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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 | 
| 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 | 
|  | 
| Field Detail | 
int[] rank
| Constructor Detail | 
public BasketDataStructure(int s)
s - initial size| Method 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 basket
public 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 Tree
public 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 Tree
public 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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