vg::multipath_alignment_t Class Reference

#include <multipath_alignment.hpp>

Public Types
enum	anno_type_t { Null = 0 , Double = 2 , Bool = 3 , String = 4 }

Public Member Functions
	multipath_alignment_t ()
	multipath_alignment_t (const multipath_alignment_t &other)
	multipath_alignment_t (multipath_alignment_t &&other)
	~multipath_alignment_t ()
multipath_alignment_t &	operator= (const multipath_alignment_t &other)
multipath_alignment_t &	operator= (multipath_alignment_t &&other)
const string &	sequence () const
string *	mutable_sequence ()
void	set_sequence (const string &s)
const string &	quality () const
string *	mutable_quality ()
void	set_quality (const string &q)
const vector< subpath_t > &	subpath () const
const subpath_t &	subpath (size_t i) const
vector< subpath_t > *	mutable_subpath ()
subpath_t *	mutable_subpath (size_t i)
subpath_t *	add_subpath ()
void	clear_subpath ()
size_t	subpath_size () const
int32_t	mapping_quality () const
void	set_mapping_quality (int32_t q)
const vector< uint32_t > &	start () const
uint32_t	start (size_t i) const
vector< uint32_t > *	mutable_start ()
void	set_start (size_t i, uint32_t s)
void	add_start (uint32_t s)
void	clear_start ()
size_t	start_size () const
bool	has_start () const
void	set_annotation (const string &annotation_name)
void	set_annotation (const string &annotation_name, double value)
void	set_annotation (const string &annotation_name, bool value)
void	set_annotation (const string &annotation_name, const string &value)
void	clear_annotation (const string &annotation_name)
bool	has_annotation (const string &annotation_name) const
pair< anno_type_t, const void * >	get_annotation (const string &annotation_name) const
void	for_each_annotation (function< void(const string &, anno_type_t, const void *)> lambda) const

Static Public Member Functions
template<typename AnnotationType>
static anno_type_t	anno_type_tag ()

Private Attributes
string	_sequence
string	_quality
vector< subpath_t >	_subpath
int32_t	_mapping_quality
vector< uint32_t >	_start
map< string, pair< anno_type_t, void * > >	_annotation

Member Enumeration Documentation

anno_type_t

enum vg::multipath_alignment_t::anno_type_t

Enumerator
Null
Double
Bool
String

Constructor & Destructor Documentation

multipath_alignment_t() [1/3]

vg::multipath_alignment_t::multipath_alignment_t

(

)

multipath_alignment_t() [2/3]

vg::multipath_alignment_t::multipath_alignment_t

(

const multipath_alignment_t &

other

)

multipath_alignment_t() [3/3]

vg::multipath_alignment_t::multipath_alignment_t

(

multipath_alignment_t &&

other

)

~multipath_alignment_t()

vg::multipath_alignment_t::~multipath_alignment_t

(

)

Member Function Documentation

add_start()

void vg::multipath_alignment_t::add_start ( uint32_t s )

inline

add_subpath()

subpath_t * vg::multipath_alignment_t::add_subpath ( )

inline

anno_type_tag()

template<typename AnnotationType>

multipath_alignment_t::anno_type_t vg::multipath_alignment_t::anno_type_tag ( )

static

Function to get the right tag to use to look for an annotation of a particular type.

clear_annotation()

void vg::multipath_alignment_t::clear_annotation

(

const string &

annotation_name

)

clear_start()

void vg::multipath_alignment_t::clear_start ( )

inline

clear_subpath()

void vg::multipath_alignment_t::clear_subpath ( )

inline

for_each_annotation()

void vg::multipath_alignment_t::for_each_annotation

(

function< void(const string &, anno_type_t, const void *)>

lambda

)

const

get_annotation()

pair< multipath_alignment_t::anno_type_t, const void * > vg::multipath_alignment_t::get_annotation

(

const string &

annotation_name

)

const

has_annotation()

bool vg::multipath_alignment_t::has_annotation

(

const string &

annotation_name

)

const

has_start()

bool vg::multipath_alignment_t::has_start ( ) const

inline

mapping_quality()

int32_t vg::multipath_alignment_t::mapping_quality ( ) const

inline

mutable_quality()

string * vg::multipath_alignment_t::mutable_quality ( )

inline

mutable_sequence()

string * vg::multipath_alignment_t::mutable_sequence ( )

inline

mutable_start()

vector< uint32_t > * vg::multipath_alignment_t::mutable_start ( )

inline

mutable_subpath() [1/2]

vector< subpath_t > * vg::multipath_alignment_t::mutable_subpath ( )

inline

mutable_subpath() [2/2]

subpath_t * vg::multipath_alignment_t::mutable_subpath ( size_t i )

inline

operator=() [1/2]

multipath_alignment_t & vg::multipath_alignment_t::operator=

(

const multipath_alignment_t &

other

)

operator=() [2/2]

multipath_alignment_t & vg::multipath_alignment_t::operator=

(

multipath_alignment_t &&

other

)

quality()

const string & vg::multipath_alignment_t::quality ( ) const

inline

sequence()

const string & vg::multipath_alignment_t::sequence ( ) const

inline

set_annotation() [1/4]

void vg::multipath_alignment_t::set_annotation

(

const string &

annotation_name

)

set_annotation() [2/4]

void vg::multipath_alignment_t::set_annotation	(	const string &	annotation_name,
		bool	value )

set_annotation() [3/4]

void vg::multipath_alignment_t::set_annotation	(	const string &	annotation_name,
		const string &	value )

set_annotation() [4/4]

void vg::multipath_alignment_t::set_annotation	(	const string &	annotation_name,
		double	value )

set_mapping_quality()

void vg::multipath_alignment_t::set_mapping_quality ( int32_t q )

inline

set_quality()

void vg::multipath_alignment_t::set_quality ( const string & q )

inline

set_sequence()

void vg::multipath_alignment_t::set_sequence ( const string & s )

inline

set_start()

void vg::multipath_alignment_t::set_start ( size_t i, uint32_t s )

inline

start() [1/2]

const vector< uint32_t > & vg::multipath_alignment_t::start ( ) const

inline

start() [2/2]

uint32_t vg::multipath_alignment_t::start ( size_t i ) const

inline

start_size()

size_t vg::multipath_alignment_t::start_size ( ) const

inline

subpath() [1/2]

const vector< subpath_t > & vg::multipath_alignment_t::subpath ( ) const

inline

subpath() [2/2]

const subpath_t & vg::multipath_alignment_t::subpath ( size_t i ) const

inline

subpath_size()

size_t vg::multipath_alignment_t::subpath_size ( ) const

inline

Member Data Documentation

_annotation

map<string, pair<anno_type_t, void*> > vg::multipath_alignment_t::_annotation

private

_mapping_quality

int32_t vg::multipath_alignment_t::_mapping_quality

private

_quality

string vg::multipath_alignment_t::_quality

private

_sequence

string vg::multipath_alignment_t::_sequence

private

_start

vector<uint32_t> vg::multipath_alignment_t::_start

private

_subpath

vector<subpath_t> vg::multipath_alignment_t::_subpath

private

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

• src/multipath_alignment.hpp
• src/multipath_alignment.cpp