import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.sdi.SDIR;
import org.forester.sdi.SDIse;
import org.forester.util.ForesterUtil;
import org.forester.sdi.SDIR;
import org.forester.sdi.SDIse;
import org.forester.util.ForesterUtil;
* 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
* 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
*/
public static void infer( final File indir,
final File species_tree_file,
*/
public static void infer( final File indir,
final File species_tree_file,
final boolean write_trees,
final boolean minimize_mapping_cost,
boolean minimize_sum_of_dup,
final boolean write_trees,
final boolean minimize_mapping_cost,
boolean minimize_sum_of_dup,
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]
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]