// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// 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;
  /**
      @brief DataFilter array providing some convenience functions

      @note For features the meta data filtering works on the MetaDataInterface of the Feature.
      For peaks it works on the FloatDataArrays defined in MSSpectrum.
  */
  class OPENMS_DLLAPI DataFilters
  {
public:
    DataFilters();

    ///Information to filter
    enum FilterType
    {
      INTENSITY,                ///< Filter the intensity value
      QUALITY,                    ///< Filter the overall quality value
      CHARGE,                       ///< Filter the charge value
      SIZE,                   ///< Filter the number of subordinates/elements
      META_DATA                     ///< Filter meta data
    };
    ///Filter operation
    enum FilterOperation
    {
      GREATER_EQUAL,          ///< Greater than the value or equal to the value
      EQUAL,                    ///< Equal to the value
      LESS_EQUAL,               ///< Less than the value or equal to the value
      EXISTS                        ///< Only for META_DATA filter type, tests if meta data exists
    };

    ///Representation of a peak/feature filter combining FilterType, FilterOperation and a value
    struct OPENMS_DLLAPI DataFilter
    {
      ///Default constructor
      DataFilter();

      ///Field to filter
      FilterType field;
      ///Filter operation
      FilterOperation op;
      ///Value for comparison
      double value;
      ///String value for comparison (for meta data)
      String value_string;
      ///Name of the considered meta information
      String meta_name;
      ///Bool value that indicates if the specified value is numerical
      bool value_is_numerical;

      /// Returns a string representation of the filter
      String toString() const;

      /**
          @brief Parses @p filter and sets the filter properties accordingly

          This method accepts the format provided by toString().

          @exception Exception::InvalidValue is thrown when the filter is not formatted properly
      */
      void fromString(const String & filter);

      ///Equality operator
      bool operator==(const DataFilter & rhs) const;

      ///Inequality operator
      bool operator!=(const DataFilter & rhs) const;

    };

    ///Filter count
    Size size() const;

    /**
      @brief Filter accessor

      @exception Exception::IndexOverflow is thrown for invalid indices
    */
    const DataFilter & operator[](Size index) const;

    ///Adds a filter
    void add(const DataFilter & filter);

    /**
      @brief Removes the filter corresponding to @p index

      @exception Exception::IndexOverflow is thrown for invalid indices
    */
    void remove(Size index);

    /**
      @brief Replaces the filter corresponding to @p index

      @exception Exception::IndexOverflow is thrown for invalid indices
    */
    void replace(Size index, const DataFilter & filter);

    ///Removes all filters
    void clear();

    ///Enables/disables the all the filters
    void setActive(bool is_active);

    /**
        @brief Returns if the filters are enabled

        They are automatically enabled when a filter is added and
        automatically disabled when the last filter is removed
    */
    inline bool isActive() const
    {
      return is_active_;
    }

    ///Returns if the @p feature fulfills the current filter criteria
    bool passes(const Feature & feature) const;

    ///Returns if the @p consensus_feature fulfills the current filter criteria
    bool passes(const ConsensusFeature & consensus_feature) const;

    ///Returns if the @p peak fulfills the current filter criteria
    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:
    ///Array of DataFilters
    std::vector<DataFilter> filters_;
    ///Vector of meta indices acting as index cache
    std::vector<Size> meta_indices_;

    ///Determines if the filters are activated
    bool is_active_;

    ///Returns if the meta value at @p index of @p meta_interface (a peak or feature) passes the @p filter
    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

