int => long for node id

[jalview.git] / forester / java / src / org / forester / sdi / SDIR.java

diff --git a/forester/java/src/org/forester/sdi/SDIR.java b/forester/java/src/org/forester/sdi/SDIR.java
index ce7fc00..88a2f2c 100644 (file)
--- 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;
 
@@ -222,7 +222,7 @@ public class SDIR {
                               final boolean return_trees,
                               int max_trees_to_return ) throws SDIException {
         init();
-        SDIse sdise = null;
+        SDI sdise = null;
         final ArrayList<Phylogeny> trees = new ArrayList<Phylogeny>();
         Phylogeny[] tree_array = null;
         List<PhylogenyBranch> branches = null;
@@ -282,7 +282,7 @@ public class SDIR {
         g.reRoot( g.getFirstExternalNode() );
         branches = SDIR.getBranchesInPreorder( g );
         if ( minimize_mapping_cost || minimize_sum_of_dup ) {
-            sdise = new SDIse( g, species_tree );
+            sdise = new SDI( g, species_tree );
             duplications = sdise.getDuplicationsSum();
         }
         final Set<PhylogenyBranch> used_root_placements = new HashSet<PhylogenyBranch>();
@@ -418,7 +418,7 @@ public class SDIR {
                     height = height__diff[ 0 ];
                     diff = height__diff[ 1 ];
                     if ( Math.abs( diff ) < SDIR.ZERO_DIFF ) {
-                        sdise = new SDIse( g, species_tree );
+                        sdise = new SDI( g, species_tree );
                         min_duplications = sdise.getDuplicationsSum();
                         min_height = height;
                         min_diff = Math.abs( diff );
@@ -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() ) ) {