vdj_pipe
pipeline for processing DNA sequence data
Public Member Functions | Static Public Member Functions | Private Types | Private Attributes | List of all members
vdj_pipe::Pipeline< Config > Class Template Reference

#include <pipeline.hpp>

Collaboration diagram for vdj_pipe::Pipeline< Config >:
Collaboration graph
[legend]

Public Member Functions

 Pipeline (Pipe_environment const &pe)
 
 Pipeline (boost::property_tree::ptree const &pt, Pipe_environment const &pe)
 
void add_step (boost::property_tree::ptree const &pt)
 
void add_step (processing_step const &step)
 
vm_access const & value_map () const
 
vm_accessvalue_map ()
 
void process_read ()
 
std::size_t size () const
 
processing_step const & step (const std::size_t n) const
 
void run ()
 
void finalize ()
 

Static Public Member Functions

static std::string const & name ()
 

Private Types

typedef Config::input_step input_step
 
typedef Config::processing_step processing_step
 
typedef Config::value_map_access vm_access
 
typedef std::vector< processing_stepstep_vector
 

Private Attributes

Pipe_environment pe_
 
input_step ins_
 
step_vector sv_
 
vm_access vma_
 

Member Typedef Documentation

template<class Config >
typedef Config::input_step vdj_pipe::Pipeline< Config >::input_step
private
template<class Config >
typedef Config::processing_step vdj_pipe::Pipeline< Config >::processing_step
private
template<class Config >
typedef std::vector<processing_step> vdj_pipe::Pipeline< Config >::step_vector
private
template<class Config >
typedef Config::value_map_access vdj_pipe::Pipeline< Config >::vm_access
private

Constructor & Destructor Documentation

template<class Config >
vdj_pipe::Pipeline< Config >::Pipeline ( Pipe_environment const &  pe)
inlineexplicit
template<class Config >
vdj_pipe::Pipeline< Config >::Pipeline ( boost::property_tree::ptree const &  pt,
Pipe_environment const &  pe 
)
inline

Member Function Documentation

template<class Config >
void vdj_pipe::Pipeline< Config >::add_step ( boost::property_tree::ptree const &  pt)
inline
template<class Config >
void vdj_pipe::Pipeline< Config >::add_step ( processing_step const &  step)
inline
template<class Config >
void vdj_pipe::Pipeline< Config >::finalize ( )
inline
template<class Config >
static std::string const& vdj_pipe::Pipeline< Config >::name ( )
inlinestatic
template<class Config >
void vdj_pipe::Pipeline< Config >::process_read ( )
inline
template<class Config >
void vdj_pipe::Pipeline< Config >::run ( )
inline
template<class Config >
std::size_t vdj_pipe::Pipeline< Config >::size ( ) const
inline
template<class Config >
processing_step const& vdj_pipe::Pipeline< Config >::step ( const std::size_t  n) const
inline
template<class Config >
vm_access const& vdj_pipe::Pipeline< Config >::value_map ( ) const
inline
template<class Config >
vm_access& vdj_pipe::Pipeline< Config >::value_map ( )
inline

Member Data Documentation

template<class Config >
input_step vdj_pipe::Pipeline< Config >::ins_
private
template<class Config >
Pipe_environment vdj_pipe::Pipeline< Config >::pe_
private
template<class Config >
step_vector vdj_pipe::Pipeline< Config >::sv_
private
template<class Config >
vm_access vdj_pipe::Pipeline< Config >::vma_
private

The documentation for this class was generated from the following file: