vdj_pipe
pipeline for processing DNA sequence data
Public Member Functions | List of all members
vdj_pipe::Vm_access_paired_emid Class Reference

Access to value map for paired eMID read pipeline and processing steps. More...

#include <value_map_access_paired.hpp>

Inheritance diagram for vdj_pipe::Vm_access_paired_emid:
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Collaboration diagram for vdj_pipe::Vm_access_paired_emid:
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Public Member Functions

seq_type const & emid_fwd () const
 
void emid_fwd (seq_type const &seq)
 
seq_type const & emid_rev () const
 
void emid_rev (seq_type const &seq)
 
std::string const & emid_path_fwd () const
 
std::string const & emid_path_rev () const
 
void emid_path_fwd (std::string const &s)
 
void emid_path_rev (std::string const &s)
 
- Public Member Functions inherited from vdj_pipe::Vm_access_paired
std::string const & description_fwd () const
 
void description_fwd (std::string const &descr)
 
std::string const & description_rev () const
 
void description_rev (std::string const &descr)
 
seq_type const & sequence_fwd () const
 
std::string sequence_fwd (const bool trim) const
 
void sequence_fwd (seq_type const &seq)
 
seq_type const & sequence_rev () const
 
std::string sequence_rev (const bool trim, const bool reverse) const
 
void sequence_rev (seq_type const &seq)
 
qual_type const & quality_fwd () const
 
qual_type quality_fwd (const bool trim) const
 
void quality_fwd (qual_type const &qual)
 
qual_type const & quality_rev () const
 
qual_type quality_rev (const bool trim, const bool reverse) const
 
void quality_rev (qual_type const &qual)
 
sequence_interval interval_fwd () const
 
void interval_fwd (sequence_interval const &si)
 
sequence_interval interval_rev () const
 
void interval_rev (sequence_interval const &si)
 
std::string const & sequence_path_fwd () const
 
void sequence_path_fwd (std::string const &s)
 
std::string const & sequence_path_rev () const
 
void sequence_path_rev (std::string const &s)
 
std::string const & quality_path_fwd () const
 
void quality_path_fwd (std::string const &s)
 
std::string const & quality_path_rev () const
 
void quality_path_rev (std::string const &s)
 
- Public Member Functions inherited from vdj_pipe::Value_map
iterator begin () const
 
iterator end () const
 
std::size_t size () const
 
void clear_values ()
 
std::string const & name (const Val_id vid) const
 
Val_id insert_name (std::string const &name)
 
Val_id insert_new_name (std::string const &name)
 
Val_id const * find_id (std::string const &name) const
 
Val_id value_id (std::string const &name) const
 
value_variant const & operator[] (const Val_id vid) const
 
value_variant & operator[] (const Val_id vid)
 
long read_count () const
 
void read_count_reset ()
 
void read_count_incr ()
 
long file_read_count () const
 
void file_read_count_reset ()
 
void file_read_count_incr ()
 
std::string const & seq_file_name () const
 
void seq_file_name (std::string const &fn)
 
std::string const & read_id_nothrow () const
 
std::string const & read_id () const
 
void read_id (std::string const &id)
 
template<typename T >
T const & value (std::string const &name) const
 
template<typename T >
T const * value_ptr (std::string const &name) const
 
template<typename T >
T const & value (const Val_id id) const
 
template<typename T >
T const * value_ptr (const Val_id id) const
 
std::string const & str_nothrow (const Val_id id) const
 

Additional Inherited Members

- Public Types inherited from vdj_pipe::Vm_access_paired
typedef Seq_record::sequence seq_type
 
typedef Qual_record::quality qual_type
 
- Public Types inherited from vdj_pipe::Value_map
typedef map_type::iterator iterator
 
typedef iterator const_iterator
 
- Protected Member Functions inherited from vdj_pipe::Value_map
std::string sequence (const Val_id seq_id, const Val_id trim_id, const bool trimmed, const bool reverse_compl) const
 
Qual_record::quality quality (const Val_id qual_id, const Val_id trim_id, const bool trimmed, const bool reverse_compl) const
 
- Protected Attributes inherited from vdj_pipe::Vm_access_paired
Value_ids_paired ids_
 

Detailed Description

Access to value map for paired eMID read pipeline and processing steps.


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