Trees       Indices       Help   
MEDITE
Package medite :: Package MediteAppli :: Module suffix_tree :: Class TrueGeneralisedSuffixTree
[hide private]
[frames] | no frames]

Class TrueGeneralisedSuffixTree

source code

             object --+        
                      |        
    SuffixTreeInterface --+    
                          |    
             object --+   |    
                      |   |    
_suffix_tree.SuffixTree --+    
                          |    
                 SuffixTree --+
                              |
                             TrueGeneralisedSuffixTree
A suffix tree for a set of strings.

Instance Methods [hide private]
 
__init__(self, sequences)
Build a generalised suffix tree.		 source code
 
_translate_index(self, idx)
Translate a concat-string index into a (string_no,idx) pair.		 source code
 
_annotate_nodes(self)
Ajoute à chaque noeud interne(répété) ses positions dans la séquence.		 source code
 
shared_substrings(self, minimum_length=0)
Iterator through shared sub-strings.		 source code
 
inter_inclus(self, i, d) source code
 
shared_substrings2naif(self, long_min_pivots)
Iterator through shared sub-strings.		 source code
 
shared_substrings2(self, long_min_pivots)
Iterator through shared sub-strings.		 source code
 
shared_substrings3(self, long_min_pivots)
Iterator through shared sub-strings.		 source code
 
get_repeat(self, min_size=1)
Renvoie un dictionnaire de toutes les chaines répétées.		 source code
 
get_seq_repeat_list(self, min_size=1) source code
 
get_seq_repeat(self, min_size=1) source code
 
get_seq_repeat2(self, min_size=1) source code

Inherited from SuffixTreeInterface: generate_MEM, generate_inner_nodes, generate_inner_nodes_2, generate_leaves, generate_post_order_nodes, generate_post_order_nodes_max, generate_pre_order_nodes, get_MEM

Inherited from _suffix_tree.SuffixTree: __new__, substring

Inherited from object: __delattr__, __getattribute__, __hash__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Properties [hide private]

Inherited from SuffixTreeInterface: MEM, inner_nodes, inner_nodes_2, leaves, post_order_nodes, post_order_nodes_max, pre_order_nodes

Inherited from _suffix_tree.SuffixTree: root

Inherited from object: __class__

Method Details [hide private]

__init__(self, sequences)
(Constructor)

source code 
Build a generalised suffix tree. The strings must not contain the special symbols $ or ascii numbers from 1 to the number of sequences.
Overrides: SuffixTree.__init__

_annotate_nodes(self)

source code 
Ajoute à chaque noeud interne(répété) ses positions dans la séquence.
Overrides: SuffixTreeInterface._annotate_nodes
(inherited documentation)

shared_substrings(self, minimum_length=0)

source code 
Iterator through shared sub-strings. Returned as a list of triples (sequence,from,to).

shared_substrings2naif(self, long_min_pivots)

source code 
Iterator through shared sub-strings. Returned as a list of triples (sequence,from,to).

shared_substrings2(self, long_min_pivots)

source code 
Iterator through shared sub-strings. Returned as a list of triples (sequence,from,to).

shared_substrings3(self, long_min_pivots)

source code 
Iterator through shared sub-strings. Returned as a list of triples (sequence,from,to).

get_repeat(self, min_size=1)

source code 

Renvoie un dictionnaire de toutes les chaines répétées.

Indexé par la taille des chaines. En valeur une liste de positions. min_size: taille mini des chaines répétées Linéaire(nb de noeuds de l'arbre)=linéaire(taille de la séquence)

   Trees       Indices       Help   
MEDITE
Generated by Epydoc 3.0beta1 on Wed Aug 13 15:25:31 2008 http://epydoc.sourceforge.net