X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FRIO.java;h=028881cfcc48a333fa5cbf98092892fb19c2d2eb;hb=4acc1443d8c6c6f47c26a7c57357bdcdad27ecf8;hp=2da3a706413ae43d11d13e513e3af6d1376cdc9e;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

diff --git a/forester/java/src/org/forester/sdi/RIO.java b/forester/java/src/org/forester/sdi/RIO.java
index 2da3a70..028881c 100644
--- a/forester/java/src/org/forester/sdi/RIO.java
+++ b/forester/java/src/org/forester/sdi/RIO.java
@@ -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();