PackedSequenceData Class Reference

Inheritance diagram for PackedSequenceData:

Collaboration diagram for PackedSequenceData:

Public Member Functions
void	reserve (size_t baseCount)
size_t	size ()
void	clear ()
uint8_t	operator[] (size_t index)
void	push_back (uint8_t base)
char	operator[] (PackedVectorIndex_t baseIndex)
void	set (PackedVectorIndex_t baseIndex, char value)
void	push_back (char value)
Public Member Functions inherited from PackedVector< PackedAccess_4Bit, PackedAssign_4Bit, Packed4BitElementCount2Bytes >
uint32_t	operator[] (uint32_t i)
void	set (uint32_t i, uint32_t v)
size_t	getElementCount () const
double	getUtilization ()
void	reserve (uint32_t reserveElements)
size_t	size ()
void	resize (uint32_t newSize)
void	push_back (uint32_t value)

Additional Inherited Members
Protected Attributes inherited from PackedVector< PackedAccess_4Bit, PackedAssign_4Bit, Packed4BitElementCount2Bytes >
std::vector< uint8_t >	m_data
size_t	m_elementCount
double	m_growthRateMultiplier
double	m_growthRateAdder

Detailed Description

Definition at line 381 of file GenomeSequence.cpp.

Member Function Documentation

clear()

void PackedSequenceData::clear ( )

inline

Definition at line 398 of file GenomeSequence.cpp.

{m_packedBases.clear(); m_baseCount = 0;}

operator[]() [1/2]

char PackedSequenceData::operator[] ( PackedVectorIndex_t baseIndex )

inline

Definition at line 253 of file ReferenceSequence.h.

    {
        return BaseAsciiMap::int2base[ (static_cast<PackedVector4Bit_t>(*this))[baseIndex]];
    }

operator[]() [2/2]

uint8_t PackedSequenceData::operator[] ( size_t index )

inline

Definition at line 399 of file GenomeSequence.cpp.

    {
        return (m_packedBases[index>>1] >> ((index&0x1)<<2)) & 0xf;
    }

push_back()

void PackedSequenceData::push_back ( char value )

inline

Definition at line 261 of file ReferenceSequence.h.

    {
        this->PackedVector4Bit_t::push_back(BaseAsciiMap::base2int[(uint32_t) value]);
    }

reserve()

void PackedSequenceData::reserve ( size_t baseCount )

inline

Definition at line 396 of file GenomeSequence.cpp.

{m_packedBases.reserve(baseCount/2);}

set()

void PackedSequenceData::set ( PackedVectorIndex_t baseIndex, char value )

inline

Definition at line 257 of file ReferenceSequence.h.

    {
        this->PackedVector4Bit_t::set(baseIndex, BaseAsciiMap::base2int[(uint32_t) value]);
    }

size()

size_t PackedSequenceData::size ( )

inline

Definition at line 397 of file GenomeSequence.cpp.

{return m_baseCount;}

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The documentation for this class was generated from the following files:

• general/GenomeSequence.cpp
• general/ReferenceSequence.h