BasicPharmacophore.hpp

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/* 
 * BasicPharmacophore.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_PHARM_BASICPHARMACOPHORE_HPP
#define CDPL_PHARM_BASICPHARMACOPHORE_HPP
 
#include <vector>
 
#include <boost/iterator/indirect_iterator.hpp>
 
#include "CDPL/Pharm/APIPrefix.hpp"
#include "CDPL/Pharm/Pharmacophore.hpp"
#include "CDPL/Pharm/BasicFeature.hpp"
#include "CDPL/Util/ObjectPool.hpp"
 
 
namespace CDPL
{
 
    namespace Pharm
    {
 
        class CDPL_PHARM_API BasicPharmacophore : public Pharmacophore
        {
 
            typedef Util::ObjectPool<BasicFeature>    FeatureCache;
            typedef FeatureCache::SharedObjectPointer FeaturePointer;
            typedef std::vector<FeaturePointer>       FeatureList;
 
          public:
            typedef std::shared_ptr<BasicPharmacophore> SharedPointer;
 
            typedef boost::indirect_iterator<FeatureList::iterator, BasicFeature>             FeatureIterator;
            typedef boost::indirect_iterator<FeatureList::const_iterator, const BasicFeature> ConstFeatureIterator;
 
            BasicPharmacophore();
 
            BasicPharmacophore(const BasicPharmacophore& pharm);
 
            BasicPharmacophore(const Pharmacophore& pharm);
 
            explicit BasicPharmacophore(const FeatureContainer& cntnr);
 
            ~BasicPharmacophore();
 
            void clear();
 
            std::size_t getNumFeatures() const;
 
            ConstFeatureIterator getFeaturesBegin() const;
 
            FeatureIterator getFeaturesBegin();
 
            ConstFeatureIterator getFeaturesEnd() const;
 
            FeatureIterator getFeaturesEnd();
 
            const BasicFeature& getFeature(std::size_t idx) const;
 
            BasicFeature& getFeature(std::size_t idx);
 
            BasicFeature& addFeature();
 
            void removeFeature(std::size_t idx);
 
            FeatureIterator removeFeature(const FeatureIterator& it);
 
            bool containsFeature(const Feature& feature) const;
 
            std::size_t getFeatureIndex(const Feature& feature) const;
 
            BasicPharmacophore& operator=(const BasicPharmacophore& pharm);
 
            using Pharmacophore::operator=;
 
            BasicPharmacophore& operator+=(const BasicPharmacophore& pharm);
 
            using Pharmacophore::operator+=;
 
            Pharmacophore::SharedPointer clone() const;
 
            void copy(const BasicPharmacophore& pharm);
 
            void copy(const Pharmacophore& pharm);
 
            void copy(const FeatureContainer& cntnr);
 
            void append(const BasicPharmacophore& pharm);
 
            void append(const Pharmacophore& pharm);
 
            void append(const FeatureContainer& cntnr);
 
            void remove(const FeatureContainer& cntnr);
 
            void orderFeatures(const FeatureCompareFunction& func);
 
          private:
            template <typename T>
            void doCopy(const T& pharm);
 
            template <typename T>
            void doAppend(const T& pharm);
 
            void clearFeatures();
 
            void renumberFeatures(std::size_t idx);
 
            BasicFeature* createFeature();
 
            static void destroyFeature(BasicFeature* feature);
            static void clearFeature(BasicFeature& feature);
 
            FeatureCache featureCache;
            FeatureList  features;
        };
    } // namespace Pharm
} // namespace CDPL
 
#endif // CDPL_PHARM_BASICPHARMACOPHORE_HPP