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FORESTER 1.9 | |||||||
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java.lang.Object | +--forester.datastructures.BasketDataStructure
An implementation of the "Basket" datastructure. This datastructure is used in Eulenstein's algorithm for gene duplication inference ("forester/tools/OE").
Reference: Oliver Eulenstein (1998) Vorhersage von Genduplikationen und deren Entwicklung in der Evolution. GMD Research Series, No 20/1998 GMD - Forschungszentrum Informationstechnik GmbH. - Sankt Augustin (http://www.gmd.de/publications/research/1998/020/)
More information about FORESTER (including download) is available at: http://www.genetics.wustl.edu/eddy/people/zmasek/forester/
Field Summary | |
(package private) int[] |
rank
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Constructor Summary | |
BasketDataStructure(int s)
Constructs a BasketDataStructure of size s. |
Method Summary | |
void |
createBasket(int g,
int s)
Creates a basket( s ), which is affiliated with the Node s of the species Tree and which contains the Node g of the gene Tree. |
int |
findBasket(int g)
Finds the basket containing the Node g of the gene Tree. |
void |
insertIntoBasket(int g,
int s)
Inserts gene Tree Node g into basket( s ). |
void |
mergeBasket(int s1,
int s2)
Adds the elements of basket( s1 ) to the elements of basket( s2 ) and deletes basket( s1 ). |
void |
moveBasket(int s1,
int s2)
Changes the affiliation of basket( s1 ) from s1 to s2. |
java.lang.String |
toString()
Transfers this to a String. |
Methods inherited from class java.lang.Object |
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Field Detail |
int[] rank
Constructor Detail |
public BasketDataStructure(int s)
s
- initial sizeMethod Detail |
public void createBasket(int g, int s)
g
- a Node ID of the gene Trees
- a Node ID of the species Tree which will become
the representative of a basketpublic void moveBasket(int s1, int s2)
s1
- a Node ID of the species Tree
and representative of a existing basket( s1 )s2
- a Node ID of the species Treepublic void mergeBasket(int s1, int s2)
s1
- a Node ID of the species Tree
and representative of a existing basket( s1 )s2
- a Node ID of the species Tree
and representative of a existing basket( s2 )public int findBasket(int g)
g
- a Node ID of the gene Treepublic void insertIntoBasket(int g, int s)
g
- a Node ID of the gene Trees
- a Node ID of the species Tree
and representative of a existing basket( s1 )public java.lang.String toString()
toString
in class java.lang.Object
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