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