BulkSimilarityCalculator.hpp

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/* 
 * BulkSimilarityCalculator.hpp 
 *
 * This file is part of the Chemical Data Processing Toolkit
 *
 * Copyright (C) 2003 Thomas Seidel <thomas.seidel@univie.ac.at>
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2 of the License, or (at your option) any later version.
 *
 * This library 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
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this library; see the file COPYING. If not, write to
 * the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
 * Boston, MA 02111-1307, USA.
 */
 
#ifndef CDPL_DESCR_BULKSIMILARITYCALCULATOR_HPP
#define CDPL_DESCR_BULKSIMILARITYCALCULATOR_HPP
 
#include <vector>
#include <cstddef>
#include <functional>
#include <memory>
#include <utility>
#include <algorithm>
 
#include <boost/iterator/indirect_iterator.hpp>
 
#include "CDPL/Descr/SimilarityFunctors.hpp"
#include "CDPL/Base/Exceptions.hpp"
 
 
namespace CDPL
{
 
    namespace Descr
    {
 
        template <typename DT = Util::BitSet, typename SVT = double>
        class BulkSimilarityCalculator
        {
 
          public:
            typedef DT                                        Descriptor;
            typedef std::shared_ptr<DT>                       DescriptorPointer;
            typedef SVT                                       SimilarityValue;
            typedef std::function<SVT(const DT&, const DT&)>  SimilarityFunction;
            typedef std::pair<std::size_t, SVT>               Result;
            typedef std::shared_ptr<BulkSimilarityCalculator> SharedPointer;
 
          private:
            typedef std::vector<DescriptorPointer> DescriptorList;
            typedef std::vector<Result>            ResultList;
 
          public:
            typedef boost::indirect_iterator<typename DescriptorList::const_iterator, DT>
                ConstDescriptorIterator;
            typedef boost::indirect_iterator<typename DescriptorList::iterator, DT>
                DescriptorIterator;
 
            typedef typename ResultList::const_iterator ConstResultIterator;
            
            BulkSimilarityCalculator() = default;
 
            BulkSimilarityCalculator(const BulkSimilarityCalculator& calc) = default;
            BulkSimilarityCalculator(BulkSimilarityCalculator&& calc) = default;
            
            template <typename SF>
            BulkSimilarityCalculator(SF&& sim_func):
                simFunc(std::forward<SF>(sim_func)) {}
 
            BulkSimilarityCalculator& operator=(const BulkSimilarityCalculator& calc) = default;
            BulkSimilarityCalculator& operator=(BulkSimilarityCalculator&& calc) = default;
            
            const SimilarityFunction& getSimilarityFunction() const;
 
            template <typename SF>
            void setSimilarityFunction(SF&& func);
            
            void clear();
 
            DescriptorIterator getDescriptorsBegin();
            DescriptorIterator getDescriptorsEnd();
 
            ConstDescriptorIterator getDescriptorsBegin() const;
            ConstDescriptorIterator getDescriptorsEnd() const;
 
            std::size_t getNumDescriptors() const;
 
            void addDescriptor(const Descriptor& descr);
            void addDescriptor(const DescriptorPointer& descr_ptr);
 
            bool containsDescriptor(const Descriptor& descr) const;
 
            const Descriptor& getDescriptor(std::size_t idx) const;
 
            void removeDescriptor(std::size_t idx);
            DescriptorIterator removeDescriptor(const DescriptorIterator& it);
 
            void calculate(const Descriptor& descr, bool sort = false, bool sort_desc = true);
 
            ConstResultIterator getResultsBegin() const;
            ConstResultIterator getResultsEnd() const;
 
            ConstResultIterator begin() const;
            ConstResultIterator end() const;
 
            const Result& getResult(std::size_t idx) const;
 
            const SimilarityValue& getSimilarity(std::size_t idx) const;
            std::size_t getDescriptorIndex(std::size_t idx) const;
 
          private:
            SimilarityFunction simFunc{TanimotoSimilarity()};
            DescriptorList     descriptors;
            ResultList         results;
        };
 
