/**
 * Project     : CASAVA
 * Module      : $RCSfile: AnomalousReadMgr.hh,v $
 * @author     : Richard Shaw
 * Copyright   : Copyright (c) Illumina 2010. All rights reserved.
 *
 ** This software is covered by the "Illumina Genome Analyzer Software
 ** License Agreement" and the "Illumina Source Code License Agreement",
 ** and certain third party copyright/licenses, and any user of this
 ** source file is bound by the terms therein (see accompanying files
 ** Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
 ** Illumina_Source_Code_License_Agreement.pdf and third party
 ** copyright/license notices).
 *
 */

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#ifndef ANOMALOUS_READ_MGR_HH
#define ANOMALOUS_READ_MGR_HH

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#include <vector>
#include <map>

#include "variance/AnomalousRead.hh"
#include "variance/AnomReadGroup.hh"

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namespace ca {
namespace variance_detection {

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class AnomalousReadMgr {
public:
    AnomalousReadMgr(long clusterMaxInterBreakPtDist);
    ~AnomalousReadMgr();

    void addRead(AnomalousRead::Type anomalousReadType,
                 Singleton* singletonPtr);
    unsigned long totalNumReadsAdded() const; // including duplicates

    typedef std::vector<Singleton*> SingletonPtrVec;
    typedef SingletonPtrVec::const_iterator SingletonPtrVecCIter;

    SingletonPtrVec& getVec(AnomalousRead::Type anomalousReadType);
    const SingletonPtrVec& getVec(AnomalousRead::Type anomalousReadType) const;

    // FIXME : Ultimately AnomalousReadMgr should encapsulate the clustering
    //         and writing out of clusters but for now expose its innards
    //         to ClusterFinderImpl to minimise disruption.
    typedef std::vector<AnomalousRead::Type> TypeVec;
    typedef TypeVec::const_iterator TypeVecCIter;

    void getAnomPairTypeVec(TypeVec& typeVec) const; 

    typedef std::vector<SingletonEvent> SingletonEventVec;
    typedef SingletonEventVec::iterator SingletonEventVecIter;
    typedef SingletonEventVec::const_iterator SingletonEventVecCIter;

    void
    getSortedAnomReads(AnomalousRead::Type anomalousReadType,
                       SingletonEventVec& sortedAnomReads) const;

    typedef std::vector<AnomReadGroup> AnomReadGroupVec;
    typedef AnomReadGroupVec::iterator AnomReadGroupVecIter;
    typedef AnomReadGroupVec::const_iterator AnomReadGroupVecCIter;

    void
    clusterAnomPairReads(AnomalousRead::Type anomReadType,
                         SingletonEventVec& sortedEvents,
                         AnomReadGroupVec& clusters);

private:
    typedef std::map<AnomalousRead::Type,
                     SingletonPtrVec> TypeSingletonPtrVecMap;
    typedef TypeSingletonPtrVecMap::const_iterator TypeSingletonPtrVecMapCIter;

    const SingletonPtrVec myEmptySingletonPtrVec;

    TypeSingletonPtrVecMap myTypeSingletonPtrVecMap;

    long myClusterMaxInterBreakPtDist;
};

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} // namespace variance_detection
} // namespace ca

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#endif // ANOMALOUS_READ_MGR_HH

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