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/filesystem/path.hpp>
  10 namespace fs = boost::filesystem;
  11
  12 #include <boost/shared_ptr.hpp>
  13
  14 #include <string>
  15 #include "alg/glsequence.hpp"
  16
  17 void export_sequence()
  18 {
  19   void (Sequence::*load_fasta_piii)(const fs::path, int, int, int) = &Sequence::load_fasta;
  20
  21   class_<Sequence>("Sequence")
  22     .def(init<std::string>())
  23     .def("__len__", &Sequence::size, "return the length of the sequence")
  24     .def("__repr__", &Sequence::get_sequence, "display as string")
  25     .def("__str__", &Sequence::get_sequence, "cast to string")
  26     .def("add_annotation", &Sequence::add_annotation, "append an annotation")
  27     //.def("annotations", &Sequence::annotations, "return list of annotations")
  28     .def("add_motif", &Sequence::add_motif, "add a motif sequenence")
  29     .def("clear", &Sequence::clear, "clear the sequence and its annotations")
  30     .def("empty", &Sequence::empty, "Is the sequence empty")
  31     .def("load_fasta", load_fasta_piii, "Load fasta")
  32     .add_property("header", &Sequence::get_fasta_header, &Sequence::set_fasta_header, "the fasta header")
  33     .def("rcseq", &Sequence::rev_comp, return_value_policy<return_by_value>())
  34     .def("size", &Sequence::size, "return the length of the sequence")
  35     .add_property("species", &Sequence::get_species, &Sequence::set_species)
  36     .def("subseq", &Sequence::subseq, "return a subsequence")
  37   ;
  38
  39   register_ptr_to_python< boost::shared_ptr<Sequence> >();
  40 }