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
+        return PhylogenyMethods.obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
     }
 
     public static boolean test() {

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index 1a0a07d..ab83ebf 100644 (file)
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -374,7 +374,7 @@ public final class SurfacingUtil {
                 }
                 for( int i = 0; i < nodes.size() - 1; ++i ) {
                     for( int j = i + 1; j < nodes.size(); ++j ) {
-                        final PhylogenyNode lca = PhylogenyMethods.getInstance().obtainLCA( nodes.get( i ),
+                        final PhylogenyNode lca = PhylogenyMethods.obtainLCA( nodes.get( i ),
                                                                                             nodes.get( j ) );
                         String rank = "unknown";
                         if ( lca.getNodeData().isHasTaxonomy()

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index b7eff50..9c67685 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -3210,200 +3210,199 @@ public final class Test {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
             final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
                                                  new NHXParser() )[ 0 ];
-            final PhylogenyMethods pm = PhylogenyMethods.getInstance();
-            final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
+            final PhylogenyNode A = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
             if ( !A.getName().equals( "A" ) ) {
                 return false;
             }
-            final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
+            final PhylogenyNode gh = PhylogenyMethods.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
             if ( !gh.getName().equals( "gh" ) ) {
                 return false;
             }
-            final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
+            final PhylogenyNode ab = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
             if ( !ab.getName().equals( "ab" ) ) {
                 return false;
             }
-            final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
+            final PhylogenyNode ab2 = PhylogenyMethods.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
             if ( !ab2.getName().equals( "ab" ) ) {
                 return false;
             }
-            final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
+            final PhylogenyNode gh2 = PhylogenyMethods.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
             if ( !gh2.getName().equals( "gh" ) ) {
                 return false;
             }
-            final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
+            final PhylogenyNode gh3 = PhylogenyMethods.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
             if ( !gh3.getName().equals( "gh" ) ) {
                 return false;
             }
-            final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
+            final PhylogenyNode abc = PhylogenyMethods.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
             if ( !abc.getName().equals( "abc" ) ) {
                 return false;
             }
-            final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
+            final PhylogenyNode abc2 = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
             if ( !abc2.getName().equals( "abc" ) ) {
                 return false;
             }
-            final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
+            final PhylogenyNode abcd = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
             if ( !abcd.getName().equals( "abcd" ) ) {
                 return false;
             }
-            final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
+            final PhylogenyNode abcd2 = PhylogenyMethods.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
             if ( !abcd2.getName().equals( "abcd" ) ) {
                 return false;
             }
-            final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
+            final PhylogenyNode abcdef = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
             if ( !abcdef.getName().equals( "abcdef" ) ) {
                 return false;
             }
-            final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
+            final PhylogenyNode abcdef2 = PhylogenyMethods.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
             if ( !abcdef2.getName().equals( "abcdef" ) ) {
                 return false;
             }
-            final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
+            final PhylogenyNode abcdef3 = PhylogenyMethods.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
             if ( !abcdef3.getName().equals( "abcdef" ) ) {
                 return false;
             }
-            final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
+            final PhylogenyNode abcdef4 = PhylogenyMethods.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
             if ( !abcdef4.getName().equals( "abcdef" ) ) {
                 return false;
             }
-            final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
+            final PhylogenyNode abcde = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
             if ( !abcde.getName().equals( "abcde" ) ) {
                 return false;
             }
-            final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
+            final PhylogenyNode abcde2 = PhylogenyMethods.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
             if ( !abcde2.getName().equals( "abcde" ) ) {
                 return false;
             }
-            final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
+            final PhylogenyNode r = PhylogenyMethods.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
             if ( !r.getName().equals( "abcdefgh" ) ) {
                 return false;
             }
-            final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
+            final PhylogenyNode r2 = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
             if ( !r2.getName().equals( "abcdefgh" ) ) {
                 return false;
             }
-            final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
+            final PhylogenyNode r3 = PhylogenyMethods.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
             if ( !r3.getName().equals( "abcdefgh" ) ) {
                 return false;
             }
-            final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
+            final PhylogenyNode abcde3 = PhylogenyMethods.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
             if ( !abcde3.getName().equals( "abcde" ) ) {
                 return false;
             }
-            final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
+            final PhylogenyNode abcde4 = PhylogenyMethods.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
             if ( !abcde4.getName().equals( "abcde" ) ) {
                 return false;
             }
-            final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
