#include <pbdata/FASTASequence.hpp>

#include <cstdlib>

FASTASequence::FASTASequence() : DNASequence()
{
    title = NULL;
    titleLength = 0;
    deleteTitleOnExit = false;
    // If deleteTitleOnExist is false, whether to delete title
    // or not should depend on deleteOnExit; otherwise, delete title
    // regardless of deleteOnExit.
}

void FASTASequence::PrintSeq(std::ostream &out, int lineLength, char delim) const
{
    out << delim;
    if (title) out << title;
    out << std::endl;
    static_cast<const DNASequence *>(this)->PrintSeq(out, lineLength);
}

int FASTASequence::GetStorageSize() const
{
    if (!title) return DNASequence::GetStorageSize();
    return strlen(title) + DNASequence::GetStorageSize();
}

std::string FASTASequence::GetName() const
{
    std::string name;
    int i;
    for (i = 0; i < titleLength; i++) {
        if (title[i] != ' ' && title[i] != '\t' && title[i] != '\n' && title[i] != '\r') {
            name.push_back(title[i]);
        } else {
            break;
        }
    }
    return name;
}

void FASTASequence::ShallowCopy(const FASTASequence &rhs)
{
    CheckBeforeCopyOrReference(rhs, "FASTASequence");
    FASTASequence::Free();

    static_cast<DNASequence *>(this)->ShallowCopy(rhs);

    title = rhs.title;
    titleLength = rhs.titleLength;
    deleteTitleOnExit = false;
}

std::string FASTASequence::GetTitle() const { return std::string(title); }

// Delete title if this FASTASequence is under control or
// only title is under control.
void FASTASequence::DeleteTitle()
{
    if (deleteOnExit or deleteTitleOnExit) {
        if (title != NULL) {
            delete[] title;
        }
    }  // otherwise, title is controlled by another obj
    title = NULL;
    titleLength = 0;
    deleteTitleOnExit = false;
}

void FASTASequence::CopyTitle(const char *str, int strlen)
{
    FASTASequence::DeleteTitle();

    // No segfault when str is NULL;
    if (str == NULL) {
        title = NULL;
        titleLength = 0;
    } else {
        title = new char[strlen + 1];
        memcpy(title, str, strlen);
        titleLength = strlen;
        title[titleLength] = '\0';
    }

    // In some cases, (e.g., when ReferenceSubstring and CopyTitle
    // are called together), this Sequence may only have control over
    // title but not seq.
    deleteTitleOnExit = true;
}

void FASTASequence::CopyTitle(std::string str)
{
    FASTASequence::CopyTitle(str.c_str(), str.size());
}

void FASTASequence::GetFASTATitle(std::string &fastaTitle) const
{
    // look for the first space, and return the string until there.
    int i;
    for (i = 0; i < titleLength; i++) {
        if (title[i] == ' ' or title[i] == '\t') {
            break;
        }
    }
    fastaTitle.assign(title, i);
}

// Copy rhs.seq[readStart:readEnd] to this Sequence.
void FASTASequence::CopySubsequence(FASTASequence &rhs, int readStart, int readEnd)
{
    CheckBeforeCopyOrReference(rhs, "FASTASequence");

    // Free before copying anything
    FASTASequence::Free();

    if (readEnd == -1) {
        readEnd = rhs.length;
    }

    if (readEnd > readStart) {
        length = readEnd - readStart;
        DNASequence::Copy(rhs, readStart, length);
    } else {
        seq = NULL;
        length = 0;
        deleteOnExit = true;
    }
    FASTASequence::CopyTitle(rhs.title);
}

void FASTASequence::AppendToTitle(std::string str)
{
    int newLength = titleLength + str.size() + 1;
    if (newLength == 0) {
        DeleteTitle();
        return;
    }

    char *tmpTitle = new char[newLength];
    memcpy(tmpTitle, title, titleLength);
    memcpy(&tmpTitle[titleLength], str.c_str(), str.size());
    tmpTitle[newLength - 1] = '\0';
    delete[] title;
    title = tmpTitle;
    titleLength = newLength;
    deleteTitleOnExit = true;
}

void FASTASequence::Assign(FASTASequence &rhs) { *this = (FASTASequence &)rhs; }

// Create a reverse complement FASTASequence of *this and assign to rhs.
void FASTASequence::MakeRC(FASTASequence &rhs, DNALength rhsPos, DNALength rhsLength)
{
    rhs.Free();
    DNASequence::MakeRC((DNASequence &)rhs, rhsPos, rhsLength);
    if (title != NULL) {
        (static_cast<FASTASequence *>(&rhs))->CopyTitle(title);
    }
}

// Reverse complement sequence, don't change the title
FASTASequence &FASTASequence::ReverseComplementSelf(void)
{
    FASTASequence rc;
    MakeRC(rc);
    Copy(rc);
    return *this;
}

void FASTASequence::operator=(const FASTASequence &rhs)
{
    CheckBeforeCopyOrReference(rhs, "FASTASequence");

    // Free before copying anything
    FASTASequence::Free();

    // Copy seq from rhs
    ((DNASequence *)this)->Copy((DNASequence &)rhs);

    assert(deleteOnExit);

    // Copy title from rhs
    FASTASequence::CopyTitle(rhs.title, rhs.titleLength);

    assert(deleteOnExit);
}

void FASTASequence::Copy(const std::string &rhsTitle, const std::string &rhsSeq)
{
    this->Copy(rhsSeq);
    this->CopyTitle(rhsTitle);
}

void FASTASequence::Copy(const std::string &rhsSeq)
{
    (static_cast<DNASequence *>(this))->Copy(rhsSeq);
}

void FASTASequence::Copy(const FASTASequence &rhs) { *this = (FASTASequence &)rhs; }

#ifdef USE_PBBAM
void FASTASequence::Copy(const PacBio::BAM::BamRecord &record)
{
    FASTASequence::Copy(record.Impl().Name(), record.Sequence());
}
#endif

void FASTASequence::Free()
{
    // Delete title if title is under control, reset deleteTitleOnExit.
    FASTASequence::DeleteTitle();

    // Delete seq if under control, reset deleteOnExit.
    // Don't call Free() before calling DeleteTitle().
    DNASequence::Free();
}

template DNALength ResizeSequence<FASTASequence>(FASTASequence &, DNALength);