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;
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>();
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 );