X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FSDIR.java;h=dbab2265d481dc55ecfc7bb1b28cc41c197ff393;hb=4ac270d05ca87fd5eb6e1794eefbd85a58451d30;hp=2b72221c21e890e86a059c5b2ef0785580425d2b;hpb=6c0feb7d2e02c6287d1328e61353cecff062bcd3;p=jalview.git

diff --git a/forester/java/src/org/forester/sdi/SDIR.java b/forester/java/src/org/forester/sdi/SDIR.java
index 2b72221..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;
 
@@ -212,7 +212,7 @@ public class SDIR {
      *            Array) must be no lower than 1
      * @return array of rooted Trees with duplication vs. speciation assigned if
      *         return_trees is set to true, null otherwise
-     * @throws SdiException 
+     * @throws SDIException 
      */
     public Phylogeny[] infer( final Phylogeny gene_tree,
                               final Phylogeny species_tree,
@@ -220,9 +220,9 @@ public class SDIR {
                               boolean minimize_sum_of_dup,
                               final boolean minimize_height,
                               final boolean return_trees,
-                              int max_trees_to_return ) throws SdiException {
+                              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;
@@ -266,26 +266,23 @@ public class SDIR {
             final PhylogenyNode n = iter.next();
             if ( n.isRoot() ) {
                 if ( ( n.getNumberOfDescendants() != 2 ) && ( n.getNumberOfDescendants() != 3 ) ) {
-                    throw new IllegalArgumentException( "attempt to run SDI on gene tree with "
-                            + n.getNumberOfDescendants() + " child nodes at its root" );
+                    throw new SDIException( "gene tree has " + n.getNumberOfDescendants() + " descendents at its root" );
                 }
             }
             else if ( !n.isExternal() && ( n.getNumberOfDescendants() != 2 ) ) {
-                throw new IllegalArgumentException( "attempt to run SDI on gene tree which is not completely binary [found node with "
-                        + n.getNumberOfDescendants() + " child nodes]" );
+                throw new SDIException( "gene tree is not completely binary" );
             }
         }
         for( final PhylogenyNodeIterator iter = species_tree.iteratorPostorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
             if ( !n.isExternal() && ( n.getNumberOfDescendants() != 2 ) ) {
-                throw new IllegalArgumentException( "attempt to run SDI with a species tree which is not completely binary (after stripping) [found node with "
-                        + n.getNumberOfDescendants() + " child nodes]" );
+                throw new SDIException( "species tree (after stripping) is not completely binary" );
             }
         }
         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>();
@@ -295,7 +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 );
             }
@@ -421,7 +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 );
@@ -497,8 +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() ) ) {