org.forester.sdi
public class SDIR extends java.lang.Object
Constructor and Description |
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SDIR()
Default contructor which creates an "empty" object..
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Modifier and Type | Method and Description |
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static java.util.List<PhylogenyBranch> |
getBranchesInPreorder(Phylogeny t) |
int |
getCount()
Returns the number of differently rooted trees which minimize the
(rooting) "criterion" - as determined by method "infer".
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double |
getMinimalDiffInSubTreeHeights()
Returns the (absolue value of the) minimal difference in tree heights of
the two subtrees at the root (of the (re)rooted gene tree) - as
determined by method "infer" - if minimize_height is set to true.
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int |
getMinimalDuplications()
Returns the minimal number of duplications - as determined by method
"infer".
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int |
getMinimalMappingCost()
Returns the minimal mapping cost L - as determined by method "infer" - if
minimize_mapping_cost is set to true.
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double |
getMinimalTreeHeight()
Returns the minimal tree height - as determined by method "infer" - if
minimize_height is set to true.
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long |
getTimeSumSDI()
Returns the sum of times (in ms) needed to run method infer of class SDI.
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Phylogeny[] |
infer(Phylogeny gene_tree,
Phylogeny species_tree,
boolean minimize_mapping_cost,
boolean minimize_sum_of_dup,
boolean minimize_height,
boolean return_trees,
int max_trees_to_return)
Infers gene duplications on a possibly unrooted gene Phylogeny gene_tree.
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public int getCount()
#infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
public double getMinimalDiffInSubTreeHeights()
If a tree is midpoint rooted this number is zero.
IMPORTANT : If minimize_mapping_cost or minimize_sum_of_dup are also set to true, then this returns the minimal difference in tree heights of the trees which minimize the first criterion, and is therefore not necessarily zero.
(Last modified: 01/22/00)
#infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
public int getMinimalDuplications()
IMPORTANT : 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.
#infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
public int getMinimalMappingCost()
(Last modified: 11/07/00)
#infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
public double getMinimalTreeHeight()
(Last modified: 01/12/00)
#infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
public long getTimeSumSDI()
public Phylogeny[] infer(Phylogeny gene_tree, Phylogeny species_tree, boolean minimize_mapping_cost, boolean minimize_sum_of_dup, boolean minimize_height, boolean return_trees, int max_trees_to_return)
Conditions:
(Last modified: 10/01/01)
gene_tree
- a binary (except deepest node) gene Phylogenyspecies_tree
- a rooted binary species Phylogenyminimize_mapping_cost
- set to true to root by minimizing the mapping cost L (and also
the sum of duplications)minimize_sum_of_dup
- set to true to root by minimizing the sum of duplicationsminimize_height
- set to true to root by minimizing the tree height - if
minimize_mapping_cost is set to true or minimize_sum_of_dup is
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 chosenreturn_trees
- set to true to return Array of Trees, otherwise null is
returnedmax_trees_to_return
- maximal number of Trees to return (=maximal size of returned
Array) must be no lower than 1public static java.util.List<PhylogenyBranch> getBranchesInPreorder(Phylogeny t)