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 679c2d6..058e10f 100644 (file)
--- a/forester/java/src/org/forester/sdi/RIOn.java
+++ b/forester/java/src/org/forester/sdi/RIOn.java
@@ -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 ) throws SdiException {
+    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();