X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fpccx%2FModelingUtils.java;h=f8d40623985510638715105b138e36bbfe117a0d;hb=d4d61f9d2969283e821f650d031c169899fb3870;hp=44eb20fa1a608563e00bf2f2f7763cb5a9a52d9b;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/pccx/ModelingUtils.java b/forester/java/src/org/forester/pccx/ModelingUtils.java
index 44eb20f..f8d4062 100644
--- a/forester/java/src/org/forester/pccx/ModelingUtils.java
+++ b/forester/java/src/org/forester/pccx/ModelingUtils.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,13 +15,13 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.pccx;
 
@@ -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.calculateLCA( 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.calculateLCA( n1, n2 );
         return ModelingUtils.calculateBranchSumHelper( n1, lca ) + ModelingUtils.calculateBranchSumHelper( n2, lca );
     }