DataFilters.h

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// --------------------------------------------------------------------------
//                   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.
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// 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
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/KERNEL/Mobilogram.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSChromatogram.h>
 
namespace OpenMS
{
  class Feature;
  class ConsensusFeature;
  class OPENMS_DLLAPI DataFilters
  {
public:
    DataFilters() = default;
 
    enum FilterType
    {
      INTENSITY,      
      QUALITY,        
      CHARGE,         
      SIZE,           
      META_DATA       
    };
    enum FilterOperation
    {
      GREATER_EQUAL,  
      EQUAL,          
      LESS_EQUAL,     
      EXISTS          
    };
 
    struct OPENMS_DLLAPI DataFilter
    {
      DataFilter(){};
      DataFilter(const FilterType type, const FilterOperation op, const double val, const String& meta_name = "")
        : field(type), op(op), value(val), value_string(), meta_name(meta_name), value_is_numerical(true)
      {};
      DataFilter(const FilterType type, const FilterOperation op, const String& val, const String& meta_name = "")
        : field(type), op(op), value(0.0), value_string(val), meta_name(meta_name), value_is_numerical(false)
      {};
      FilterType field{ DataFilters::INTENSITY };
      FilterOperation op{ DataFilters::GREATER_EQUAL} ;
      double value{ 0.0 };
      String value_string;
      String meta_name;
      bool value_is_numerical{ false };
 
      String toString() const;
 
      void fromString(const String & filter);
 
      bool operator==(const DataFilter & rhs) const;
 
      bool operator!=(const DataFilter & rhs) const;
 
    };
 
    Size size() const;
 
    const DataFilter & operator[](Size index) const;
 
    void add(const DataFilter & filter);
 
    void remove(Size index);
 
    void replace(Size index, const DataFilter & filter);
 
    void clear();
 
    void setActive(bool is_active);
 
    inline bool isActive() const
    {
      return is_active_;
    }
 
    bool passes(const Feature& feature) const;
 
    bool passes(const ConsensusFeature& consensus_feature) const;
 
    inline bool passes(const MSSpectrum& spectrum, Size peak_index) const
    {
      if (!is_active_) return true;
 
      for (Size i = 0; i < filters_.size(); i++)
      {
        const DataFilters::DataFilter & filter = filters_[i];
        if (filter.field == INTENSITY)
        {
          switch (filter.op)
          {
          case GREATER_EQUAL:
            if (spectrum[peak_index].getIntensity() < filter.value) return false;
 
            break;
 
          case EQUAL:
            if (spectrum[peak_index].getIntensity() != filter.value) return false;
 
            break;
 
          case LESS_EQUAL:
            if (spectrum[peak_index].getIntensity() > filter.value) return false;
 
            break;
 
          default:
            break;
          }
        }
        else if (filter.field == META_DATA)
        {
          const auto& f_arrays = spectrum.getFloatDataArrays();
          //find the right meta data array
          SignedSize f_index = -1;
          for (Size j = 0; j < f_arrays.size(); ++j)
          {
            if (f_arrays[j].getName() == filter.meta_name)
            {
              f_index = j;
              break;
            }
          }
          //if it is present, compare it
          if (f_index != -1)
          {
            if (filter.op == EQUAL && f_arrays[f_index][peak_index] != filter.value) return false;
            else if (filter.op == LESS_EQUAL && f_arrays[f_index][peak_index] > filter.value) return false;
            else if (filter.op == GREATER_EQUAL && f_arrays[f_index][peak_index] < filter.value) return false;
          }
 
          //if float array not found, search in integer arrays
          const typename MSSpectrum::IntegerDataArrays & i_arrays = spectrum.getIntegerDataArrays();
          //find the right meta data array
          SignedSize i_index = -1;
          for (Size j = 0; j < i_arrays.size(); ++j)
          {
            if (i_arrays[j].getName() == filter.meta_name)
            {
              i_index = j;
              break;
            }
          }
          //if it is present, compare it
          if (i_index != -1)
          {
            if (filter.op == EQUAL && i_arrays[i_index][peak_index] != filter.value) return false;
            else if (filter.op == LESS_EQUAL && i_arrays[i_index][peak_index] > filter.value) return false;
            else if (filter.op == GREATER_EQUAL && i_arrays[i_index][peak_index] < filter.value) return false;
          }
 
