Page MenuHomec4science
Files F60928645

ProbToModelApplication.hpp
No OneTemporary
Actions

File Metadata

Created
Fri, May 3, 11:02

ProbToModelApplication.hpp
View Options

#ifndef PROBTOMODELAPPLICATION_HPP
#define PROBTOMODELAPPLICATION_HPP
#include <ApplicationInterface.hpp>
#include <iostream>
#include <string>
#include <Matrix2D.hpp>
#include <Matrix3D.hpp>
#include <Matrix4D.hpp>
/*!
* \brief The ProbToModelApplication class is a wrapper around an ModelReferenceComputer
* instance creating an autonomous application to compute data models given the
* data and the results of the classification procedure (the posterior probability
* matrix).
*/
class ProbToModelApplication : public ApplicationInterface
{
public:
ProbToModelApplication() = delete ;
ProbToModelApplication(const ProbToModelApplication& 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.
*/
ProbToModelApplication(int argn, char** argv) ;
/*!
* \brief Destructor.
*/
virtual ~ProbToModelApplication() override ;
/*!
* \brief Runs the application. The data 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 Checks that both matrices have
* compatible dimensions.
* For this, both matrices should have the
* same number of rows (1st dimension) and
* the data number of columns should not be
* smaller than the probability matrix 3rd
* dimension (shifting freedom incompatible
* with data width).
* \param data the data matrix.
* \param prob the probability matrix.
* \throw std::runtime_error with a descriptive
* message if both matrices are not compatible.
*/
void check_dimensions(const Matrix2D<int>& data,
const Matrix4D<double>& prob) const ;
/*!
* \brief Checks that both matrices have
* compatible dimensions.
* For this, both matrices should have the
* 1st dimension size and the data 2nd
* dimensions should not be smaller than
* the probability matrix 3rd dimensions
* (shifting freedom incompatible
* with data width).
* Additionaly, the data matrix should have
* a 3rd dimension of size 4 (for A,C,G,T).
* \param data the data matrix.
* \param prob the probability matrix.
* \throw std::runtime_error with a descriptive
* message if both matrices are not compatible.
*/
void check_dimensions(const Matrix3D<double>& data,
const Matrix4D<double>& prob) const ;
/*!
* \brief the path to the file containing the
* read count data.
*/
std::string file_read ;
/*!
* \brief the path to the file containing the
* sequence data.
*/
std::string file_seq ;
/*!
* \brief the path to the file containing the
* consensus sequence data.
*/
std::string file_consseq ;
/*!
* \brief the path to the file containing the
* classification posterior probabilities.
*/
std::string file_prob ;
/*!
* \brief the path to the file containing the
* (0-based) index of the rows to filter out
* from the data.
*/
std::string file_filter ;
/*!
* \brief whether the last class of the
* classification (posterior probabilities) is a
* background class.
*/
bool bckg_class ;
/*!
* \brief the number of threads.
*/
size_t n_threads ;
/*!
* \brief whether run() can be called.
*/
bool runnable ;
} ;
#endif // PROBTOMODELAPPLICATION_HPP

Event Timeline

c4science · Help