cgreylag.i

   1 // SWIG interface definition for module cgreylag
   2
   3 //     Copyright (C) 2006-2007, Stowers Institute for Medical Research
   4 //
   5 //     This program is free software; you can redistribute it and/or modify
   6 //     it under the terms of the GNU General Public License as published by
   7 //     the Free Software Foundation; either version 2 of the License, or
   8 //     (at your option) any later version.
   9 //
  10 //     This program is distributed in the hope that it will be useful,
  11 //     but WITHOUT ANY WARRANTY; without even the implied warranty of
  12 //     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13 //     GNU General Public License for more details.
  14 //
  15 //     You should have received a copy of the GNU General Public License along
  16 //     with this program; if not, write to the Free Software Foundation, Inc.,
  17 //     51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  18
  19
  20 %module cgreylag
  21
  22
  23 // Declare this read-only, to suppress a warning about a possible memory leak.
  24 %immutable mass_trace_item::description;
  25
  26
  27 %feature("autodoc");
  28
  29 %{
  30 #include "cgreylag.hpp"
  31 %}
  32
  33
  34 // catch STL exceptions, etc
  35 %include "exception.i"
  36 %exception {
  37     try {
  38         $action
  39     } catch (const std::exception& e) {
  40         SWIG_exception(SWIG_RuntimeError, e.what());
  41     } catch (...) {
  42         PyErr_SetString(PyExc_RuntimeError,"unknown C++ (swig) exception");
  43         return NULL;
  44     }
  45 }
  46
  47 // not sure these are useful--just avoiding SWIG warning
  48 %rename(ion_increment) operator++(ion &);
  49 %rename(ion_post_increment) operator++(ion &, int);
  50
  51
  52 %include std_string.i
  53 %apply const std::string & { std::string *name };
  54
  55 // %include std_list.i
  56 %include std_vector.i
  57
  58 // Note: SWIG currently only exposes the outermost vector (in a vector of
  59 // vector of X) as a modifiable object.  Inner vectors appear as tuples, and
  60 // are thus unmodifiable.  They must therefore be assigned all at once.  This
  61 // shortcoming will probably be fixed in a future version of SWIG.
  62
  63 %template(vector_int) std::vector<int>;
  64 %template(vector_double) std::vector<double>;
  65 %template(vector_sequence_run) std::vector<sequence_run>;
  66 %template(vector_peak) std::vector<peak>;
  67 %template(vector_spectrum) std::vector<spectrum>;
  68 %template(vector_match) std::vector<match>;
  69 %template(vector_mass_regime_parameters) std::vector<mass_regime_parameters>;
  70 %template(vector_mass_trace_item) std::vector<mass_trace_item>;
  71 %template(vector_vector_int) std::vector< std::vector<int> >;
  72 %template(vector_vector_double) std::vector< std::vector<double> >;
  73 %template(vector_vector_match) std::vector< std::vector<match> >;
  74 %template(vector_vector_vector_double) std::vector< std::vector< std::vector<double> > >;
  75
  76
  77 %include std_pair.i
  78 %include std_map.i
  79 %include std_multimap.i
  80
  81 %template(pair_double_vector_size_type)
  82     std::pair<double, std::vector<spectrum>::size_type>;
  83
  84 // These two lines seem to be required to make the multimap template work.
  85 // The multimap is only exposed for debugging purposes, anyway, though.
  86 %template() std::pair<swig::PyObject_ptr, swig::PyObject_ptr>;
  87 %template(pymap) std::map<swig::PyObject_ptr, swig::PyObject_ptr>;
  88
  89 %template(multimap_double_vector_size_type)
  90     std::multimap<double, std::vector<spectrum>::size_type>;
  91
  92 // currently unused
  93 //%template(pair_char_int) std::pair<char, int>;
  94 //%template(pair_char_double) std::pair<char, double>;
  95
  96 //%template(map_char_int) std::map<char, int>;
  97 //%template(map_char_double) std::map<char, double>;
  98
  99
 100 %include "typemaps.i"
 101 %apply int *OUTPUT { int *peak_count };
 102
 103
 104 %include file.i
 105
 106
 107 %naturalvar search_context::pca_residues;
 108
 109 %include "cgreylag.hpp"