py/seq_span.cpp

   1 #include <boost/iterator.hpp>
   2
   3 #include <boost/python.hpp>
   4 #include <boost/python/return_value_policy.hpp>
   5
   6 #include <boost/python/register_ptr_to_python.hpp>
   7 using namespace boost::python;
   8
   9 #include "alg/seq_span.hpp"
  10
  11 #include "stl_container_adapter.hpp"
  12
  13 void export_seq_span()
  14 {
  15   enum_<SeqSpan::strand_type>("strand_type")
  16     .value("unknown", SeqSpan::UnknownStrand)
  17     .value("minus", SeqSpan::MinusStrand)
  18     .value("plus", SeqSpan::PlusStrand)
  19     .value("both", SeqSpan::BothStrand)
  20     .value("same", SeqSpan::SameStrand)
  21     .value("opposite", SeqSpan::OppositeStrand)
  22     .value("single", SeqSpan::SingleStrand)
  23     ;
  24
  25
  26   class_<SeqSpan>("SeqSpan",
  27                   init<std::string, optional<AlphabetRef,
  28                                              SeqSpan::strand_type>
  29                       >() )
  30     .def("__len__", &SeqSpan::size)
  31     .def("__getitem__", &std_item<SeqSpan>::get_const,
  32         return_value_policy<copy_const_reference>())
  33     .def("__str__", &SeqSpan::sequence)
  34     .def("empty", &SeqSpan::empty)
  35     .add_property("start", &SeqSpan::start, &SeqSpan::setStart,
  36                   "start position relative to root sequence")
  37     .add_property("stop", &SeqSpan::stop, &SeqSpan::setStop,
  38                   "one past the last position relative to the root sequence.")
  39     .add_property("strand", &SeqSpan::strand,
  40                   "describe which strand the span is on")
  41
  42     .add_property("parentStart", &SeqSpan::parentStart, &SeqSpan::setParentStart,
  43                   "start position relative to parent sequence")
  44     .add_property("parentStop", &SeqSpan::parentStop, &SeqSpan::setParentStop,
  45                   "one past the last position relative to the parent sequence.")
  46     .add_property("parent", &SeqSpan::parent)
  47
  48     .def("subseq", &SeqSpan::subseq)
  49     ;
  50
  51   register_ptr_to_python< boost::shared_ptr<SeqSpan> >();
  52 }