/**
 * Project     : CASAVA
 * Module      : $RCSfile: AnomReadVec.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).
 *
 */

/*****************************************************************************/

#ifndef ANOM_READ_VEC_HH
#define ANOM_READ_VEC_HH

/*****************************************************************************/

#include <string>
#include <vector>
#include <set>
#include <iostream>

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

/*****************************************************************************/

namespace ca {
namespace variance_detection {

/*****************************************************************************/

struct AnomReadVec : public std::vector<Singleton*>
{
    AnomReadVec(unsigned int groupNum = 0);
    AnomReadVec(AnomalousRead::Type anomReadType,
                unsigned int groupNum = 0);
    void updateBreakPoints(PairStats& pairStats);
    unsigned int numCommonReads(const AnomReadVec& anomReadVec);
    void absorb(AnomReadVec& anomReadVec);

    AnomalousRead::Type myAnomReadType;

    typedef std::vector<AnomalousRead::Type> AnomReadTypeVec;
    typedef AnomReadTypeVec::const_iterator AnomReadTypeVecCIter;
    AnomReadTypeVec myExtraAnomReadTypeVec;

    int myPos;
    unsigned int myGroupNum;
    int myLeftBreakPos;
    int myRightBreakPos;

private:
    void ensureReadIdSetPopulated(bool forceUpdate=false);

    typedef std::set<std::string> ReadIdSet;
    typedef ReadIdSet::const_iterator ReadIdSetCIter;
    ReadIdSet myReadIdSet;
};

typedef AnomReadVec::iterator AnomReadVecIter;
typedef AnomReadVec::const_iterator AnomReadVecCIter;

/*****************************************************************************/

std::istream& operator>>(std::istream& istrm, AnomReadVec& anomReadVec);
std::ostream& operator<<(std::ostream& ostrm, const AnomReadVec& anomReadVec);

/*****************************************************************************/
// Sorting by left breakpoint then right breakpoint, should cause only
// DeletionPair clusters for larger deletions to move within the list,
// so the ordering should otherwise be the same.

class SortAnomReadVecByLeftBrk
{
public:
    bool operator()(const AnomReadVec& anomReadVecA,
                    const AnomReadVec& anomReadVecB) {
        return (anomReadVecA.myLeftBreakPos < anomReadVecB.myLeftBreakPos);
    }
};

/*****************************************************************************/

class SortAnomReadVecByRightBrk
{
public:
    bool operator()(const AnomReadVec& anomReadVecA,
                    const AnomReadVec& anomReadVecB) {
        return (anomReadVecA.myRightBreakPos < anomReadVecB.myRightBreakPos);
    }
};

/*****************************************************************************/

class SortAnomReadVecByGroupNum
{
public:
    bool operator()(const AnomReadVec& anomReadVecA,
                    const AnomReadVec& anomReadVecB) {
        return (anomReadVecA.myGroupNum < anomReadVecB.myGroupNum);
    }
};

/*****************************************************************************/

} // namespace variance_detection
} // namespace ca

/*****************************************************************************/

#endif // ! ANOM_READ_GROUP_HH

/*****************************************************************************/