MASA-Core: SpecialRowReader Class Reference

MASA-Core

Detailed Description

Definition at line 39 of file SpecialRowReader.hpp.

#include <SpecialRowReader.hpp>

List of all members.

Public Member Functions
	SpecialRowReader (string directory, const score_params_t *score_params, bool firstRowGapped=false)
virtual	~SpecialRowReader ()
int	getCol () const
int	getRow () const
void	open (int start)
void	close ()
int	read (cell_t *buf, int offset, int len)
int	getCurrentPosition ()
string	getFilename (int row=-1, int col=-1)
bool	nextSpecialRow (int row, int col, int min_dist)
int	getLargestInterval (int max_i, int max_j)
Private Member Functions
void	loadSpecialRows ()
Private Attributes
int	j0
int	j1
string	directory
const score_params_t *	score_params
FILE *	file
vector< coordinate_t >	specialRowCoordinates
int	id
int	start
int	min_step
int	current
int	firstRowGapped

Constructor & Destructor Documentation

SpecialRowReader::SpecialRowReader	(	string	directory,
		const score_params_t *	score_params,
		bool	firstRowGapped = `false`
	)

Definition at line 36 of file SpecialRowReader.cpp.

SpecialRowReader::~SpecialRowReader ( ) [virtual]

Definition at line 46 of file SpecialRowReader.cpp.

Member Function Documentation

void SpecialRowReader::close ( )

Definition at line 86 of file SpecialRowReader.cpp.

int SpecialRowReader::getCol ( ) const

Definition at line 50 of file SpecialRowReader.cpp.

int SpecialRowReader::getCurrentPosition ( )

Definition at line 94 of file SpecialRowReader.cpp.

string SpecialRowReader::getFilename	(	int	row = `-1`,
		int	col = `-1`
	)

Definition at line 58 of file SpecialRowReader.cpp.

int SpecialRowReader::getLargestInterval	(	int *	max_i,
		int *	max_j
	)

Definition at line 210 of file SpecialRowReader.cpp.

int SpecialRowReader::getRow ( ) const

Definition at line 54 of file SpecialRowReader.cpp.

void SpecialRowReader::loadSpecialRows ( ) [private]

Definition at line 149 of file SpecialRowReader.cpp.

bool SpecialRowReader::nextSpecialRow	(	int	row,
		int	col,
		int	min_dist
	)

Definition at line 182 of file SpecialRowReader.cpp.

void SpecialRowReader::open ( int start )

Definition at line 70 of file SpecialRowReader.cpp.

int SpecialRowReader::read	(	cell_t *	buf,
		int	offset,
		int	len
	)

Definition at line 98 of file SpecialRowReader.cpp.

Member Data Documentation

int SpecialRowReader::current [private]

Definition at line 68 of file SpecialRowReader.hpp.

string SpecialRowReader::directory [private]

Definition at line 60 of file SpecialRowReader.hpp.

FILE* SpecialRowReader::file [private]

Definition at line 62 of file SpecialRowReader.hpp.

int SpecialRowReader::firstRowGapped [private]

Definition at line 69 of file SpecialRowReader.hpp.

int SpecialRowReader::id [private]

Definition at line 64 of file SpecialRowReader.hpp.

int SpecialRowReader::j0 [private]

Definition at line 58 of file SpecialRowReader.hpp.

int SpecialRowReader::j1 [private]

Definition at line 59 of file SpecialRowReader.hpp.

int SpecialRowReader::min_step [private]

Definition at line 67 of file SpecialRowReader.hpp.

const score_params_t* SpecialRowReader::score_params [private]

Definition at line 61 of file SpecialRowReader.hpp.

vector<coordinate_t> SpecialRowReader::specialRowCoordinates [private]

Definition at line 63 of file SpecialRowReader.hpp.

int SpecialRowReader::start [private]

Definition at line 66 of file SpecialRowReader.hpp.

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