cgreylag.i

   1 // SWIG interface definition for module cgreylag
   2
   3 //     greylag, a collection of programs for MS/MS protein analysis
   4 //     Copyright (C) 2006-2008  Stowers Institute for Medical Research
   5 //
   6 //     This program is free software: you can redistribute it and/or modify
   7 //     it under the terms of the GNU General Public License as published by
   8 //     the Free Software Foundation, either version 3 of the License, or
   9 //     (at your option) any later version.
  10 //
  11 //     This program is distributed in the hope that it will be useful,
  12 //     but WITHOUT ANY WARRANTY; without even the implied warranty of
  13 //     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  14 //     GNU General Public License for more details.
  15 //
  16 //     You should have received a copy of the GNU General Public License
  17 //     along with this program.  If not, see <http://www.gnu.org/licenses/>.
  18 //
  19 //     Contact: Mike Coleman
  20 //              Stowers Institute for Medical Research
  21 //              1000 East 50th Street
  22 //              Kansas City, Missouri  64110
  23 //              USA
  24
  25
  26 %module cgreylag
  27
  28
  29 %feature("autodoc");
  30
  31 %{
  32 #include "cgreylag.hpp"
  33 %}
  34
  35
  36 // catch STL exceptions, etc
  37 %include "exception.i"
  38 %exception {
  39     try {
  40         $action
  41     } catch (const std::exception& e) {
  42         SWIG_exception(SWIG_RuntimeError, e.what());
  43     } catch (...) {
  44         PyErr_SetString(PyExc_RuntimeError,"unknown C++ (swig) exception");
  45         return NULL;
  46     }
  47 }
  48
  49
  50 %include std_string.i
  51 %apply const std::string & { std::string *name };
  52
  53 // %include std_list.i
  54 %include std_vector.i
  55
  56 // Note: SWIG currently only exposes the outermost vector (in a vector of
  57 // vector of X) as a modifiable object.  Inner vectors appear as tuples, and
  58 // are thus unmodifiable.  They must therefore be assigned all at once.  This
  59 // shortcoming will probably be fixed in a future version of SWIG.
  60
  61 %template(vector_int) std::vector<int>;
  62 %template(vector_double) std::vector<double>;
  63 %template(vector_sequence_run) std::vector<sequence_run>;
  64 %template(vector_peak) std::vector<peak>;
  65 %template(vector_spectrum) std::vector<spectrum>;
  66 %template(vector_match) std::vector<match>;
  67 %template(vector_mass_regime_parameters) std::vector<mass_regime_parameters>;
  68 %template(vector_mass_trace_item) std::vector<mass_trace_item>;
  69 %template(vector_string) std::vector<std::string>;
  70 %template(vector_vector_int) std::vector< std::vector<int> >;
  71 %template(vector_vector_double) std::vector< std::vector<double> >;
  72 %template(vector_vector_match) std::vector< std::vector<match> >;
  73
  74
  75 %include std_pair.i
  76 %include std_map.i
  77 %include std_multimap.i
  78
  79 %template(pair_double_vector_size_type)
  80     std::pair<double, std::vector<spectrum>::size_type>;
  81
  82 // These two lines seem to be required to make the multimap template work.
  83 // The multimap is only exposed for debugging purposes, anyway, though.
  84 %template() std::pair<swig::PyObject_ptr, swig::PyObject_ptr>;
  85 %template(pymap) std::map<swig::PyObject_ptr, swig::PyObject_ptr>;
  86
  87 %template(multimap_double_vector_size_type)
  88     std::multimap<double, std::vector<spectrum>::size_type>;
  89
  90
  91 %include file.i
  92
  93
  94 %naturalvar search_context::pca_residues;
  95
  96 %include "cgreylag.hpp"