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WhichNullRowsApplication.hpp
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Wed, Aug 28, 10:35

WhichNullRowsApplication.hpp
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#ifndef WHICHNULLROWSAPPLICATION_HPP
#define WHICHNULLROWSAPPLICATION_HPP
#include <ApplicationInterface.hpp>
#include <string>
/*!
* \brief The WhichNullRowsApplication class implements an
* autonomous application that reads a read density 2D matrix in
* text format and returns the indices of the rows that contain
* no signal (no read). The matrix dimensions should be :
* 1) the number of regions
* 2) the number of bins per region
*/
class WhichNullRowsApplication : public ApplicationInterface
{
public:
WhichNullRowsApplication() = delete ;
WhichNullRowsApplication(const WhichNullRowsApplication& other) = delete ;
/*!
* \brief Constructs an object from the command line
* options.
* \param argn the number of options passed to the
* main() function.
* \param argv the vector of options passed to the
* main() function.
*/
WhichNullRowsApplication(int argn, char** argv) ;
/*!
* \brief Runs the application. The data are classified
* using the given settings and the posterior probability
* matrix is returned through the stdout.
* The matrix is a 4D matrix with dimensions :
* regions, class, shift flip.
* \return an exit code EXIT_SUCCESS or EXIT_FAILURE
* to return to the OS.
*/
virtual int run() override ;
private:
/*!
* \brief Parses the program command line options and
* sets the object field accordingly.
* If the help option is detected, the "runnable"
* field is set to false and subsequent calls to
* run() will produce nothing.
* \param argn the number of options passed to the
* main() function.
* \param argv the vector of options passed to the
* main() function.
* \throw std::invalid_argument if an error is found
* in the program options.
*/
void parseOptions(int argn, char** argv) ;
/*!
* \brief the path to the file containing the matrix.
*/
std::string file_matrix ;
/*!
* \brief a flag indicating whether the core of run() can be
* run or not.
*/
bool runnable ;
} ;
#endif // WHICHNULLROWSAPPLICATION_HPP

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