DataFilters.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 2002-2018.
//
// 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: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/KERNEL/MSSpectrum.h>

namespace OpenMS
{
  class Feature;
  class ConsensusFeature;
  class OPENMS_DLLAPI DataFilters
  {
public:
    DataFilters();

    enum FilterType
    {
      INTENSITY,                
      QUALITY,                    
      CHARGE,                       
      SIZE,                   
      META_DATA                     
    };
    enum FilterOperation
    {
      GREATER_EQUAL,          
      EQUAL,                    
      LESS_EQUAL,               
      EXISTS                        
    };

    struct OPENMS_DLLAPI DataFilter
    {
      DataFilter();

      FilterType field;
      FilterOperation op;
      double value;
      String value_string;
      String meta_name;
      bool value_is_numerical;

      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 typename MSSpectrum::FloatDataArrays & 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;
    }

protected:
    std::vector<DataFilter> filters_;
    std::vector<Size> meta_indices_;

    bool is_active_;

    inline bool metaPasses_(const MetaInfoInterface & meta_interface, const DataFilters::DataFilter & filter, Size index) const
    {
      if (!meta_interface.metaValueExists((UInt)index)) return false;
      else if (filter.op != EXISTS)
      {
        const DataValue & data_value = meta_interface.getMetaValue((UInt)index);
        if (!filter.value_is_numerical)
        {
          if (data_value.valueType() != DataValue::STRING_VALUE) return false;
          else
          {
            // for string values, equality is the only valid operation (besides "exists", see above)
            if (filter.op != EQUAL) return false;
            else if (filter.value_string != data_value.toString()) return false;
          }
        }
        else             // value_is_numerical
        {
          if (data_value.valueType() == DataValue::STRING_VALUE || data_value.valueType() == DataValue::EMPTY_VALUE) return false;
          else
          {
            if (filter.op == EQUAL && (double)data_value != filter.value) return false;
            else if (filter.op == LESS_EQUAL && (double)data_value > filter.value) return false;
            else if (filter.op == GREATER_EQUAL && (double)data_value < filter.value) return false;
          }
        }
      }
      return true;
    }

  };

} //namespace