* <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>
* <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>
/**
* Returns the number of differently rooted trees which minimize the
* (rooting) "criterion" - as determined by method "infer".
/**
* 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
*/
* @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
* @return number of differently rooted trees which minimized the criterion
*/
* @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
* @return the minimal difference in tree heights -- IF calculated by
* "infer"
* @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.
* <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
*/
* @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
* @return (minimal) number of duplications
*/
* @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
* @return the minimal mapping cost "L" -- IF calculated by "infer"
*/
* @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
* @return the minimal mapping cost "L" -- IF calculated by "infer"
*/
* @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
* @return the minimal tree height -- IF calculated by "infer"
*/
* @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.
/**
* Returns the sum of times (in ms) needed to run method infer of class SDI.
* Final variable TIME needs to be set to true.
* 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
* 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
*/
public Phylogeny[] infer( final Phylogeny gene_tree,
final Phylogeny species_tree,
*/
public Phylogeny[] infer( final Phylogeny gene_tree,
final Phylogeny species_tree,