    } // namespace Descr
} // namespace CDPL
 
 
// Implementation
 
template <typename DT, typename SVT>
const typename CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::SimilarityFunction&
CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::getSimilarityFunction() const
{
    return simFunc;
}
 
template <typename DT, typename SVT>
template <typename SF>
void CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::setSimilarityFunction(SF&& func)
{
    simFunc = std::forward<SF>(func);
}
 
template <typename DT, typename SVT>
void CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::clear()
{
    descriptors.clear();
    results.clear();
}
 
template <typename DT, typename SVT>
typename CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::DescriptorIterator
CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::getDescriptorsBegin()
{
    return descriptors.begin();
}
 
template <typename DT, typename SVT>
typename CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::DescriptorIterator
CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::getDescriptorsEnd()
{
    return descriptors.end();
}
 
template <typename DT, typename SVT>
typename CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::ConstDescriptorIterator
CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::getDescriptorsBegin() const
{
    return descriptors.begin();
}
 
template <typename DT, typename SVT>
typename CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::ConstDescriptorIterator
CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::getDescriptorsEnd() const
{
    return descriptors.end();
}
 
template <typename DT, typename SVT>
std::size_t CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::getNumDescriptors() const
{
    return descriptors.size();
}
 
template <typename DT, typename SVT>
void CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::addDescriptor(const Descriptor& descr)
{
    descriptors.emplace_back(DescriptorPointer(new Descriptor(descr)));
}
 
template <typename DT, typename SVT>
void CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::addDescriptor(const DescriptorPointer& descr_ptr)
{
    descriptors.emplace_back(descr_ptr);
}
 
template <typename DT, typename SVT>
bool CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::containsDescriptor(const Descriptor& descr) const
{
    for (auto& dp : descriptors)
        if (*dp == descr)
            return true;
 
    return false;
}
 
template <typename DT, typename SVT>
const typename CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::Descriptor&
CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::getDescriptor(std::size_t idx) const
{
    if (idx >= descriptors.size())
        throw Base::IndexError("BulkSimilarityCalculator: descriptor index out of bounds");
 
    return *descriptors[idx];
}
 
template <typename DT, typename SVT>
void CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::removeDescriptor(std::size_t idx)
{
    if (idx >= descriptors.size())
        throw Base::IndexError("BulkSimilarityCalculator: descriptor index out of bounds");
 
    descriptors.erase(descriptors.begin() + idx);
}
 
template <typename DT, typename SVT>
typename CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::DescriptorIterator
CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::removeDescriptor(const DescriptorIterator& it)
{
    auto& b_it = it.base();
 
    if ((b_it < descriptors.begin()) || (b_it >= descriptors.end()))
        throw Base::RangeError("BulkSimilarityCalculator: descriptor iterator out of valid range");
 
    return descriptors.erase(b_it);
}
 
template <typename DT, typename SVT>
void CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::calculate(const Descriptor& descr, bool sort, bool sort_desc)
{
    results.clear();
    results.reserve(descriptors.size());
 
    for (std::size_t i = 0, num_descrs = descriptors.size(); i < num_descrs; i++)
        results.emplace_back(i, simFunc(descr, *descriptors[i]));
 
    if (!sort)
        return;
 
    if (sort_desc)
        std::sort(results.begin(), results.end(),
                  [](const Result& r1, const Result& r2) {
                      return (r1.second > r2.second);
                  });
    else
        std::sort(results.begin(), results.end(),
                  [](const Result& r1, const Result& r2) {
                      return (r1.second < r2.second);
                  });
}
 
template <typename DT, typename SVT>
typename CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::ConstResultIterator
CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::getResultsBegin() const
{
    return results.begin();
}
 
template <typename DT, typename SVT>
typename CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::ConstResultIterator
CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::getResultsEnd() const
{
    return results.end();
}
 
template <typename DT, typename SVT>
typename CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::ConstResultIterator
CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::begin() const
{
    return results.begin();
}
 
template <typename DT, typename SVT>
typename CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::ConstResultIterator
CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::end() const
{
    return results.end();
}
 
template <typename DT, typename SVT>
const typename CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::Result&
CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::getResult(std::size_t idx) const
{
    if (idx >= results.size())
        throw Base::IndexError("BulkSimilarityCalculator: result index out of bounds");
 
    return results[idx];
}
 
template <typename DT, typename SVT>
const typename CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::SimilarityValue&
CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::getSimilarity(std::size_t idx) const
{
    if (idx >= results.size())
        throw Base::IndexError("BulkSimilarityCalculator: result index out of bounds");
 
    return results[idx].second;
}
 
template <typename DT, typename SVT>
std::size_t CDPL::Descr::BulkSimilarityCalculator<DT, SVT>::getDescriptorIndex(std::size_t idx) const
{
    if (idx >= results.size())
        throw Base::IndexError("BulkSimilarityCalculator: result index out of bounds");
 
    return results[idx].first;
}
 
#endif // CDPL_DESCR_BULKSIMILARITYCALCULATOR_HPP