#ifndef _BLASR_FILE_SAM_HEADER_PRINTER_
#define _BLASR_FILE_SAM_HEADER_PRINTER_

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

#include <pbdata/Enumerations.h>
#include <pbdata/Types.h>
#include <alignment/datastructures/alignmentset/SAMSupplementalQVList.hpp>
#include <alignment/files/BaseSequenceIO.hpp>
#include <alignment/files/ReaderAgglomerate.hpp>
#include <pbdata/StringUtils.hpp>

/// This is a simple implementation for generating SAM Headers.
/// It is provided such that libblasr can compile with and without
/// linking to lib PBBAM.
/// * When compiled without linking to lib PBBAM, blasr should be
///   able to produce SAM output.
/// * When compiled with lib PBBAM, blasr should be able to produce
///   SAM and BAM output. If input is one or more than one BAM files,
///   @PG and @CO info will be kept.

#define REQUEST_PBBAM_ERROR() \
    assert("libblasr must be compiled with lib PBBAM to consume bam files." == 0)

class SAMHeaderItem
{
    /// SAM Header Item: key=value
public:
    SAMHeaderItem(const std::string& key, const std::string& val) : _key(key), _val(val) {}

    SAMHeaderItem(const std::string& fromString);

    std::string ToString();

private:
    std::string _key;
    std::string _val;
};

std::vector<SAMHeaderItem> MakeSAMHeaderItems(const std::string& fromString);

class SAMHeaderTag
{
public:
    SAMHeaderTag() {}

    /// ID:12345
    SAMHeaderTag(const std::string& tagName, const std::string& tagValue)
        : _tagName(tagName), _tagValue(tagValue)
    {
    }

    /// DS:READTYPE=SUBREAD;BINDKINGKIT=123456
    SAMHeaderTag(const std::string& tagName, const std::vector<SAMHeaderItem>& tagItems)
        : _tagName(tagName), _tagItems(tagItems)
    {
    }

    SAMHeaderTag(const std::string& fromString);

public:
    std::string ToString();

    std::string TagName() const;

    void AddItem(SAMHeaderItem& item);

    void AddItem(const std::string& fromString);

    void AddItems(const std::string& fromString);

private:
    std::string _tagName;
    std::string _tagValue;
    std::vector<SAMHeaderItem> _tagItems;
};

typedef std::vector<SAMHeaderTag> SAMHeaderTags;

class SAMHeaderGroup
{
public:
    SAMHeaderGroup() {}

    SAMHeaderGroup(const std::string& groupName, const SAMHeaderTags& tags)
        : _groupName(groupName), _tags(tags)
    {
    }

    SAMHeaderGroup(const std::string& fromString);

    std::string ToString();

    /// returns true if this SAMHeaderGroup contains a tag tagName.
    bool HasTag(std::string tagName);

    /// returns value of a tag if it exists, otherwise, return an empty string.
    std::string Tag(const std::string& tagName);

protected:
    std::string _groupName;

    SAMHeaderTags _tags;
};

class SAMHeaderGroupWithID : public SAMHeaderGroup
{
public:
    SAMHeaderGroupWithID() {}

    SAMHeaderGroupWithID(const std::string& fromString);

    std::string ID() const;

protected:
    std::string _id;
};

std::ostream& operator<<(std::ostream& os, SAMHeaderGroup& g);

class SAMHeaderRG : public SAMHeaderGroupWithID
{
    /// SAM Header @RG entry, containing ID, PL, PU, DS tags.
    /// ID: Read group Id Tag, which must be unique for read groups.
    /// PL: PacBio platform Tag, e.g., PacBio.
    /// PU: PacBio platform unit Tag, e.g., m1473.....p0
    /// DS: Description Items for this @RG entry, including READTYPE, BINDKINGKIT,
    ///     SEQUENCEKIT, BASECALLERVERSION.
    /// The following is an example:
    /// @RG ID:abcdefgh PL:PacBio   PU:m1473...p0   DS:READTYPE=SUBREAD;BINDINGKIT=123456;SEQUENCINGKIT=123456;BASECALLERVERSION=2.3
public:
    SAMHeaderRG(const std::string& id, const std::string& pl, const std::string& pu,
                const std::vector<SAMHeaderItem>& dsItems);

