X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FSDIR.java;h=dbab2265d481dc55ecfc7bb1b28cc41c197ff393;hb=d0bb37d418d945966304afe70431185c3873635a;hp=7af2359389b62a1a822c1385bcc605d3a4fc9e2c;hpb=9bad57b1ba0f75075ab8c6bda1dedb906f8c6280;p=jalview.git

diff --git a/forester/java/src/org/forester/sdi/SDIR.java b/forester/java/src/org/forester/sdi/SDIR.java
index 7af2359..dbab226 100644
--- a/forester/java/src/org/forester/sdi/SDIR.java
+++ b/forester/java/src/org/forester/sdi/SDIR.java
@@ -23,7 +23,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.sdi;
 
@@ -292,7 +292,7 @@ public class SDIR {
             prev_root_c2 = prev_root.getChildNode2();
             prev_root_was_dup = prev_root.isDuplication();
             final PhylogenyBranch current_branch = branches.get( j );
-            g.reRoot( current_branch );
+            GSDIR.reRoot( current_branch, g );
             if ( minimize_mapping_cost || minimize_sum_of_dup ) {
                 duplications = sdise.updateM( prev_root_was_dup, prev_root_c1, prev_root_c2 );
             }
@@ -494,8 +494,8 @@ public class SDIR {
             branches.add( new PhylogenyBranch( t.getRoot().getChildNode1(), t.getRoot().getChildNode2() ) );
             return branches;
         }
-        final Set<Integer> one = new HashSet<Integer>();
-        final Set<Integer> two = new HashSet<Integer>();
+        final Set<Long> one = new HashSet<Long>();
+        final Set<Long> two = new HashSet<Long>();
         PhylogenyNode node = t.getRoot();
         while ( !node.isRoot() || !two.contains( node.getId() ) ) {
             if ( !node.isExternal() && !two.contains( node.getId() ) ) {