7 #ifndef EXTERNAL_MID_BASE_HPP_ 8 #define EXTERNAL_MID_BASE_HPP_ 11 #include "boost/property_tree/ptree_fwd.hpp" 12 #include "boost/shared_ptr.hpp" 21 class Pipe_environment;
50 "identify which of the given
short sequences best matches "
51 "external molecular identifier"
58 const Val_id name_val_id,
59 const Val_id score_val_id
65 boost::shared_ptr<Seq_map_short>
sms_;
66 boost::shared_ptr<Seq_map_full>
smf_;
74 std::size_t mid_size()
const;
80 const boost::string_ref seq,
Definition: sanitize_string.cpp:15
Definition: best_match_pair.hpp:16
int min_score_
Definition: external_mid_base.hpp:68
Definition: find_shared.hpp:22
VDJ_PIPE_KEYWORD_STRUCT(Character_filter::kwds,(chars))
Val_id score_val_id_
Definition: external_mid_base.hpp:71
Main namespace of vdj_pipe library.
Definition: keywords_variable.hpp:11
scoring_matrix_t const * scoring_matrix_
Definition: external_mid_base.hpp:67
Definition: pipe_environment.hpp:26
#define VDJ_PIPE_DECL
Definition: config.hpp:23
Best_match_pair< Mid_id, int > match_type
Definition: external_mid_base.hpp:31
Definition: step_base.hpp:28
Step_base::Err Err
Definition: external_mid_base.hpp:44
boost::shared_ptr< Seq_map_full > smf_
Definition: external_mid_base.hpp:66
Definition: external_mid_base.hpp:30
boost::shared_ptr< Seq_map_short > sms_
Definition: external_mid_base.hpp:65
bool require_best_
Definition: external_mid_base.hpp:69
#define VDJ_PIPE_STATIC_STRING_METHOD(name, val)
Definition: keyword_struct_macro.hpp:12
Val_id name_val_id_
Definition: external_mid_base.hpp:70
Store values mapped against name strings and value IDs.
Definition: value_map.hpp:23
bpt::ptree ptree
Definition: processing_step_utils.hpp:19