// 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;
* <li>Mapping cost L <li>Phylogeny height - which is the largest distance from
* root to external node (minimizing of which is the same as "midpoint rooting")
* </ul>
- *
+ *
* @see SDIse
- *
+ *
* @see SDI
- *
+ *
* @author Christian M. Zmasek
*/
public class SDIR {
/**
* Returns the number of differently rooted trees which minimize the
* (rooting) "criterion" - as determined by method "infer".
- *
+ *
* @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
* @return number of differently rooted trees which minimized the criterion
*/
* not necessarily zero.
* <p>
* (Last modified: 01/22/00)
- *
+ *
* @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
* @return the minimal difference in tree heights -- IF calculated by
* "infer"
* <B>IMPORTANT </B>: If the tree is not rooted by minimizing the sum of
* duplications or the mapping cost L, then this number is NOT NECESSARILY
* the MINIMAL number of duplications.
- *
+ *
* @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
* @return (minimal) number of duplications
*/
* minimize_mapping_cost is set to true.
* <p>
* (Last modified: 11/07/00)
- *
+ *
* @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
* @return the minimal mapping cost "L" -- IF calculated by "infer"
*/
* first criterion.
* <p>
* (Last modified: 01/12/00)
- *
+ *
* @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
* @return the minimal tree height -- IF calculated by "infer"
*/
/**
* Returns the sum of times (in ms) needed to run method infer of class SDI.
* Final variable TIME needs to be set to true.
- *
+ *
* @return sum of times (in ms) needed to run method infer of class SDI
*/
public long getTimeSumSDI() {
* </ul>
* <p>
* (Last modified: 10/01/01)
- *
+ *
* @param gene_tree
* a binary (except deepest node) gene Phylogeny
* @param species_tree
* 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,
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 );
}
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() ) ) {