7 #ifndef APPLY_TO_ADAPTOR_HPP_ 8 #define APPLY_TO_ADAPTOR_HPP_ 10 #include "boost/foreach.hpp" 11 #include "boost/property_tree/ptree_fwd.hpp" 12 #include "boost/variant/static_visitor.hpp" 23 class Pipe_environment;
35 "apply specified step to either forward, reverse, or merged sequences"
45 boost::apply_visitor(sv2,
step_);
58 class Visitor :
public boost::static_visitor<> {
60 Visitor(vid_vector
const& idv) : idv_(idv) {}
62 template<
typename Step>
void operator()(Step& step)
const {
64 step.reset_access(vis);
79 "apply specified step to either forward, reverse, or merged sequences"
86 : av_(idv),
step_(step) {}
93 apply_visitor(sv2,
step_);
112 "apply specified step to forward, reverse, or merged sequences"
118 static result_type make(
127 std::
string const& type
void summary(std::ostream &os) const
Definition: apply_to_adaptor.hpp:91
Visitor(vid_vector const &idv)
Definition: apply_to_adaptor.hpp:60
Definition: sanitize_string.cpp:15
void run()
Definition: apply_to_adaptor.hpp:88
Apply_to_maker type
Definition: apply_to_adaptor.hpp:134
step_variant_single step_
Definition: apply_to_adaptor.hpp:49
Apply_to_maker type
Definition: apply_to_adaptor.hpp:133
Vm_access_paired vma_type
Definition: apply_to_adaptor.hpp:30
Apply enclosed processing step once to a sequence read of specified kind: forward, reverse, or merged.
Definition: apply_to_adaptor.hpp:28
Access to value map for paired read pipeline and processing steps.
Definition: value_map_access_paired.hpp:16
std::vector< Value_ids_single > vid_vector
Definition: apply_to_adaptor.hpp:56
void operator()(Step &step) const
Definition: apply_to_adaptor.hpp:62
vid_vector idv_
Definition: apply_to_adaptor.hpp:70
Main namespace of vdj_pipe library.
Definition: keywords_variable.hpp:11
Definition: visitor.hpp:71
Definition: pipe_environment.hpp:26
#define VDJ_PIPE_DECL
Definition: config.hpp:23
step_variant_single step_
Definition: apply_to_adaptor.hpp:98
Definition: visitor.hpp:18
Provides access to standard values for single read pipeline.
Definition: value_names.hpp:33
Definition: apply_to_adaptor.hpp:58
Definition: exception.hpp:23
void finish()
Definition: apply_to_adaptor.hpp:89
VDJ_PIPE_STATIC_STRING_METHOD(comment,"apply specified step to either forward, reverse, or merged sequences") Apply_one(step_variant_single const &step)
Definition: apply_to_adaptor.hpp:33
Definition: apply_to_adaptor.hpp:107
boost::make_recursive_variant_over< step::single_read_vector >::type step_variant_single
Definition: step_variant_single_read.hpp:66
Apply enclosed processing step multiple times to sequence reads of specified kind: forward...
Definition: apply_to_adaptor.hpp:55
Visitor av_
Definition: apply_to_adaptor.hpp:97
Definition: step_maker.hpp:40
void summary(std::ostream &os) const
Definition: apply_to_adaptor.hpp:43
Definition: apply_to_adaptor.hpp:105
bpt::ptree ptree
Definition: processing_step_utils.hpp:19
Definition: visitor.hpp:35
void finish()
Definition: apply_to_adaptor.hpp:41
void run()
Definition: apply_to_adaptor.hpp:40