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MatrixCreator.hpp
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Sat, Apr 27, 15:08

MatrixCreator.hpp
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#ifndef MATRIXCREATOR_HPP
#define MATRIXCREATOR_HPP
#include <string>
#include <seqan/bed_io.h> // BedFileIn, BedRecord
#include <GenomeRegion.hpp>
#include <Matrix2D.hpp>
/*!
* \brief The MatrixCreator class is a base class
* to be derived by classes that are dedicated to
* construct data matrices which rows contains
* a signal at different positions (columns) in
* this given region.
*/
class MatrixCreator
{ public:
/*!
* \brief Returns the central position of a bed region.
* \param bed_line the region of interest.
* \return the position of the center.
*/
static int get_center_pos(const seqan::BedRecord<seqan::Bed3>& bed_line) ;
public:
/*!
* \brief Constructs an object.
* \param bed_file_path the path to the bed file
* containing the coordinates of the regions of
* interest.
* \param from the downstream most position
* to consider, relative to a set of genomic
* positions.
* \param to the upstream most position to
* consider, relative to a set of genomic
* positions
*/
MatrixCreator(const std::string& bed_file_path,
int from,
int to) ;
/*!
* Destructor.
*/
virtual ~MatrixCreator() ;
/*!
* \brief Creates and return the count matrix.
* \return the count matrix.
*/
virtual Matrix2D<int> create_matrix() = 0 ;
protected:
/*!
* \brief Opens the bed file.
* \throw std::runtime_error if the file cannot
* be open.
*/
void open_bed_file() ;
/*!
* \brief Closes the bed file.
* Does nothing if already closed.
*/
void close_bed_file() ;
/*!
* \brief Bed file path.
*/
std::string bed_path ;
/*!
* \brief An input stream to the
* bed file.
* Use open_bed_file() to open the stream
* and close_bed_file() to close it.
*/
seqan::BedFileIn bed_file ;
/*!
* \brief The smallest relative coordinate from the region
* center to consider (included).
*/
int from ;
/*!
* \brief The biggest relative coordinate from the region
* center to consider (not included).
*/
int to ;
/*!
* \brief A matrix containing the number of targets
* found at each position around each reference.
* This is the data structure to fill.
*/
Matrix2D<int> matrix_counts ;
} ;
#endif // MATRIXCREATOR_HPP

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