CassieIndexer Class Reference

#include <Cassiopee.h>

Public Member Functions
	CassieIndexer (const char *path)
void	save ()
void	load ()
void	graph ()
void	graph (int depth)
string	getSuffix (long pos)
void	index ()
tree< TreeNode > *	getTree ()
char	getCharAtSuffix (long pos)
void	filltree (long pos)
bool	index_loaded_from_file ()

Public Attributes
list< Match >	matches
bool	do_reduction
long	max_depth
long	max_index_depth
long	seq_length

Detailed Description

Cassiopee indexer

Index an input file

Constructor & Destructor Documentation

CassieIndexer::CassieIndexer

(

const char *

path

)

Main contructor

Parameters

path	Path to the sequence file, sequence must be a one-line sequence.

Member Function Documentation

void CassieIndexer::filltree

(

long

pos

)

Fills suffix tree with input suffix

Parameters

pos	Position of suffix in sequence

char CassieIndexer::getCharAtSuffix

(

long

pos

)

Get char from suffix located at position pos.

string CassieIndexer::getSuffix

(

long

pos

)

Get the suffix content from a position

Parameters

pos	Position in the file

Returns

the suffix string

tree< TreeNode > * CassieIndexer::getTree

(

)

Get the tree matching the indexed sequence

void CassieIndexer::graph

(

)

Generates a dot file representing the tree.

void CassieIndexer::graph

(

int

depth

)

Generates a dot file representing the tree up to depth

Parameters

depth

Max depth to print

void CassieIndexer::index

(

)

Launch the indexation of the input sequence

bool CassieIndexer::index_loaded_from_file

(

)

Checks if index has been loaded from a saved index or if index has been build dynamically

void CassieIndexer::load

(

)

Load index from a file

void CassieIndexer::save

(

)

Save the index in a file

Member Data Documentation

bool CassieIndexer::do_reduction

Allow tree reduction

list<Match> CassieIndexer::matches

List of positions in original sequence matching the search

long CassieIndexer::max_depth

Max depth to graph

long CassieIndexer::max_index_depth

Max depth to index, can limit index size if pattern to search are known of a maximum size

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The documentation for this class was generated from the following files:

• src/Cassiopee.h
• src/cassiopee.cxx