1 #include <boost/python.hpp>
2 namespace py = boost::python;
4 #include "alg/mussa.hpp"
5 #include "alg/sequence.hpp"
6 #include "stl_container_adapter.hpp"
10 void (Mussa::*save_string)(const std::string &) = &Mussa::save;
11 void (Mussa::*load_mupa_string)(const std::string &) = &Mussa::load_mupa_file;
12 void (Mussa::*load_string)(const std::string &) = &Mussa::load;
13 void (Mussa::*append_sequence_ref)(const Sequence&) = &Mussa::append_sequence;
14 void (Mussa::*append_sequence_ptr)(const boost::shared_ptr<Sequence>) = &Mussa::append_sequence;
16 py::class_<Mussa::vector_sequence_type>("Sequences")
17 .def("__len__", &Mussa::vector_sequence_type::size, "return length of sequences")
18 .def("__contains__", &std_item<Mussa::vector_sequence_type>::in)
19 .def("__iter__", py::iterator<Mussa::vector_sequence_type>())
20 .def("clear", &Mussa::vector_sequence_type::clear, "remove all the sequences")
21 .def("append", &std_item<Mussa::vector_sequence_type>::add,
22 py::with_custodian_and_ward<1,2>()) // to let container keep value
23 .def("__getitem__", &std_item<Mussa::vector_sequence_type>::get,
24 py::return_value_policy<py::copy_non_const_reference>())
25 .def("__setitem__", &std_item<Mussa::vector_sequence_type>::set,
26 py::with_custodian_and_ward<1,2>()) // to let container keep value
27 .def("__delitem__", &std_item<Mussa::vector_sequence_type>::del)
30 py::class_<Mussa>("_Mussa", py::no_init)
31 .def("save", save_string, "Save analysis in the specified directory")
32 .def("load", load_string, "Load previous run analysis")
33 .def("load_mupa", load_mupa_string, "Load mussa parameter file")
34 .def("clear", &Mussa::clear, "Clear the current analysis")
35 .add_property("name", &Mussa::get_name, &Mussa::set_name, "Set the name of the analysis")
36 .def("size", &Mussa::size, "Number of sequences attached to "
38 .add_property("window", &Mussa::get_window, &Mussa::set_window,
39 "the number of base pairs in the sliding window")
40 .add_property("threshold", &Mussa::get_threshold, &Mussa::set_threshold,
41 "how many base pairs must match between two windows")
42 .add_property("softThreshold", &Mussa::get_soft_threshold,
43 &Mussa::set_soft_threshold)
44 .add_property("analysisMode", &Mussa::get_analysis_mode,
45 &Mussa::set_analysis_mode)
46 .add_property("analysisModeName", &Mussa::get_analysis_mode_name)
47 .def("analyze", &Mussa::analyze, "Run the analysis")
48 .def("paths", &Mussa::paths, py::return_internal_reference<>(), "return list of paths")
49 .def("sequences", &Mussa::sequences, py::return_internal_reference<>(), "return list of sequences")
50 .def("add_sequence", append_sequence_ref, "attach a sequence to the analysis")
52 py::def("Mussa", &Mussa::init,
53 "Construct a new Mussa object.\n"
54 "You can use this to load a previous analysis or to construct\n"
56 py::register_ptr_to_python< boost::shared_ptr<Mussa> >();
58 py::enum_<Mussa::analysis_modes>("analysis_modes")
59 .value("TransitiveNway", Mussa::TransitiveNway )
60 .value("RadialNway", Mussa::RadialNway )
61 .value("EntropyNway", Mussa::EntropyNway )
62 .value("RecursiveNway", Mussa::RecursiveNway )