filtersuitestring.cpp

Go to the documentation of this file.

/**
 * \file pappsomspp/processing/filers/filtersuitestring.cpp
 * \date 17/11/2020
 * \author Olivier Langella
 * \brief build a filter suite from a string
 */
 
/*******************************************************************************
 * Copyright (c) 2020 Olivier Langella
 *<olivier.langella@universite-paris-saclay.fr>
 *
 * This file is part of the PAPPSOms++ library.
 *
 *     PAPPSOms++ 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 3 of the License, or
 *     (at your option) any later version.
 *
 *     PAPPSOms++ is distributed in the hope that it will be useful,
 *     but WITHOUT ANY WARRANTY; without even the implied warranty of
 *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *     GNU General Public License for more details.
 *
 *     You should have received a copy of the GNU General Public License
 *     along with PAPPSOms++.  If not, see <http://www.gnu.org/licenses/>.
 *
 ******************************************************************************/
 
#include "filtersuitestring.h"
#include "filterchargedeconvolution.h"
#include "filtercomplementionenhancer.h"
#include "filterpass.h"
#include "filtermorpho.h"
#include <QStringList>
#include <QDebug>
#include "pappsomspp/core/exception/exceptionnotrecognized.h"
#include "filterexclusionmz.h"
 
 
namespace pappso
{
FilterSuiteString::FilterSuiteString(const QString &strBuildParams)
{
  buildFilterFromString(strBuildParams);
}
 
FilterSuiteString::~FilterSuiteString()
{
}
 
 
pappso::Trace &
FilterSuiteString::filter(pappso::Trace &data_points) const
{
 
  qDebug();
  for(auto &&filter : m_filterVector)
    {
 
      qDebug() << filter.get();
      qDebug() << filter->toString();
      filter->filter(data_points);
    }
 
  qDebug();
  return data_points;
}
 
 
QString
pappso::FilterSuiteString::name() const
{
  // FIXME: check if this makes sense
  return "Suite of filters";
}
 
 
QString
FilterSuiteString::toString() const
{
  QStringList filter_str_list;
  for(auto &&filter : m_filterVector)
    {
      filter_str_list << filter->toString();
    }
 
  return filter_str_list.join(" ");
}
 
 
void
FilterSuiteString::buildFilterFromString(const QString &strBuildParams)
{
  // qInfo() << strBuildParams;
  QStringList filters = strBuildParams.split(" ", Qt::SkipEmptyParts);
  for(QString filter_str : filters)
    {
      if(filter_str.startsWith("complementIonEnhancer|"))
        {
          m_filterVector.push_back(std::make_shared<FilterComplementIonEnhancer>(filter_str));
        }
      else if(filter_str.startsWith("chargeDeconvolution|"))
        {
          m_filterVector.push_back(std::make_shared<FilterChargeDeconvolution>(filter_str));
        }
      else if(filter_str.startsWith("mzExclusion|"))
        {
          m_filterVector.push_back(std::make_shared<FilterMzExclusion>(filter_str));
        }
      else if(filter_str.startsWith("passQuantileBasedRemoveY|"))
        {
          m_filterVector.push_back(std::make_shared<FilterQuantileBasedRemoveY>(filter_str));
        }
 
      else if(filter_str.startsWith("antiSpike|"))
        {
          m_filterVector.push_back(std::make_shared<FilterMorphoAntiSpike>(filter_str));
        }
      else if(filter_str.startsWith("morphoBackground|"))
        {
          m_filterVector.push_back(std::make_shared<FilterMorphoBackground>(filter_str));
        }
      else if(filter_str.startsWith("removeY|"))
        {
          m_filterVector.push_back(std::make_shared<FilterRemoveY>(filter_str));
        }
 
      else if(filter_str.startsWith("morphoMean|"))
        {
          m_filterVector.push_back(std::make_shared<FilterMorphoMean>(filter_str));
        }
      else
        {
          throw pappso::ExceptionNotRecognized(QString("building Filter from string %1 is "
                                                       "not possible")
                                                 .arg(filter_str));
        }
    }
}
 
void
FilterSuiteString::addFilterFromString(const QString &strBuildParams)
{
  buildFilterFromString(strBuildParams);
}
 
void
pappso::FilterSuiteString::addFilter(const pappso::FilterNameInterfaceSPtr &filter)
{
  m_filterVector.push_back(filter);
}
 
FilterSuiteString::FilterNameType::const_iterator
FilterSuiteString::begin()
{
  return m_filterVector.begin();
};
FilterSuiteString::FilterNameType::const_iterator
FilterSuiteString::end()
{
  return m_filterVector.end();
};
 
} // namespace pappso