    SAMHeaderRG(const std::string& fromString);
};

class SAMHeaderPG : public SAMHeaderGroupWithID
{
public:
    SAMHeaderPG(const std::string& id, const std::string& progName, const std::string& progVersion,
                const std::string& commandLine);

    SAMHeaderPG(const std::string& fromString);
};

class SAMHeaderSQ : public SAMHeaderGroup
{
public:
    SAMHeaderSQ(const std::string& sn, const DNALength& ln, const std::string& md5);

    SAMHeaderSQ(const std::string& sn, const std::string& ln, const std::string& md5);

    SAMHeaderSQ(const std::string& fromString);
};

template <class T>
class SAMHeaderGroups
{
public:
    SAMHeaderGroups() {}

    // Add a SAM Header group regardless
    void Add(const T& group);

    void Append(const std::vector<T>& groups);

    std::string ToString();

protected:
    std::vector<T> _groups;
};

template <class T>
class SAMHeaderGroupsWithID : public SAMHeaderGroups<T>
{
public:
    SAMHeaderGroupsWithID() : SAMHeaderGroups<T>() {}

    /// Add a SAM Header group with unique ID if it does not exist.
    void Add(const T& g);

    /// Check whether a group already exists or not.
    /// \returns true if g.ID() already exists in _groups, otherwise false.
    bool Contain(const T& g);
};

typedef SAMHeaderGroupsWithID<SAMHeaderRG> SAMHeaderRGs;
// FIXME: @PG groups should have unique IDs according to SAM spec v1.5,
// However, PacBio tools such as blasr and bax2bam use prog name as prog id.
typedef SAMHeaderGroups<SAMHeaderPG> SAMHeaderPGs;
typedef SAMHeaderGroups<SAMHeaderSQ> SAMHeaderSQs;
typedef SAMHeaderGroups<std::string> SAMHeaderCOs;

class SAMHeaderPrinter
{
public:
    /// SAMHeaderPrinter constructor
    /// \param[in] sortingOrder - sorting order of alignments.
    /// \param[in] seqdb - database of target sequences.
    /// \param[in] readsFiles - input reads files, file format
    /// can be FASTA, FASTQ, BAS.H5, BAX.H5, BAM.
    /// \param[in] samQVs - samQVs that will be printed.
    /// \param[in] readType - read type, must be either SUBREAD or CCS or UNKNOWN
    /// \param[in] progName - program which calls SMAHeaderPrinter
    /// \param[in] progVersion - program version.
    /// \param[in] commandLine - command line to call program.
    SAMHeaderPrinter(const std::string& sortingOrder, SequenceIndexDatabase<FASTASequence>& seqdb,
                     const std::vector<std::string>& readsFiles,
                     const ReadType::ReadTypeEnum& readType, const SupplementalQVList& samQVs,
                     const std::string& progName, const std::string& progVersion,
                     const std::string& commandLine);

    /// \returns SAM header in string.
    std::string ToString();

public:
#ifdef USE_PBBAM
    /// Converts this SAMHeader to PacBio::BAM::BamHeader, must be compiled with pbbam
    /// \returns a PacBio::BAM::BamHeader.
    PacBio::BAM::BamHeader ToBamHeader();
#endif

    /// Add a SAM Header @RG entry, including the following tags:
    /// ID (identifier), PL (platform), PU (platform unit),
    /// DS (description, which may have many items)
    SAMHeaderPrinter& AddRG(std::string& id, std::string& pl, std::string& pu, std::string& ds);

    /// Add a SAM Header @RG entry from string, which may contain arbitary tags.
    SAMHeaderPrinter& AddRG(const std::string& fromString);

