7 #ifndef PIPE_ENVIRONMENT_HPP_ 8 #define PIPE_ENVIRONMENT_HPP_ 10 #include "boost/property_tree/ptree_fwd.hpp" 11 #include "boost/shared_ptr.hpp" 12 #include "boost/chrono/process_cpu_clocks.hpp" 22 class Step_variant_store;
29 BOOST_STATIC_CONSTANT(std::size_t, unset = static_cast<std::size_t>(-1));
30 static void input_csv(
32 std::vector<std::string>& vs
54 max_reads() <= (std::size_t)vm_.read_count() ||
55 max_file_reads() <= (std::size_t)vm_.file_read_count()
57 reads_skipped_ =
true;
63 std::size_t read_count()
const;
70 std::string
const& path
73 void start_file(std::string
const& fn);
77 boost::shared_ptr<Step_variant_store>
steps_;
83 boost::chrono::process_real_cpu_clock::time_point t1_, t2_,
t3_;
89 std::ostream& print_summary(std::ostream& os)
const;
Step_variant_store const & steps() const
Definition: pipe_environment.hpp:42
out_manager_ptr om_
Definition: pipe_environment.hpp:79
Definition: pipe_environment.hpp:36
Output_manager & output()
Definition: pipe_environment.hpp:47
Value_map vm_
Definition: pipe_environment.hpp:86
boost::shared_ptr< Step_variant_store > steps_
Definition: pipe_environment.hpp:77
bool reads_skipped_
Definition: pipe_environment.hpp:85
std::size_t max_reads_
Definition: pipe_environment.hpp:80
boost::shared_ptr< Input_manager > in_manager_ptr
Definition: pipe_environment.hpp:27
Input_manager const & input() const
Definition: pipe_environment.hpp:44
boost::shared_ptr< Output_manager > out_manager_ptr
Definition: pipe_environment.hpp:28
Main namespace of vdj_pipe library.
Definition: keywords_variable.hpp:11
bool process_more()
Definition: pipe_environment.hpp:52
Input_manager & input()
Definition: pipe_environment.hpp:45
char delimiter() const
Definition: pipe_environment.hpp:48
bool is_running_
Definition: pipe_environment.hpp:84
in_manager_ptr im_
Definition: pipe_environment.hpp:78
Definition: pipe_environment.hpp:26
#define VDJ_PIPE_DECL
Definition: config.hpp:23
std::size_t max_file_reads() const
Definition: pipe_environment.hpp:50
boost::chrono::process_real_cpu_clock::time_point t3_
Definition: pipe_environment.hpp:83
Output_manager const & output() const
Definition: pipe_environment.hpp:46
Definition: step_variant_store.hpp:40
Definition: exception.hpp:23
Step_variant_store & steps()
Definition: pipe_environment.hpp:43
Definition: output_manager.hpp:20
Store values mapped against name strings and value IDs.
Definition: value_map.hpp:23
std::string summary_output_path_
Definition: pipe_environment.hpp:82
std::size_t max_file_reads_
Definition: pipe_environment.hpp:81
bpt::ptree ptree
Definition: processing_step_utils.hpp:19
std::size_t max_reads() const
Definition: pipe_environment.hpp:49