+            final PhylogenyNode ab3 = PhylogenyMethods.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
             if ( !ab3.getName().equals( "ab" ) ) {
                 return false;
             }
-            final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
+            final PhylogenyNode ab4 = PhylogenyMethods.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
             if ( !ab4.getName().equals( "ab" ) ) {
                 return false;
             }
             final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
-            final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
+            final PhylogenyNode cd = PhylogenyMethods.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
             if ( !cd.getName().equals( "cd" ) ) {
                 return false;
             }
-            final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
+            final PhylogenyNode cd2 = PhylogenyMethods.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
             if ( !cd2.getName().equals( "cd" ) ) {
                 return false;
             }
-            final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
+            final PhylogenyNode cde = PhylogenyMethods.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
             if ( !cde.getName().equals( "cde" ) ) {
                 return false;
             }
-            final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
+            final PhylogenyNode cde2 = PhylogenyMethods.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
             if ( !cde2.getName().equals( "cde" ) ) {
                 return false;
             }
-            final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
+            final PhylogenyNode cdef = PhylogenyMethods.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
             if ( !cdef.getName().equals( "cdef" ) ) {
                 return false;
             }
-            final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
+            final PhylogenyNode cdef2 = PhylogenyMethods.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
             if ( !cdef2.getName().equals( "cdef" ) ) {
                 return false;
             }
-            final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
+            final PhylogenyNode cdef3 = PhylogenyMethods.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
             if ( !cdef3.getName().equals( "cdef" ) ) {
                 return false;
             }
-            final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
+            final PhylogenyNode rt = PhylogenyMethods.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
             if ( !rt.getName().equals( "r" ) ) {
                 return false;
             }
             final Phylogeny p3 = factory
                     .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
                              new NHXParser() )[ 0 ];
-            final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
+            final PhylogenyNode bc_3 = PhylogenyMethods.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
             if ( !bc_3.getName().equals( "bc" ) ) {
                 return false;
             }
-            final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
+            final PhylogenyNode ac_3 = PhylogenyMethods.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
             if ( !ac_3.getName().equals( "abc" ) ) {
                 return false;
             }
-            final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
+            final PhylogenyNode ad_3 = PhylogenyMethods.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
             if ( !ad_3.getName().equals( "abcde" ) ) {
                 return false;
             }
-            final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
+            final PhylogenyNode af_3 = PhylogenyMethods.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
             if ( !af_3.getName().equals( "abcdef" ) ) {
                 return false;
             }
-            final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
+            final PhylogenyNode ag_3 = PhylogenyMethods.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
             if ( !ag_3.getName().equals( "" ) ) {
                 return false;
             }
             if ( !ag_3.isRoot() ) {
                 return false;
             }
-            final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
+            final PhylogenyNode al_3 = PhylogenyMethods.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
             if ( !al_3.getName().equals( "" ) ) {
                 return false;
             }
             if ( !al_3.isRoot() ) {
                 return false;
             }
-            final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
+            final PhylogenyNode kl_3 = PhylogenyMethods.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
             if ( !kl_3.getName().equals( "" ) ) {
                 return false;
             }
             if ( !kl_3.isRoot() ) {
                 return false;
             }
-            final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
+            final PhylogenyNode fl_3 = PhylogenyMethods.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
             if ( !fl_3.getName().equals( "" ) ) {
                 return false;
             }
             if ( !fl_3.isRoot() ) {
                 return false;
             }
-            final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
+            final PhylogenyNode gk_3 = PhylogenyMethods.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
             if ( !gk_3.getName().equals( "ghijk" ) ) {
                 return false;
             }
             final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
-            final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
+            final PhylogenyNode r_4 = PhylogenyMethods.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
             if ( !r_4.getName().equals( "r" ) ) {
                 return false;
             }
             final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
-            final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
+            final PhylogenyNode r_5 = PhylogenyMethods.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
             if ( !r_5.getName().equals( "root" ) ) {
                 return false;
             }
             final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
-            final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
+            final PhylogenyNode r_6 = PhylogenyMethods.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
             if ( !r_6.getName().equals( "rot" ) ) {
                 return false;
             }
             final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
-            final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
+            final PhylogenyNode r_7 = PhylogenyMethods.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
             if ( !r_7.getName().equals( "rott" ) ) {
                 return false;
             }