    /// Add a SAM Header @PG entry, including the following tags:
    /// ID, progName, progVersion, commandLine. @PG must have unique ID.
    SAMHeaderPrinter& AddPG(std::string& id, std::string& progName, std::string& progVersion,
                            std::string& commandLine);

    /// Add a SAM Header @PG entry from string, which may contain arbitary tags.
    SAMHeaderPrinter& AddPG(const std::string& fromString);

    /// Add a SAM Header @CO entry from string.
    SAMHeaderPrinter& AddCO(const std::string& fromString);

private:
    const std::string& _sortingOrder;
    const std::vector<std::string>& _readsFiles;
    SequenceIndexDatabase<FASTASequence>& _seqdb;
    FileType fileType;

    SAMHeaderGroup _hd;  //@HD VN:? SO:? pb:?
    SAMHeaderSQs _sqs;   //@SQ SN:? LN:? M5:?
    SAMHeaderRGs _rgs;   //@RG ID:? PU:? PL:? DS:key=val;key=val;key=val
    SAMHeaderPGs _pgs;   //@PG VN:? CL:?
    SAMHeaderCOs _cos;   //@CO

private:
    /// \returns SAMHeaderGroup @HD
    static SAMHeaderGroup MakeHD(const std::string& sortingOrder);

    /// \returns SAMHeaderSQs, SAM Header @SQ groups
    SAMHeaderSQs MakeSQs(SequenceIndexDatabase<FASTASequence>& seqdb);

    /// \returns SAMHeaderRGs @RG groups
    /// \param[in] readsFiles - incoming reads files in BAM or other formats
    /// \param[in] readType - read type, must be either SUBREAD or CCS or UNKNOWN
    /// \param[in] samQVs - SupplementalQVList, an object that handles which
    ///                      QVs to print in SAM/BAM file.
    SAMHeaderRGs MakeRGs(const std::vector<std::string>& readsFiles,
                         const ReadType::ReadTypeEnum& readType, const SupplementalQVList& samQVs);

    /// \returns SAMHeaderPGs @PG groups
    /// \param[in] readsFiles - incoming reads files in BAM or other formats
    /// \param[in] progName - program which calls SMAHeaderPrinter
    /// \param[in] progVersion - program version.
    /// \param[in] commandLine - command line to call program.
    SAMHeaderPGs MakePGs(const std::vector<std::string>& readsFiles, const std::string& progName,
                         const std::string& progVersion, const std::string& commandLine);

    /// \returns SAMHeaderPGs @CO groups
    /// \param[in] readsFiles - incoming reads files in BAM or other formats
    SAMHeaderCOs MakeCOs(const std::vector<std::string>& readsFiles);
};

// template<class T> SAMHeaderGroups
template <class T>
void SAMHeaderGroups<T>::Add(const T& group)
{
    this->_groups.push_back(group);
}

template <class T>
void SAMHeaderGroups<T>::Append(const std::vector<T>& groups)
{
    for (int i = 0; i < int(groups.size()); i++) {
        this->Add(groups[i]);
    }
}

template <class T>
std::string SAMHeaderGroups<T>::ToString()
{
    std::stringstream ss;
    for (size_t i = 0; i < this->_groups.size(); i++) {
        ss << this->_groups[i] << std::endl;
    }
    return ss.str();
}

// template<class T> SAMHeaderGroupsWithID
template <class T>
void SAMHeaderGroupsWithID<T>::Add(const T& g)
{
    if (not this->Contain(g)) {
        this->_groups.push_back(g);
    }
}

template <class T>
bool SAMHeaderGroupsWithID<T>::Contain(const T& g)
{
    typename std::vector<T>::iterator it;
    for (it = this->_groups.begin(); it < this->_groups.end(); it++) {
        if ((*it).ID() == g.ID()) {
            return true;
        }
    }
    return false;
}
#endif