          //if it is not present, abort
          if (f_index == -1 && i_index == -1) return false;
        }
      }
      return true;
    }
 
    inline bool passes(const MSChromatogram& chrom, Size peak_index) const
    {
      if (!is_active_) return true;
 
      for (Size i = 0; i < filters_.size(); i++)
      {
        const DataFilters::DataFilter& filter = filters_[i];
        if (filter.field == INTENSITY)
        {
          switch (filter.op)
          {
            case GREATER_EQUAL:
              if (chrom[peak_index].getIntensity() < filter.value)
                return false;
 
              break;
 
            case EQUAL:
              if (chrom[peak_index].getIntensity() != filter.value)
                return false;
 
              break;
 
            case LESS_EQUAL:
              if (chrom[peak_index].getIntensity() > filter.value)
                return false;
 
              break;
 
            default:
              break;
          }
        }
        else if (filter.field == META_DATA)
        {
          const auto& f_arrays = chrom.getFloatDataArrays();
          // find the right meta data array
          SignedSize f_index = -1;
          for (Size j = 0; j < f_arrays.size(); ++j)
          {
            if (f_arrays[j].getName() == filter.meta_name)
            {
              f_index = j;
              break;
            }
          }
          // if it is present, compare it
          if (f_index != -1)
          {
            if (filter.op == EQUAL && f_arrays[f_index][peak_index] != filter.value) return false;
            else if (filter.op == LESS_EQUAL && f_arrays[f_index][peak_index] > filter.value) return false;
            else if (filter.op == GREATER_EQUAL && f_arrays[f_index][peak_index] < filter.value) return false;
          }
 
          // if float array not found, search in integer arrays
          const typename MSSpectrum::IntegerDataArrays& i_arrays = chrom.getIntegerDataArrays();
          // find the right meta data array
          SignedSize i_index = -1;
          for (Size j = 0; j < i_arrays.size(); ++j)
          {
            if (i_arrays[j].getName() == filter.meta_name)
            {
              i_index = j;
              break;
            }
          }
          // if it is present, compare it
          if (i_index != -1)
          {
            if (filter.op == EQUAL && i_arrays[i_index][peak_index] != filter.value) return false;
            else if (filter.op == LESS_EQUAL && i_arrays[i_index][peak_index] > filter.value) return false;
            else if (filter.op == GREATER_EQUAL && i_arrays[i_index][peak_index] < filter.value) return false;
          }
 
          // if it is not present, abort
          if (f_index == -1 && i_index == -1) return false;
        }
      }
      return true;
    }
 
    inline bool passes(const Mobilogram& mobilogram, Size peak_index) const
    {
      if (!is_active_) {
        return true;
      }
        
 
      for (Size i = 0; i < filters_.size(); i++)
      {
        const DataFilters::DataFilter& filter = filters_[i];
        if (filter.field == INTENSITY)
        {
          switch (filter.op)
          {
            case GREATER_EQUAL:
              if (mobilogram[peak_index].getIntensity() < filter.value)
                return false;
 
              break;
 
            case EQUAL:
              if (mobilogram[peak_index].getIntensity() != filter.value)
                return false;
 
              break;
 
            case LESS_EQUAL:
              if (mobilogram[peak_index].getIntensity() > filter.value)
                return false;
 
              break;
 
            default:
              break;
          }
        }
        else if (filter.field == META_DATA)
        { // no metadata arrays so far...
          return false;
        }
      }
      return true;
    }
 
  protected:
    std::vector<DataFilter> filters_;
    std::vector<Size> meta_indices_;
 
    bool is_active_ = false;
 
    bool metaPasses_(const MetaInfoInterface& meta_interface, const DataFilters::DataFilter& filter, Size index) const;
  };
 
} //namespace