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java.lang.Object
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+--forester.tools.SDI
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+--forester.tools.SDIse
Implements our algorithm for speciation - duplication inference (SDI).
Reference:
The initialization is accomplished by:
The recursion part is accomplished by this class' method "geneTreePostOrderTraversal(Node)".
Requires JDK 1.2 or greater.
SDI.linkExtNodesOfG(),
Tree.preorderReID(int),
SDI.stripTree(Tree,Tree),
geneTreePostOrderTraversal(Node)| Fields inherited from class forester.tools.SDI |
c, duplications, genetree, speciestree |
| Constructor Summary | |
SDIse(Tree gene_tree,
Tree species_tree)
Constructor which sets the gene tree and the species tree to be compared. |
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| Method Summary | |
(package private) void |
geneTreePostOrderTraversal(Node g)
Traverses the subtree of Node g in postorder, calculating the mapping function M, and determines which nodes represent speciation events and which ones duplication events. |
int |
infer(boolean strip_species_tree)
Infers for each Node of gene_tree (set in constructor) whether it represents a speciation or duplication event by calculating and interpreting the mapping function M. |
(package private) int |
inferR(boolean was_old_root_dup)
Calculates the mapping for the root of the gene tree and its two children. |
| Methods inherited from class forester.tools.SDI |
computeMappingCost, linkExtNodesOfG, main, stripTree |
| Methods inherited from class java.lang.Object |
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| Constructor Detail |
public SDIse(Tree gene_tree,
Tree species_tree)
throws java.lang.Exception
(Last modified: 01/11/01)
gene_tree - reference to a rooted binary gene Tree to which assign
duplication vs speciation, must have species names in
the species name fields for all external nodesspecies_tree - reference to a rooted binary species Tree which might
get stripped in the process, must have species names in
the species name fields for all external nodesinfer(boolean),
SDI.computeMappingCost()| Method Detail |
public int infer(boolean strip_species_tree)
throws java.lang.Exception
(Last modified: 01/11/01)
infer in class SDIstrip_species_tree - set to true to remove from the species tree
species not found in the gene tree prior
to analysis (optional)SDIse(Tree,Tree)void geneTreePostOrderTraversal(Node g)
Preconditions: Mapping M for external nodes must have been calculated and the species tree must be labelled in preorder.
(Last modified: 01/11/01)
g - starting node of a gene tree - normally the root
int inferR(boolean was_old_root_dup)
throws java.lang.Exception
Is to be used ONLY by method "SDIunrooted.fastInfer(Tree,Tree)".
(Last modfied: 06/12/01)
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