X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FRIO.java;h=4db4648c82219a59ffe6f1798e647ca4af690319;hb=c8ff981282f66e8a7bb5435aad13686236651c14;hp=d2c79ee6186f16ed155962a7b7c15bf4e4d5b4ed;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/sdi/RIO.java b/forester/java/src/org/forester/sdi/RIO.java
index d2c79ee..4db4648 100644
--- a/forester/java/src/org/forester/sdi/RIO.java
+++ b/forester/java/src/org/forester/sdi/RIO.java
@@ -7,7 +7,7 @@
 // Copyright (C) 2000-2001 Washington University School of Medicine
 // and Howard Hughes Medical Institute
 // 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
@@ -17,7 +17,7 @@
 // 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
@@ -231,9 +231,10 @@ public final class RIO {
      * @param query
      *            the sequence name of the squence whose orthologs are to be
      *            inferred
+     * @throws SdiException 
      */
     public void inferOrthologs( final File gene_trees_file, final Phylogeny species_tree, final String query )
-            throws IOException {
+            throws IOException, SdiException {
         int bs = 0;
         if ( RIO.TIME ) {
             _time = System.currentTimeMillis();
@@ -281,7 +282,8 @@ public final class RIO {
 
     // Helper method which performs the actual ortholog inference for
     // the external node with seqname query.
-    private void inferOrthologsHelper( final Phylogeny gene_tree, final Phylogeny species_tree, final String query ) {
+    private void inferOrthologsHelper( final Phylogeny gene_tree, final Phylogeny species_tree, final String query )
+            throws SdiException {
         Phylogeny assigned_tree = null;
         List<PhylogenyNode> nodes = null;
         final SDIR sdiunrooted = new SDIR();