py/seq_span.cpp

   1 #include <boost/iterator.hpp>
   2
   3 #include <boost/python.hpp>
   4 #include <boost/python/return_value_policy.hpp>
   5 #include <boost/python/manage_new_object.hpp>
   6
   7 #include <boost/python/register_ptr_to_python.hpp>
   8 using namespace boost::python;
   9
  10 #include "alg/seq_span.hpp"
  11
  12 #include "stl_container_adapter.hpp"
  13
  14 SeqSpanRef seq_span_factory(
  15   const std::string& s,
  16   AlphabetRef a = dna_alphabet,
  17   SeqSpan::strand_type strand = SeqSpan::PlusStrand)
  18 {
  19   SeqSpanRef seq(new SeqSpan(s, a, strand));
  20   return seq;
  21 }
  22
  23 BOOST_PYTHON_FUNCTION_OVERLOADS(
  24   seq_span_factory_overloads,
  25   seq_span_factory,
  26   1, // minimum arguments
  27   3 // maximum arguments
  28 );
  29
  30 void export_seq_span()
  31 {
  32   enum_<SeqSpan::strand_type>("strand")
  33     .value("unknown", SeqSpan::UnknownStrand)
  34     .value("minus", SeqSpan::MinusStrand)
  35     .value("plus", SeqSpan::PlusStrand)
  36     .value("both", SeqSpan::BothStrand)
  37     .value("same", SeqSpan::SameStrand)
  38     .value("opposite", SeqSpan::OppositeStrand)
  39     .value("single", SeqSpan::SingleStrand)
  40     ;
  41
  42   def("SeqSpan", seq_span_factory,
  43       seq_span_factory_overloads(args("sequence", "alphabet", "strand"))
  44       );
  45
  46   class_<SeqSpan>("_SeqSpan", no_init)
  47     .def("__getitem__", &std_item<SeqSpan>::get_const,
  48         return_value_policy<copy_const_reference>())
  49     .def("__len__", &SeqSpan::size)
  50     .def("__str__", &SeqSpan::sequence)
  51     .def("empty", &SeqSpan::empty)
  52     //.add_property("alphabet",
  53     //              make_getter(&SeqSpan::get_alphabet,
  54     //                          return_value_policy<copy_const_reference>()))
  55     .add_property("annotations", &SeqSpan::annotations,
  56                                  &SeqSpan::setAnnotations)
  57     .add_property("start", &SeqSpan::start, &SeqSpan::setStart,
  58                   "start position relative to root sequence")
  59     .add_property("stop", &SeqSpan::stop, &SeqSpan::setStop,
  60                   "one past the last position relative to the root sequence.")
  61     .add_property("strand", &SeqSpan::strand,
  62                   "describe which strand the span is on")
  63
  64     .add_property("parentStart", &SeqSpan::parentStart, &SeqSpan::setParentStart,
  65                   "start position relative to parent sequence")
  66     .add_property("parentStop", &SeqSpan::parentStop, &SeqSpan::setParentStop,
  67                   "one past the last position relative to the parent sequence.")
  68     // doesn't work because I keep getting new python objects for the same
  69     // shared ptr
  70     //.def("parent", &SeqSpan::parent)
  71     .def("subseq", &SeqSpan::subseq)
  72     ;
  73
  74   register_ptr_to_python< SeqSpanRef >();
  75 }