pout_parser.h

/*   Copyright 2014 Henric Zazzi

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

       http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.
*/
// This sample parser implementation was generated by CodeSynthesis XSD,
// an XML Schema to C++ data binding compiler. You may use it in your
// programs without any restrictions.
//

#ifndef POUT_PARSER_H
#define POUT_PARSER_H

#include "global.h"
#include "xmlio.h"
#include "percolator_out-pskel.hxx"
//------------------------------------------------------------------------------
using namespace std;
//------------------------------------------------------------------------------
namespace poutXML {
  class probability_t_pimpl: public virtual probability_t_pskel {
    public:
      string probability_t;

      virtual void _characters (const ::xml_schema::ro_string&);
    };
//------------------------------------------------------------------------------
  class peptide_pimpl: public virtual peptide_pskel {
    public:
      probability_t_pimpl *probability_p;
      string pq_value;
      string ppep;
      bool pdecoy;

      virtual void pre(probability_t_pimpl *probability_p);
      virtual void q_value();
      virtual void pep();
      virtual void decoy(bool);
    };
//------------------------------------------------------------------------------
  class psm_ids_pimpl: public virtual psm_ids_pskel {
    public:
      PercolatorOutI *percolator;
      peptide_pimpl *peptide_p;

      virtual void pre(PercolatorOutI *percolator,peptide_pimpl *peptide_p);
      virtual void psm_id(const ::std::string&);
      virtual void post_psm_ids();
    };
//------------------------------------------------------------------------------
  class psm_pimpl: public virtual psm_pskel {
    public:
      PercolatorOutI *percolator;
      probability_t_pimpl* probability_p;
      string psmid,psmidfile;
      bool psm_decoy;

      virtual void pre(PercolatorOutI *percolator,probability_t_pimpl *probability_p);
      virtual void svm_score(double);
      virtual void q_value();
      virtual void pep();
      virtual void p_value();
      virtual void psm_id (const ::std::string&);
      virtual void decoy(bool);
    };
//------------------------------------------------------------------------------
  class aa_seq_t_pimpl: public virtual aa_seq_t_pskel,public ::xml_schema::string_pimpl {};
//------------------------------------------------------------------------------
  }

#endif // POUT_PARSER_H