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SequenceMatrixCreatorApplication.hpp
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Sat, May 11, 17:16

SequenceMatrixCreatorApplication.hpp
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#ifndef SEQUENCEMATRIXCREATORAPPLICATION_HPP
#define SEQUENCEMATRIXCREATORAPPLICATION_HPP
#include <ApplicationInterface.hpp>
#include <string>
/*!
* \brief The SequenceMatrixCreatorApplication class is a wrapper around a
* SequenceMatrixCreator instance creating an autonomous application to
* compute a sequence matrix from a bed file containing the regions of interest
* and a fasta file containing the genome sequences by directly passing all the
* options and parameters from the command line.
*/
class CorrelationMatrixCreatorApplication: public ApplicationInterface
{
public:
CorrelationMatrixCreatorApplication() = delete ;
CorrelationMatrixCreatorApplication(const CorrelationMatrixCreatorApplication& app) = 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.
*/
CorrelationMatrixCreatorApplication(int argn, char** argv) ;
/*!
* \brief Runs the application. A matrix containing the
* sequences around the center of the bed regions, +/-
* the given offsets is created by searching the fasta file
* and printed on the stdout.
* The matrix is a 2D matrix with dimensions :
* 1) number of regions
* 2) length of region (to - from + 1).
* \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 bed file.
*/
std::string file_bed ;
/*!
* \brief the path to the fasta file.
*/
std::string file_fasta ;
/*!
* \brief a relative coordinate indicating the
* most downstream position to consider around
* each region in the bed file.
*/
int from ;
/*!
* \brief a relative coordinate indicating the
* most upstream position to consider around
* each region in the bed file.
*/
int to ;
/*!
* \brief a flag indicating whether the core of run() can be
* run or not.
*/
bool runnable ;
} ;
#endif // SEQUENCEMATRIXCREATORAPPLICATION_HPP

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