Extend the python mussa interface.

[mussa.git] / py / mussa.cpp

diff --git a/py/mussa.cpp b/py/mussa.cpp
index 5f42599fb78111ea323fda0813c1dc3f43598c0f..cd46d4941ff1e9de5f168e82ac595e7b7d48c268 100644 (file)
--- a/py/mussa.cpp
+++ b/py/mussa.cpp
@@ -7,7 +7,9 @@ namespace py = boost::python;
 
 void export_mussa()
 {
-  void (Mussa::*load_mupa_string)(std::string) = &Mussa::load_mupa_file;
+  void (Mussa::*save_string)(const std::string &) = &Mussa::save;
+  void (Mussa::*load_mupa_string)(const std::string &) = &Mussa::load_mupa_file;
+  void (Mussa::*load_string)(const std::string &) = &Mussa::load;
   void (Mussa::*append_sequence_ref)(const Sequence&) = &Mussa::append_sequence;
   void (Mussa::*append_sequence_ptr)(const boost::shared_ptr<Sequence>) = &Mussa::append_sequence;
 
@@ -26,8 +28,8 @@ void export_mussa()
   ;
  
   py::class_<Mussa>("_Mussa", py::no_init)
-    .def("save", &Mussa::save)
-    .def("load", &Mussa::load, "Load previous run analysis")
+    .def("save", save_string, "Save analysis in the specified directory")
+    .def("load", load_string, "Load previous run analysis")
     .def("load_mupa", load_mupa_string, "Load mussa parameter file")
     .def("clear", &Mussa::clear, "Clear the current analysis")
     .add_property("name", &Mussa::get_name, &Mussa::set_name, "Set the name of the analysis")
@@ -37,7 +39,8 @@ void export_mussa()
                   "the number of base pairs in the sliding window")
     .add_property("threshold", &Mussa::get_threshold, &Mussa::set_threshold,
                   "how many base pairs must match between two windows")
-    .def("softThreshold", &Mussa::set_soft_threshold)
+    .add_property("softThreshold", &Mussa::get_soft_threshold,
+                  &Mussa::set_soft_threshold)
     .add_property("analysisMode", &Mussa::get_analysis_mode, 
                                    &Mussa::set_analysis_mode)
     .add_property("analysisModeName", &Mussa::get_analysis_mode_name)
@@ -46,7 +49,10 @@ void export_mussa()
     .def("sequences", &Mussa::sequences, py::return_internal_reference<>(), "return list of sequences")
     .def("add_sequence", append_sequence_ref, "attach a sequence to the analysis")  
   ;
-  py::def("Mussa", &Mussa::init, "Construct a new Mussa object");
+  py::def("Mussa", &Mussa::init, 
+          "Construct a new Mussa object.\n"
+          "You can use this to load a previous analysis or to construct\n"
+          "a new analysis.\n");
   py::register_ptr_to_python< boost::shared_ptr<Mussa> >();
   
   py::enum_<Mussa::analysis_modes>("analysis_modes")