// ***************************************************************************
// BamToolsIndex.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 November 2011 (DB)
// ---------------------------------------------------------------------------
// Provides index operations for the BamTools index format (".bti")
// ***************************************************************************

#ifndef BAMTOOLS_INDEX_FORMAT_H
#define BAMTOOLS_INDEX_FORMAT_H

#include "api/api_global.h"

//  -------------
//  W A R N I N G
//  -------------
//
// This file is not part of the BamTools API.  It exists purely as an
// implementation detail.  This header file may change from version to
// version without notice, or even be removed.
//
// We mean it.

#include <map>
#include <string>
#include <vector>
#include "api/BamAux.h"
#include "api/BamIndex.h"
#include "api/IBamIODevice.h"

namespace BamTools {
namespace Internal {

// contains data for each 'block' in a BTI index
struct API_NO_EXPORT BtiBlock
{

    // data members
    int32_t MaxEndPosition;
    int64_t StartOffset;
    int32_t StartPosition;

    // ctor
    BtiBlock(const int32_t& maxEndPosition = 0, const int64_t& startOffset = 0,
             const int32_t& startPosition = 0)
        : MaxEndPosition(maxEndPosition)
        , StartOffset(startOffset)
        , StartPosition(startPosition)
    {}
};

// convenience typedef for describing a a list of BTI blocks on a reference
typedef std::vector<BtiBlock> BtiBlockVector;

// contains all fields necessary for building, loading, & writing
// full BTI index data for a single reference
struct API_NO_EXPORT BtiReferenceEntry
{

    // data members
    int32_t ID;
    BtiBlockVector Blocks;

    // ctor
    BtiReferenceEntry(const int& id = -1)
        : ID(id)
    {}
};

// provides (persistent) summary of BtiReferenceEntry's index data
struct API_NO_EXPORT BtiReferenceSummary
{

    // data members
    int NumBlocks;
    uint64_t FirstBlockFilePosition;

    // ctor
    BtiReferenceSummary()
        : NumBlocks(0)
        , FirstBlockFilePosition(0)
    {}
};

// convenience typedef for describing a full BTI index file summary
typedef std::vector<BtiReferenceSummary> BtiFileSummary;

class API_NO_EXPORT BamToolsIndex : public BamIndex
{

    // keep a list of any supported versions here
    // (might be useful later to handle any 'legacy' versions if the format changes)
    // listed for example like: BTI_1_0 = 1, BTI_1_1 = 2, BTI_1_2 = 3, BTI_2_0 = 4, and so on
    //
    // so a change introduced in BTI_1_2 may be handled from then on by:
    //
    // if ( indexVersion >= BTI_1_2 )
    //   do something new
    // else
    //   do the old thing
    enum Version
    {
        BTI_1_0 = 1,
        BTI_1_1,
        BTI_1_2,
        BTI_2_0
    };

    // ctor & dtor
public:
    BamToolsIndex(Internal::BamReaderPrivate* reader);
    ~BamToolsIndex();

    // BamIndex implementation
public:
    // builds index from associated BAM file & writes out to index file
    bool Create();
    // returns whether reference has alignments or no
    bool HasAlignments(const int& referenceID) const;
    // attempts to use index data to jump to @region, returns success/fail
    // a "successful" jump indicates no error, but not whether this region has data
    //   * thus, the method sets a flag to indicate whether there are alignments
    //     available after the jump position
    bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion);
    // loads existing data from file into memory
    bool Load(const std::string& filename);
    BamIndex::IndexType Type() const
    {
        return BamIndex::BAMTOOLS;
    }

public:
    // returns format's file extension
    static const std::string Extension();

    // internal methods
private:
    // index file ops
    void CheckMagicNumber();
    void CheckVersion();
    void CloseFile();
    bool IsDeviceOpen() const;
    void OpenFile(const std::string& filename, IBamIODevice::OpenMode mode);
    void Seek(const int64_t& position, const int origin);
    int64_t Tell() const;

    // index-creation methods
    void ClearReferenceEntry(BtiReferenceEntry& refEntry);
    void WriteBlock(const BtiBlock& block);
    void WriteBlocks(const BtiBlockVector& blocks);
    void WriteHeader();
    void WriteReferenceEntry(const BtiReferenceEntry& refEntry);

    // random-access methods
    void GetOffset(const BamRegion& region, int64_t& offset, bool* hasAlignmentsInRegion);
    void ReadBlock(BtiBlock& block);
    void ReadBlocks(const BtiReferenceSummary& refSummary, BtiBlockVector& blocks);
    void ReadReferenceEntry(BtiReferenceEntry& refEntry);

    // BTI summary data methods
    void InitializeFileSummary(const int& numReferences);
    void LoadFileSummary();
    void LoadHeader();
    void LoadNumBlocks(int& numBlocks);
    void LoadNumReferences(int& numReferences);
    void LoadReferenceSummary(BtiReferenceSummary& refSummary);
    void SkipBlocks(const int& numBlocks);

    // data members
private:
    bool m_isBigEndian;
    BtiFileSummary m_indexFileSummary;
    uint32_t m_blockSize;
    int32_t m_inputVersion;  // Version is serialized as int
    Version m_outputVersion;

    struct RaiiWrapper
    {
        IBamIODevice* Device;
        RaiiWrapper();
        ~RaiiWrapper();
    };
    RaiiWrapper m_resources;

    // static constants
private:
    static const uint32_t DEFAULT_BLOCK_LENGTH;
    static const std::string BTI_EXTENSION;
    static const char* const BTI_MAGIC;
    static const int SIZEOF_BLOCK;
};

}  // namespace Internal
}  // namespace BamTools

#endif  // BAMTOOLS_INDEX_FORMAT_H
