pout_parser.cpp

/*   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.
//
//------------------------------------------------------------------------------
#include <iostream>
#include "pout_parser.h"
//------------------------------------------------------------------------------
namespace poutXML {
  void probability_t_pimpl::_characters(const ::xml_schema::ro_string &s) {
    probability_t=s;
    }
//------------------------------------------------------------------------------
  void peptide_pimpl::pre(probability_t_pimpl *probability_p) {
    this->probability_p=probability_p;
    }
//------------------------------------------------------------------------------
  void peptide_pimpl::q_value() {
    pq_value=probability_p->probability_t;
    }
//------------------------------------------------------------------------------
  void peptide_pimpl::pep() {
    ppep=probability_p->probability_t;
    }
//------------------------------------------------------------------------------
  void peptide_pimpl::decoy(bool decoy) {
    pdecoy=decoy;
    }
//------------------------------------------------------------------------------
  void psm_ids_pimpl::pre(PercolatorOutI *percolator,peptide_pimpl *peptide_p) {
    this->percolator=percolator;
    this->peptide_p=peptide_p;
    this->peptide_p->pq_value="";
    this->peptide_p->ppep="";
    }
//------------------------------------------------------------------------------
  void psm_ids_pimpl::post_psm_ids() {
    peptide_p->pq_value="";
    peptide_p->ppep="";
    }
//------------------------------------------------------------------------------
  void psm_ids_pimpl::psm_id(const ::std::string &psm_id) {
    string psmid,psmidfile;

    if (!percolator->checkDecoy(peptide_p->pdecoy))
      return;
    psmid=percolator->convertPSMID(psm_id);
    if (psmid.length()==0)
      THROW_ERROR_VALUE(PRINT_TEXT::WRONG_FORMAT_PSM,psm_id);
    psmidfile=percolator->convertPSMIDFileName(psm_id);
    if (psmidfile.length()==0 && percolator->multiplemzidfiles)
      THROW_ERROR(PRINT_TEXT::NO_UNIQUE_MZID_FILE);
    if (psmidfile.length()>0) {
      cout <<"-";
      if (!percolator->multiplemzidfiles)
        THROW_ERROR(PRINT_TEXT::MULTIPLE_MZID_FILES);
      if (!percolator->addFilenames(psmidfile,true))
        THROW_ERROR("");
      }
    if (peptide_p->ppep.length()>0)
      percolator->pout_values[PercolatorOutFeatures(psmidfile,psmid,PERCOLATOR_PARAM::PEPTIDE_PEP)]=peptide_p->ppep;
    if (peptide_p->pq_value.length()>0)
      percolator->pout_values[PercolatorOutFeatures(psmidfile,psmid,PERCOLATOR_PARAM::PEPTIDE_Q_VALUE)]=peptide_p->pq_value;
    }
//------------------------------------------------------------------------------
  void psm_pimpl::pre(PercolatorOutI *percolator,probability_t_pimpl *probability_p) {
    this->percolator=percolator;
    this->probability_p=probability_p;
    }
//------------------------------------------------------------------------------
  void psm_pimpl::svm_score(double svm_score) {
    if (psm_decoy)
      percolator->pout_values[PercolatorOutFeatures(psmidfile,psmid,PERCOLATOR_PARAM::SVM_SCORE)]=global::to_string(svm_score);
    }
//------------------------------------------------------------------------------
  void psm_pimpl::q_value() {
    if (psm_decoy)
      percolator->pout_values[PercolatorOutFeatures(psmidfile,psmid,PERCOLATOR_PARAM::Q_VALUE)]=probability_p->probability_t;
    }
//------------------------------------------------------------------------------
  void psm_pimpl::pep() {
    if (psm_decoy)
      percolator->pout_values[PercolatorOutFeatures(psmidfile,psmid,PERCOLATOR_PARAM::PEP)]=probability_p->probability_t;
    }
//------------------------------------------------------------------------------
  void psm_pimpl::p_value() {
    if (psm_decoy)
      percolator->pout_values[PercolatorOutFeatures(psmidfile,psmid,PERCOLATOR_PARAM::P_VALUE)]=probability_p->probability_t;
    }
//------------------------------------------------------------------------------
  void psm_pimpl::psm_id(const ::std::string &psm_id) {
    psmid=percolator->convertPSMID(psm_id);
    if (psmid.length()==0)
      THROW_ERROR_VALUE(PRINT_TEXT::WRONG_FORMAT_PSM,psm_id);
    psmidfile=percolator->convertPSMIDFileName(psm_id);
    if (psmidfile.length()==0 && percolator->multiplemzidfiles)
      THROW_ERROR(PRINT_TEXT::NO_UNIQUE_MZID_FILE);
    if (psmidfile.length()>0) {
      if (!percolator->multiplemzidfiles)
        THROW_ERROR(PRINT_TEXT::MULTIPLE_MZID_FILES);
      if (!percolator->addFilenames(psmidfile,true))
        THROW_ERROR("");
      }
    }
//------------------------------------------------------------------------------
  void psm_pimpl::decoy(bool decoy) {
    psm_decoy=percolator->checkDecoy(decoy);
    }
//------------------------------------------------------------------------------
  }