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#ifndef _BLASR_QUALITY_VALUE_VECTOR_IMPL_HPP_
#define _BLASR_QUALITY_VALUE_VECTOR_IMPL_HPP_
#include <pbdata/NucConversion.hpp>
template <typename T_QV>
T_QV &QualityValueVector<T_QV>::operator[](unsigned int pos) const
{
return data[pos];
}
template <typename T_QV>
QualityValueVector<T_QV>::QualityValueVector()
{
data = NULL;
// Default to phred.
qvScale = PHRED;
_length = 0;
}
template <typename T_QV>
QualityProbability QualityValueVector<T_QV>::ToProbability(unsigned int pos)
{
return QualityValueToProbability(data[pos], qvScale);
}
template <typename T_QV>
T_QV QualityValueVector<T_QV>::ToPhred(unsigned int pos)
{
if (qvScale == PHRED) {
return data[pos];
} else {
return PacBioQVToPhred(data[pos]);
}
}
template <typename T_QV>
void QualityValueVector<T_QV>::Copy(const QualityValueVector<T_QV> &rhs, const DNALength length)
{
Free();
if (rhs.Empty()) {
return;
}
Allocate(length);
std::memcpy(data, rhs.data, length * sizeof(T_QV));
}
template <typename T_QV>
void QualityValueVector<T_QV>::Copy(const std::string &rhs)
{
// Char to QualityValue
Free();
if (rhs.size() == 0) return;
Allocate(static_cast<DNALength>(rhs.size()));
for (size_t i = 0; i < rhs.size(); i++) {
data[i] = static_cast<T_QV>(rhs[i] - FASTQ_CHAR_TO_QUALITY);
}
}
template <typename T_QV>
void QualityValueVector<T_QV>::Free()
{
if (data != NULL) {
delete[] data;
data = NULL;
}
_length = 0;
}
template <typename T_QV>
void QualityValueVector<T_QV>::Allocate(unsigned int length)
{
Free();
data = ProtectedNew<T_QV>(length);
_length = static_cast<DNALength>(length);
}
template <typename T_QV>
void QualityValueVector<T_QV>::Fill(const T_QV &value)
{
memset(data, value, sizeof(T_QV) * _length);
}
template <typename T_QV>
void QualityValueVector<T_QV>::Fill(const DNALength thisStart, const DNALength fillLength,
const QualityValueVector<T_QV> &rhs, const DNALength rhsStart)
{
assert(this->_length >= thisStart + fillLength);
assert(rhs.Length() >= rhsStart + fillLength);
memcpy(&this->data[thisStart], &rhs.data[rhsStart], sizeof(T_QV) * fillLength);
}
template <typename T_QV>
bool QualityValueVector<T_QV>::Empty() const
{
return data == NULL;
}
template <typename T_QV>
void QualityValueVector<T_QV>::ShallowCopy(const QualityValueVector<T_QV> &ref, int pos,
const DNALength &length)
{
data = &ref.data[pos];
qvScale = ref.qvScale;
_length = static_cast<DNALength>(length);
}
template <typename T_QV>
void QualityValueVector<T_QV>::ResetShallowData(void)
{
data = NULL;
qvScale = PHRED;
_length = 0;
}
template <typename T_QV>
std::string QualityValueVector<T_QV>::ToString(void)
{
if (data == NULL) {
return "";
}
std::string str(static_cast<size_t>(_length), '0');
for (DNALength i = 0; i < _length; i++) {
str[i] = static_cast<char>(data[i] + FASTQ_CHAR_TO_QUALITY);
}
return str;
}
template <typename T_QV>
DNALength QualityValueVector<T_QV>::Length(void) const
{
return _length;
}
template class QualityValueVector<QualityValue>;
#endif
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