/**
 * Project     : CASAVA
 * Module      : $RCSfile: AnomalousRead.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_HH
#define ANOMALOUS_READ_HH

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#include "common/PairStats.hh"
#include "variance/SingletonEvent.hh"

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using casava::common::PairStats;

namespace ca {
namespace variance_detection {

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class AnomalousRead : public Singleton
{
public:
    typedef enum { ShadowOrSemiAligned, // FIXME : split these later
                   InsertionPair,
                   DeletionPair,
                   DuplicationPair,
                   InversionPair,
                   ChimericPair } Type;

    AnomalousRead(const Alignment& alignment, bool noReverse = false);

    // Singleton is responsible for telling the world the start and end of
    // the interval within which it might lie ...
    virtual void populateBounds
    (vector<SingletonEvent>& eventStarts,
     vector<SingletonEvent>& eventEnds)=0;
    // ... and for assigning a p-value to every position within that interval
    virtual void populateMetric(IndelMetricStore& indelMetric)=0;

    long mostLikelyBreakPt() const { return myMostLikelyBreakPt; }

protected:
    // For an anomalous pair read on same chrom, the mid-point of the pair.
    // For a chimeric pair read : where mid-point of pair was expected.
    long myMostLikelyBreakPt;
};

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std::ostream& operator<<(std::ostream& ostrm,
                         const AnomalousRead::Type& anomalousReadType);

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std::istream& operator>>(std::istream& istrm,
                         AnomalousRead::Type& anomalousReadType);

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// Class that simply preserves the alignment and positions given to it.
// In particular, there is no reversing of R-mapped read and quality strings.
// The populateBounds and populateMetric methods are deliberately no-ops.

class IdentityAnomRead : public AnomalousRead
{
public:
    IdentityAnomRead(const Alignment& alignment, int minPos, int maxPos)
        : AnomalousRead(alignment, true) {
        minPos_ = minPos;
        maxPos_ = maxPos;
    }

    virtual void populateBounds
    (vector<SingletonEvent>& ,
     vector<SingletonEvent>& ) { }

    virtual void populateMetric(IndelMetricStore& ) { }
};

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class SingleChromPairAnomRead : public AnomalousRead
{
public:
    SingleChromPairAnomRead(const Alignment& alignment,
                            long leftPos,
                            unsigned int insertSize);

    virtual void populateBounds(vector<SingletonEvent>& eventStarts,
                                vector<SingletonEvent>& eventEnds);
    virtual void populateMetric(IndelMetricStore& indelMetric);
};

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class ChimericPairAnomRead : public AnomalousRead
{
public:
    ChimericPairAnomRead(const Alignment& alignment,
                         const PairStats& pairStats,
                         unsigned int readLen);

    virtual void populateBounds(vector<SingletonEvent>& eventStarts,
                                vector<SingletonEvent>& eventEnds);
    virtual void populateMetric(IndelMetricStore& indelMetric);

private:
    // double myStandardDeviation;
};

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} // namespace variance_detection
} // namespace ca

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#endif // ANOMALOUS_READ_HH

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