#include <LibBlasrConfig.h>

#ifdef USE_PBBAM

#include <hdf/HDFBaxWriter.hpp>

HDFBaxWriter::HDFBaxWriter(const std::string& filename, const std::string& basecallerVersion,
                           const std::map<char, size_t>& baseMap,
                           const std::vector<PacBio::BAM::BaseFeature>& qvsToWrite,
                           const H5::FileAccPropList& fileAccPropList)
    : HDFWriterBase(filename)
    , fileaccproplist_(fileAccPropList)
    , basecallsWriter_(nullptr)
    , regionsWriter_(nullptr)
{

    // open file
    outfile_.Open(filename_, H5F_ACC_TRUNC, fileaccproplist_);

    // Add PulseData group to the root group '/'
    AddChildGroup(outfile_.rootGroup, pulseDataGroup_, PacBio::GroupNames::pulsedata);

    if (basecallerVersion.empty()) {
        AddErrorMessage("Base caller version must be specified.");
    }
    // Create a BaseCaller writer.
    basecallsWriter_.reset(
        new HDFBaseCallsWriter(filename_, pulseDataGroup_, baseMap, basecallerVersion, qvsToWrite));
}

HDFBaxWriter::HDFBaxWriter(const std::string& filename, const std::string& basecallerVersion,
                           const std::map<char, size_t>& baseMap,
                           const std::vector<PacBio::BAM::BaseFeature>& qvsToWrite,
                           const std::vector<std::string>& regionTypes,
                           const H5::FileAccPropList& fileAccPropList)
    : HDFBaxWriter(filename, basecallerVersion, baseMap, qvsToWrite, fileAccPropList)
{
    // Create a Regions writer.
    regionsWriter_.reset(new HDFRegionsWriter(filename_, pulseDataGroup_, regionTypes));
}

HDFBaxWriter::~HDFBaxWriter(void) { this->Close(); }

void HDFBaxWriter::Flush(void)
{
    basecallsWriter_->Flush();
    if (HasRegions()) regionsWriter_->Flush();
}

std::vector<std::string> HDFBaxWriter::Errors(void)
{
    std::vector<std::string> errors = errors_;

    for (auto error : basecallsWriter_->Errors())
        errors.emplace_back(error);

    if (HasRegions()) {
        for (auto error : regionsWriter_->Errors())
            errors.emplace_back(error);
    }

    return errors;
}

void HDFBaxWriter::Close(void)
{
    if (basecallsWriter_) basecallsWriter_.reset();
    if (HasRegions() and regionsWriter_) regionsWriter_.reset();
    outfile_.Close();
}

bool HDFBaxWriter::WriteOneZmw(const SMRTSequence& seq)
{
    return basecallsWriter_->WriteOneZmw(seq);
}

bool HDFBaxWriter::WriteOneZmw(const SMRTSequence& seq,
                               const std::vector<RegionAnnotation>& regions)
{
    if (not this->WriteOneZmw(seq)) {
        return false;
    }
    if (HasRegions()) {
        if (regions.size() == 0) {
            std::vector<RegionAnnotation> fake = {
                RegionAnnotation(seq.HoleNumber(), HQRegion, 0, 0, 0)};
            return regionsWriter_->Write(fake);
        } else {
            return regionsWriter_->Write(regions);
        }
    }
    return true;
}

bool HDFBaxWriter::WriteFakeDataSets() { return basecallsWriter_->WriteFakeDataSets(); }

#endif  // end of ifdef USE_PBBAM