class to hold encoded byte arrays for individual data fields (cigar, bases, etc.) during building of a Sam More...

#include <sam_builder_data_field.h>

Public Member Functions
	SamBuilderDataField ()
	initialize a SamBuilderDataField to an empty value More...

	SamBuilderDataField (const void *copy_source, const uint32_t bytes_to_copy, const uint32_t num_elements)
	initialize a SamBuilderDataField by copying data from a raw pointer (takes no ownership of copy_source) More...

	SamBuilderDataField (std::unique_ptr< uint8_t[]> &&move_source, const uint32_t source_bytes, const uint32_t num_elements)
	initialize a SamBuilderDataField by moving an existing unique_ptr into it and taking ownership (without copying the existing data) More...

	SamBuilderDataField (SamBuilderDataField &&other)
	initialize a SamBuilderDataField via move from an existing field More...

SamBuilderDataField &	operator= (SamBuilderDataField &&other)
	move an existing SamBuildDataField into this one More...

	SamBuilderDataField (const SamBuilderDataField &other)=delete

SamBuilderDataField &	operator= (const SamBuilderDataField &other)=delete

	~SamBuilderDataField ()=default

const uint8_t *	raw_data_ptr () const
	gets a raw pointer to the data buffer More...

uint32_t	num_bytes () const
	number of bytes in the data buffer More...

uint32_t	num_elements () const
	number of elements (cigar operations, bases, etc.) in the data buffer More...

bool	empty () const
	does this field have any data? More...

void	update (const void *copy_source, const uint32_t bytes_to_copy, const uint32_t num_elements)
	update the field by copying data from a raw pointer (takes no ownership of copy_source) More...

void	update (std::unique_ptr< uint8_t[]> &&move_source, const uint32_t source_bytes, const uint32_t num_elements)
	update the field by moving an existing unique_ptr into it and taking ownership (without copying the existing data) More...

uint8_t *	copy_into (uint8_t *destination) const
	copy this field's byte array into an arbitrary location More...

Detailed Description

class to hold encoded byte arrays for individual data fields (cigar, bases, etc.) during building of a Sam

Fields can be created/updated either by copying data from raw pointers, or by moving managed pointers into them without copying. Eg.,

auto field = SamBuilderDataField{raw_pointer, num_bytes, num_elements}; // does a copy auto field = SamBuilderDataField{move(unique_ptr), num_bytes, num_elements}; // no copy

After construction, a field's value can be altered via the update() functions

Constructor & Destructor Documentation

gamgee::SamBuilderDataField::SamBuilderDataField ( )

initialize a SamBuilderDataField to an empty value

gamgee::SamBuilderDataField::SamBuilderDataField	(	const void *	copy_source,
		const uint32_t	bytes_to_copy,
		const uint32_t	num_elements
	)

explicit

initialize a SamBuilderDataField by copying data from a raw pointer (takes no ownership of copy_source)

initialize a SamBuilderDataField by copying data from a raw pointer

Note: takes no ownership of copy_source

gamgee::SamBuilderDataField::SamBuilderDataField	(	std::unique_ptr< uint8_t[]> &&	move_source,
		const uint32_t	source_bytes,
		const uint32_t	num_elements
	)

explicit

initialize a SamBuilderDataField by moving an existing unique_ptr into it and taking ownership (without copying the existing data)

initialize a SamBuilderDataField by moving an existing unique_ptr into it (without copying the existing data)

Note: takes ownership of the memory managed by move_source

gamgee::SamBuilderDataField::SamBuilderDataField ( SamBuilderDataField && other )

initialize a SamBuilderDataField via move from an existing field

gamgee::SamBuilderDataField::SamBuilderDataField ( const SamBuilderDataField & other )

delete

gamgee::SamBuilderDataField::~SamBuilderDataField ( )

default

Member Function Documentation

uint8_t * gamgee::SamBuilderDataField::copy_into ( uint8_t * destination ) const

copy this field's byte array into an arbitrary location

Returns: pointer to the byte just AFTER the end of the copied data

bool gamgee::SamBuilderDataField::empty ( ) const

inline

does this field have any data?

uint32_t gamgee::SamBuilderDataField::num_bytes ( ) const

inline

number of bytes in the data buffer

uint32_t gamgee::SamBuilderDataField::num_elements ( ) const

inline

number of elements (cigar operations, bases, etc.) in the data buffer

SamBuilderDataField & gamgee::SamBuilderDataField::operator= ( SamBuilderDataField && other )

move an existing SamBuildDataField into this one

SamBuilderDataField& gamgee::SamBuilderDataField::operator= ( const SamBuilderDataField & other )

delete

const uint8_t* gamgee::SamBuilderDataField::raw_data_ptr ( ) const

inline

gets a raw pointer to the data buffer

void gamgee::SamBuilderDataField::update	(	const void *	copy_source,
		const uint32_t	bytes_to_copy,
		const uint32_t	num_elements
	)

update the field by copying data from a raw pointer (takes no ownership of copy_source)

Note: any previous value of m_data is destroyed via the unique_ptr assignment

void gamgee::SamBuilderDataField::update	(	std::unique_ptr< uint8_t[]> &&	move_source,
		const uint32_t	source_bytes,
		const uint32_t	num_elements
	)

update the field by moving an existing unique_ptr into it and taking ownership (without copying the existing data)

Note: any previous value of m_data is destroyed via the unique_ptr assignment

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

gamgee/sam/sam_builder_data_field.h
gamgee/sam/sam_builder_data_field.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation