py/sequence.cpp

   1 #include <boost/python.hpp>
   2 #include <boost/iterator.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 <boost/shared_ptr.hpp>
  10
  11 #include <string>
  12 #include "alg/glsequence.hpp"
  13
  14 PyObject* seq_to_string(const Sequence& s) {
  15   ::PyString_FromStringAndSize(s.data(), s.size());
  16 }
  17
  18 void export_sequence()
  19 {
  20   class_<Sequence>("Sequence")
  21     .def(init<std::string>())
  22     .def("__str__", &seq_to_string, "cast to string")
  23     .def("__repr__", &seq_to_string, "display as string")
  24     .def("size", &Sequence::size, "return the length of the sequence")
  25     .def("__len__", &Sequence::size, "return the length of the sequence")
  26     .def("clear", &Sequence::clear, "clear the sequence and its annotations")
  27     .add_property("header", &Sequence::get_fasta_header, &Sequence::set_fasta_header, "the fasta header")
  28     .add_property("species", &Sequence::get_species, &Sequence::set_species)
  29     .def("add_annotation", &Sequence::add_annotation, "append an annotation")
  30     //.def("annotations", &Sequence::annotations, "return list of annotations")
  31     .def("rcseq", &Sequence::rev_comp, return_value_policy<return_by_value>())
  32   ;
  33
  34   register_ptr_to_python< boost::shared_ptr<Sequence> >();
  35 }