py/flp.cpp

   1 #include <boost/python.hpp>
   2 #include <boost/python/list.hpp>
   3 #include <boost/python/return_internal_reference.hpp>
   4 #include <boost/python/return_by_value.hpp>
   5 #include <boost/python/return_value_policy.hpp>
   6 #include <boost/python/register_ptr_to_python.hpp>
   7 using namespace boost::python;
   8
   9 #include "alg/flp.hpp"
  10 #include "alg/sequence.hpp"
  11
  12 struct listint_to_python {
  13   static PyObject *convert(const std::list<int> l) {
  14     PyObject *pylist = PyList_New(0);
  15     for(std::list<int>::const_iterator li = l.begin();
  16         li != l.end();
  17         ++li)
  18     {
  19       PyList_Append(pylist, PyInt_FromLong(*li));
  20     }
  21     return pylist;
  22   }
  23 };
  24
  25 void export_flps()
  26 {
  27
  28   class_<FLPs>("FLP")
  29     .def("setup", &FLPs::setup, "set window size and lowest threshold")
  30     .def("seqcomp", &FLPs::seqcomp, "compare two sequences\n"
  31                                     "takes: sequence, seqeuence, bool is_reveresed flag")
  32     .def("size", &FLPs::size, "return the length of the sequence")
  33     .def("match_locations", &FLPs::match_locations, "return list of matches at a window location")
  34     .def("thres_matches", &FLPs::thres_matches, "return list of matches at a window location above a threshold")
  35   ;
  36     //std::list<match> matches(int index) const;
  37     //void save(boost::filesystem::path save_file_path);
  38     //void load(boost::filesystem::path file_path);
  39   to_python_converter< std::list<int>, listint_to_python>();
  40 }