MRMFeatureFilter.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Douglas McCloskey, Pasquale Domenico Colaianni $
// $Authors: Douglas McCloskey, Pasquale Domenico Colaianni $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureQC.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
 
#include <OpenMS/KERNEL/MRMFeature.h>
#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/KERNEL/FeatureMap.h>
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/String.h>
 
namespace OpenMS
{
  class AbsoluteQuantitationMethod;
 
  class OPENMS_DLLAPI MRMFeatureFilter :
    public DefaultParamHandler
  {
 
public:
 
    MRMFeatureFilter();
 
    ~MRMFeatureFilter() override;
 
    void getDefaultParameters(Param& params) const;
 
    void updateMembers_() override;
 
    void FilterFeatureMap(FeatureMap& features, const MRMFeatureQC& filter_criteria,
      const TargetedExperiment& transitions);
 
    void FilterFeatureMapPercRSD(FeatureMap& features, const MRMFeatureQC& filter_criteria, const MRMFeatureQC& filter_values);
 
    void FilterFeatureMapBackgroundInterference(FeatureMap& features, const MRMFeatureQC& filter_criteria, const MRMFeatureQC& filter_values);
 
    void EstimateDefaultMRMFeatureQCValues(const std::vector<FeatureMap>& samples, MRMFeatureQC& filter_template, const TargetedExperiment& transitions, const bool& init_template_values) const;
 
    void TransferLLOQAndULOQToCalculatedConcentrationBounds(const std::vector<AbsoluteQuantitationMethod>& quantitation_method, MRMFeatureQC& filter_template);
 
    void EstimatePercRSD(const std::vector<FeatureMap>& samples, MRMFeatureQC& filter_template, const TargetedExperiment& transitions) const;
 
    void EstimateBackgroundInterferences(const std::vector<FeatureMap>& samples, MRMFeatureQC& filter_template, const TargetedExperiment& transitions) const;
 
    double calculateIonRatio(const Feature& component_1, const Feature& component_2, const String& feature_name) const;
 
    double calculateRTDifference(Feature& component_1, Feature& component_2) const;
 
    double calculateResolution(Feature& component_1, Feature& component_2) const;
 
    bool checkMetaValue(
      const Feature& component,
      const String& meta_value_key,
      const double& meta_value_l,
      const double& meta_value_u,
      bool& key_exists
    ) const;
 
    void updateMetaValue(
      const Feature& component,
      const String& meta_value_key,
      double& meta_value_l,
      double& meta_value_u,
      bool& key_exists
    ) const;
 
    void setMetaValue(
      const Feature& component,
      const String& meta_value_key,
      double& meta_value_l,
      double& meta_value_u,
      bool& key_exists
    ) const;
 
    void initMetaValue(
      const Feature& component,
      const String& meta_value_key,
      double& meta_value_l,
      double& meta_value_u,
      bool& key_exists
    ) const;
 
    std::map<String,int> countLabelsAndTransitionTypes(const Feature& component_group,
      const TargetedExperiment& transitions) const;
 
    StringList getUniqueSorted(const StringList& messages) const;
 
    void accumulateFilterValues(std::vector<MRMFeatureQC>& filter_values, const std::vector<FeatureMap>& samples, const MRMFeatureQC& filter_template, const TargetedExperiment& transitions) const;
 
    void zeroFilterValues(MRMFeatureQC& filter_zeros, const MRMFeatureQC& filter_template) const;
 
    void calculateFilterValuesMean(MRMFeatureQC& filter_mean, const std::vector<MRMFeatureQC>& filter_values, const MRMFeatureQC& filter_template) const;
 
    void calculateFilterValuesVar(MRMFeatureQC& filter_var, const std::vector<MRMFeatureQC>& filter_values, const MRMFeatureQC& filter_mean, const MRMFeatureQC& filter_template) const;
 
    void calculateFilterValuesPercRSD(MRMFeatureQC& filter_rsd, const MRMFeatureQC& filter_mean, const MRMFeatureQC& filter_var) const;
 
    template <typename T>
    bool checkRange(const T& value, const T& value_l, const T& value_u) const;
 
    template <typename T>
    void updateRange(const T& value, T& value_l, T& value_u) const;
 
    template <typename T>
    void setRange(const T& value, T& value_l, T& value_u) const;
 
    template <typename T>
    void initRange(const T& value, T& value_l, T& value_u) const;
 
private:
    // Members
    String flag_or_filter_;
  };
}