Cassiopee  1.0
Suffix indexer and search tool
Public Member Functions | Public Attributes | List of all members
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< Matchmatches
 
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::CassieIndexer ( const char *  path)

Main contructor

Parameters
pathPath to the sequence file, sequence must be a one-line sequence.

Member Function Documentation

◆ filltree()

void CassieIndexer::filltree ( long  pos)

Fills suffix tree with input suffix

Parameters
posPosition of suffix in sequence

◆ getCharAtSuffix()

char CassieIndexer::getCharAtSuffix ( long  pos)

Get char from suffix located at position pos.

◆ getSuffix()

string CassieIndexer::getSuffix ( long  pos)

Get the suffix content from a position

Parameters
posPosition in the file
Returns
the suffix string

◆ getTree()

tree< TreeNode > * CassieIndexer::getTree ( )

Get the tree matching the indexed sequence

◆ graph() [1/2]

void CassieIndexer::graph ( )

Generates a dot file representing the tree.

◆ graph() [2/2]

void CassieIndexer::graph ( int  depth)

Generates a dot file representing the tree up to depth

Parameters
depthMax depth to print

◆ index()

void CassieIndexer::index ( )

Launch the indexation of the input sequence

◆ index_loaded_from_file()

bool CassieIndexer::index_loaded_from_file ( )

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

◆ load()

void CassieIndexer::load ( )

Load index from a file

◆ save()

void CassieIndexer::save ( )

Save the index in a file

Member Data Documentation

◆ do_reduction

bool CassieIndexer::do_reduction

Allow tree reduction

◆ matches

list<Match> CassieIndexer::matches

List of positions in original sequence matching the search

◆ max_depth

long CassieIndexer::max_depth

Max depth to graph

◆ max_index_depth

long CassieIndexer::max_index_depth

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


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