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java.lang.Object | +--forester.tools.SDI
Abstract class from with classes SDIse and OE inherit. SDIse implements our SDI algorithm. OE implements Eulenstein's algorithm for gene duplication inference.
Requires JDK 1.2 or greater.
SDIse
,
OE
Field Summary | |
(package private) int |
c
|
(package private) int |
duplications
|
(package private) Tree |
genetree
|
(package private) Tree |
speciestree
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Constructor Summary | |
SDI(Tree gene_tree,
Tree species_tree)
Constructor which sets the gene tree and the species tree to be compared. |
Method Summary | |
int |
computeMappingCost()
Computes the cost of mapping the gene tree gene_tree onto the species tree species_tree. |
abstract 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) void |
linkExtNodesOfG()
Calculates the mapping function for the external nodes of the gene tree: links (sets the field "link" of Node) each external Node of gene_tree to the external Node of species_tree which has the same species name. |
static void |
main(java.lang.String[] args)
A "main method" for SDI (Speciation versus Duplication Inference). |
static int |
stripTree(Tree reference,
Tree to_be_stripped)
Removes from Tree to_be_stripped all external Nodes which are associated with a species NOT found in Tree reference. |
Methods inherited from class java.lang.Object |
|
Field Detail |
Tree genetree
Tree speciestree
int duplications
int c
Constructor Detail |
public SDI(Tree gene_tree, Tree species_tree) throws java.lang.Exception
Conditions:
(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)
,
computeMappingCost()
Method Detail |
public abstract int infer(boolean strip_species_tree) throws java.lang.Exception
(Last modified: 01/11/01)
strip_species_tree
- set to true to remove from the species tree
species not found in the gene tree prior
to analysisSDI(Tree,Tree)
public int computeMappingCost()
Reference. Zhang, L. (1997) On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies. Journal of Computational Biology 4 177-187.
(Last modified: 11/07/00)
public static int stripTree(Tree reference, Tree to_be_stripped)
(Last modified: 01/11/01)
reference
- a reference Treeto_be_stripped
- Tree to be strippedvoid linkExtNodesOfG() throws java.lang.Exception
(Last modified: 01/11/01)
public static void main(java.lang.String[] args)
(Last modified: 01/11/01)
[args[0]
- "-e" to use Eulenstein's algorithm instead of SDIse][args[0]
- "-n" input trees are in New Hampshire format instead
of NHX -- or gene tree is in NHX, but species
information in gene tree is only present in the
form of SWISS-PROT sequence names]args[0or1]
- species tree file name (in NHX format with
species names in species name fields
unless -n option is used)args[1or2]
- gene tree file name (in NHX format with
species names in species name fields and sequence names
in sequence name fields unless -n option is used)[args[2or3]
- output file name; default is "sdi_out.nhx"]
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