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SequenceModelExtenderApplication.hpp
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Sat, Oct 12, 18:22

SequenceModelExtenderApplication.hpp
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#ifndef SEQUENCEMODELEXTENDERAPPLICATION_HPP
#define SEQUENCEMODELEXTENDERAPPLICATION_HPP
#include <ApplicationInterface.hpp>
#include <iostream>
#include <string>
#include <SequenceMatrixCreator.hpp>
/*!
* \brief The SequenceModelExtenderApplication class is a class implementing an
* application to extend a sequence model of length L' (L' = L - S + 1
* where L is the number of column of the sequence matrix and S the
* shifting freedom allowed during the classification) to a new model
* length L'' = L' + E (E is the number of columns to add to the
* model) given the data matrix and the results of the classification
* (posterior probability matrix).
* To do this, the sequence count matrix from which the original model
* was computed is extended (0.5*E columns on each side) and a model
* is computed using the new matrix and the given posterior probabities.
* The extended model is returned through the stdout.
*/
class SequenceModelExtenderApplication : public ApplicationInterface
{
public:
SequenceModelExtenderApplication() = delete ;
SequenceModelExtenderApplication(const SequenceModelExtenderApplication& 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.
*/
SequenceModelExtenderApplication(int argn, char** argv) ;
/*!
* \brief Destructor.
*/
virtual ~SequenceModelExtenderApplication() override ;
/*!
* \brief Runs the application. The data new model
* is computed and displayed through the
* stdout.
* \return the exit code.
*/
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
* containing the sequences.
*/
std::string file_fasta ;
/*!
* \brief the path to the file containing the
* classification posterior probabilities.
*/
std::string file_prob ;
/*!
* \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 the number of columns to add to the
* matrix (half of this value on each side).
*/
int ext ;
/*!
* \brief the number of threads.
*/
size_t n_threads ;
/*!
* \brief whether run() can be called.
*/
bool runnable ;
} ;
#endif // SEQUENCEMODELEXTENDERAPPLICATION_HPP

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