refactoring

[jalview.git] / forester / java / src / org / forester / sdi / RIOn.java

diff --git a/forester/java/src/org/forester/sdi/RIOn.java b/forester/java/src/org/forester/sdi/RIOn.java
index 7855473..058e10f 100644 (file)
--- a/forester/java/src/org/forester/sdi/RIOn.java
+++ b/forester/java/src/org/forester/sdi/RIOn.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
@@ -15,7 +15,7 @@
 // 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
@@ -45,7 +45,7 @@ public class RIOn {
     GeneralTable<String, Integer> _super_orthologs                = null;
     GeneralTable<String, Integer> _ultra_paralogs                 = null;
 
-    private void doInferOrthologs( final Phylogeny gene_tree, final Phylogeny species_tree ) {
+    private void doInferOrthologs( final Phylogeny gene_tree, final Phylogeny species_tree ) throws SDIException {
         final SDIR sdiunrooted = new SDIR();
         final Phylogeny assigned_tree = sdiunrooted.infer( gene_tree,
                                                            species_tree,
@@ -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.calculateLCA( 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();