py/mussa.cpp

   1 #include <boost/python.hpp>
   2 namespace py = boost::python;
   3
   4 #include "alg/mussa.hpp"
   5 #include "alg/sequence.hpp"
   6 #include "stl_container_adapter.hpp"
   7
   8 void export_mussa()
   9 {
  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;
  15
  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)
  28   ;
  29
  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 "
  37                                "this analysis")
  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")
  51   ;
  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"
  55           "a new analysis.\n");
  56   py::register_ptr_to_python< boost::shared_ptr<Mussa> >();
  57
  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 )
  63   ;
  64 }