Extend the python mussa interface.

[mussa.git] / py / sequence.cpp

diff --git a/py/sequence.cpp b/py/sequence.cpp
index 3167d56b1ec9edfe6a9eb6e05e856c8e606af6c5..a4ef37981360b0b00c31b08ad82b5dbf04b08cb8 100644 (file)
--- a/py/sequence.cpp
+++ b/py/sequence.cpp
@@ -1,16 +1,49 @@
 #include <boost/python.hpp>
+#include <boost/iterator.hpp>
+#include <boost/python/return_internal_reference.hpp>
+#include <boost/python/return_by_value.hpp>
+#include <boost/python/return_value_policy.hpp>
+#include <boost/python/register_ptr_to_python.hpp>
 using namespace boost::python;
 
+#include <boost/filesystem/path.hpp>
+namespace fs = boost::filesystem;
+
+#include <boost/shared_ptr.hpp>
+
 #include <string>
 #include "alg/glsequence.hpp"
 
 void export_sequence()
 {
+  void (Sequence::*load_fasta_piii)(const fs::path, int, int, int) = &Sequence::load_fasta;
+  void (Sequence::*add_annotation_ssii)(
+          std::string, 
+          std::string, 
+          Sequence::size_type,
+          Sequence::size_type
+       ) = &Sequence::add_annotation;
+  
   class_<Sequence>("Sequence")
     .def(init<std::string>())
-    .def("__str__", &Sequence::get_seq, return_value_policy<return_by_value>())
-    .def("size", &Sequence::size)
-    .def("__len__", &Sequence::size)
-    //.add_property("header", &Sequence::get_header)
+    .def("__getitem__", &Sequence::at, "return base pair at specified location",
+         return_value_policy<return_by_value>())
+    .def("__len__", &Sequence::size, "return the length of the sequence")
+    .def("__repr__", &Sequence::get_sequence, "display as string")
+    .def("__str__", &Sequence::get_sequence, "cast to string")
+    .def("add_annotation", add_annotation_ssii, 
+         "create an annotation from name, type, start, stop")
+    //.def("annotations", &Sequence::annotations, "return list of annotations")
+    .def("add_motif", &Sequence::add_motif, "add a motif sequenence")
+    .def("clear", &Sequence::clear, "clear the sequence and its annotations")
+    .def("empty", &Sequence::empty, "Is the sequence empty")
+    .def("load_fasta", load_fasta_piii, "Load fasta")
+    .add_property("header", &Sequence::get_fasta_header, &Sequence::set_fasta_header, "the fasta header")
+    .def("rcseq", &Sequence::rev_comp, return_value_policy<return_by_value>())
+    .def("size", &Sequence::size, "return the length of the sequence")
+    .add_property("species", &Sequence::get_species, &Sequence::set_species)
+    .def("subseq", &Sequence::subseq, "return a subsequence")
   ;
+
+  register_ptr_to_python< boost::shared_ptr<Sequence> >();
 }