in progress

[jalview.git] / forester / java / src / org / forester / application / sdi_dir.java

diff --git a/forester/java/src/org/forester/application/sdi_dir.java b/forester/java/src/org/forester/application/sdi_dir.java
index fddb6e4..f23a683 100644 (file)
--- a/forester/java/src/org/forester/application/sdi_dir.java
+++ b/forester/java/src/org/forester/application/sdi_dir.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
@@ -39,6 +39,7 @@ import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.sdi.SDIException;
 import org.forester.sdi.SDIR;
 import org.forester.sdi.SDIse;
 import org.forester.util.ForesterUtil;
@@ -144,6 +145,7 @@ public class sdi_dir {
      *            set to true, then out of the resulting trees with minimal
      *            mapping cost or minimal number of duplications the tree with
      *            the minimal height is chosen
+     * @throws SDIException 
      */
     public static void infer( final File indir,
                               final File species_tree_file,
@@ -153,7 +155,7 @@ public class sdi_dir {
                               final boolean write_trees,
                               final boolean minimize_mapping_cost,
                               boolean minimize_sum_of_dup,
-                              final boolean minimize_height ) throws IOException {
+                              final boolean minimize_height ) throws IOException, SDIException {
         final int MIN_EXT_NODES = 4; // Minimal size of trees [in ext nodes]
         // to be analyzed.
         final int MAX_EXT_NODES = 5000; // Maximal size of trees [in ext nodes]