#include <alignment/simulator/QualitySample.hpp>

void QualitySample::CopyFromSequence(SMRTSequence &seq, int pos)
{
    qv[0] = seq.qual[pos];
    qv[1] = seq.deletionQV[pos];
    qv[2] = seq.insertionQV[pos];
    qv[3] = seq.substitutionQV[pos];
    tags[0] = seq.deletionTag[pos];
    tags[1] = seq.substitutionTag[pos];
    frameValues[0] = seq.pulseIndex[pos];
    frameValues[1] = seq.preBaseFrames[pos];
    frameValues[2] = seq.widthInFrames[pos];
}

void QualitySample::Write(std::ofstream &out)
{
    out.write((char *)qv, sizeof(qv[0]) * NQV);
    out.write((char *)frameValues, sizeof(frameValues[0]) * NFV);
    out.write((char *)tags, sizeof(tags[0]) * NT);
}

void QualitySample::Read(std::ifstream &in)
{
    in.read((char *)qv, sizeof(QualityValue) * NQV);
    in.read((char *)frameValues, sizeof(frameValues[0]) * NFV);
    in.read((char *)tags, sizeof(tags[0]) * NT);
}

void QualitySample::CreateFromRead(SMRTSequence &seq, DNALength pos)
{
    /*
     * For now create with a static set of values:
     * qvs:
     * 0 QualityValue
     * 1 DeletionQV
     * 2 InsertionQV
     * 3 SubstitutionQV
     * tags:
     * 0 DeletionTag
     * 1 SubstitutionTag
     * PulseData
     * 0 PulseIndex
     * 1 PreBaseFrames
     * 2 WidthInFrames
     */
    //		qv.resize(4);
    std::fill(&qv[0], &qv[NQV], 0);
    if (seq.qual.Empty() == false) {
        qv[0] = seq.qual[pos];
    }
    if (seq.deletionQV.Empty() == false) {
        qv[1] = seq.deletionQV[pos];
    }
    if (seq.insertionQV.Empty() == false) {
        qv[2] = seq.insertionQV[pos];
    }
    if (seq.substitutionQV.Empty() == false) {
        qv[3] = seq.substitutionQV[pos];
    }
    std::fill(&tags[0], &tags[NT], 0);
    if (seq.deletionTag) {
        tags[0] = seq.deletionTag[pos];
    }
    if (seq.substitutionTag) {
        tags[1] = seq.substitutionTag[pos];
    }

    std::fill(&frameValues[0], &frameValues[NFV], 0);
    if (seq.pulseIndex) {
        frameValues[0] = seq.pulseIndex[pos];
    }

    if (seq.preBaseFrames) {
        frameValues[1] = seq.preBaseFrames[pos];
    }

    if (seq.widthInFrames) {
        frameValues[2] = seq.widthInFrames[pos];
    }
}