/***************************************************************************
                          secstruct_mod.cpp  -  description
                             -------------------
    begin                : Fri Dec 30 13:17:33 2005
    copyright            : (C) 2002 by Cavalli Andrea
    email                : cavalli@bioc.unizh.ch
**************************************************************************/
/***************************************************************************
 *                                                                         *
 *   This program is free software; you can redistribute it and/or modify  *
 *   it under the terms of the GNU General Public License as published by  *
 *   the Free Software Foundation; either version 2 of the License, or     *
 *   (at your option) any later version.                                   *
 *                                                                         *
 ***************************************************************************/

#include <zeta/module.h>
#include <zeta/class.h>
#include <zeta/zextclass.h>
#include <zeta/zobj.hpp>
#include <sstream>
#include <iterator>
#include <almost.h>
#include <cheshire/pssi.h>
#include <cheshire/pred3.h>
using namespace Almost;

template<>
inline string to_string(const PSSI &){
  return "<PSSI>";
}



template<>
inline string to_string(const Pred3 &){
  return "<Pred3>";
}

extern "C" {
  void init_secstruct(){
    //declarations here

    Module mod = Module("secstruct","Compute secondary structure of proteins");

    Class<PSSI, ArgList1<string> >(mod.self(),"pssi")
      .def_method("join_prob",&PSSI::join_prob)
      .def_method("calibrate",&PSSI::calibrate)
      .def_method("use_ha",&PSSI::use_ha)
      .def_method("use_h",&PSSI::use_h)
      .def_method("use_n",&PSSI::use_n)
      .def_method("use_ca",&PSSI::use_ca)
      .def_method("use_cb",&PSSI::use_cb)
      .def_method("use_c",&PSSI::use_c)
      .def_method("ha_ref",&PSSI::ha_ref)
      .def_method("h_ref",&PSSI::h_ref)
      .def_method("n_ref",&PSSI::n_ref)
      .def_method("ca_ref",&PSSI::ca_ref)
      .def_method("cb_ref",&PSSI::cb_ref)
      .def_method("c_ref",&PSSI::c_ref)
      .def_method("ha_ref_add",&PSSI::ha_ref_add)
      .def_method("h_ref_add",&PSSI::h_ref_add)
      .def_method("n_ref_add",&PSSI::n_ref_add)
      .def_method("ca_ref_add",&PSSI::ca_ref_add)
      .def_method("cb_ref_add",&PSSI::cb_ref_add)
      .def_method("c_ref_add",&PSSI::c_ref_add)
      .def_method("ss_nat",&PSSI::ss_nat)
      .def_method("fasta",&PSSI::fasta)
      ;
    Class<Pred3, ArgList1<string> >(mod.self(),"pred3")
      .def_method("run",&Pred3::run)
      .def_method("set_lambda",&Pred3::set_lambda)
      .def_method("set_T",&Pred3::set_T)
      ;
  }
}