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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| 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. | 
| (package private)  void | decreaseDuplications()Decreases the number of duplications by one. | 
|  int | getDuplications()Returns the number of duplications. | 
|  Tree | getGeneTree()Returns the gene tree. | 
|  int | getMappingCost()Returns the mapping cost L. | 
|  Tree | getSpeciesTree()Returns the species tree. | 
| (package private)  void | increaseDuplications()Increases the number of duplications by one. | 
| 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). | 
| (package private)  void | setDuplicationsToZero()Sets the number of duplications to 0. | 
| 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 | 
|  | 
| 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()
                       throws java.lang.Exception
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 strippedpublic Tree getGeneTree()
(Last modified: 10/02/01)
public Tree getSpeciesTree()
(Last modified: 10/02/01)
public int getMappingCost()
(Last modified: 10/02/01)
public int getDuplications()
(Last modified: 10/02/01)
void setDuplicationsToZero()
(Last modified: 10/02/01)
void increaseDuplications()
(Last modified: 10/02/01)
void decreaseDuplications()
(Last modified: 10/02/01)
void 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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