handlegraph Namespace Reference

Namespaces
	algorithms

Classes
struct	BoolReturningWrapper
struct	BoolReturningWrapper< Iteratee, false >
struct	BoolReturningWrapper< Iteratee, true >
class	BuildableSnarlDecomposition
class	DeletableHandleGraph
class	ExpandingOverlayGraph
struct	handle_t
	Represents a traversal of a node in a graph in a particular direction. More...
class	HandleGraph
class	MutableHandleGraph
class	MutablePathDeletableHandleGraph
class	MutablePathHandleGraph
class	MutablePathMetadata
class	MutablePathMutableHandleGraph
class	NamedNodeBackTranslation
struct	net_handle_t
struct	number_bool_packing
	Define a way to pack an integer and an orientation bit into a handle_t. More...
struct	path_handle_t
	Represents the internal id of a path entity. More...
class	PathForEachSocket
class	PathHandleGraph
class	PathMetadata
class	PathPositionHandleGraph
class	RankedHandleGraph
struct	return_type_of
struct	return_type_of< Returns(*)(Args...)>
struct	return_type_of< Returns(Owner::*)(Args...) const >
struct	return_type_of< Returns(Owner::*)(Args...)>
class	Serializable
class	SerializableHandleGraph
class	SnarlDecomposition
struct	step_handle_t
	A step handle is an opaque reference to a single step of an oriented node on a path in a graph. More...
class	TriviallySerializable
class	VectorizableHandleGraph

Typedefs
using	oriented_node_range_t = std::tuple< nid_t, bool, size_t, size_t >
typedef long long int	nid_t
typedef nid_t	id_t
typedef std::size_t	offset_t
	Represents an offset. More...
typedef offset_t	off_t
typedef std::pair< offset_t, offset_t >	subrange_t
	Represents a range of offsets, 0-based, end-exclusive. More...
typedef std::tuple< nid_t, bool, offset_t >	pos_t
	Represents a position. More...
typedef std::pair< handle_t, handle_t >	edge_t
	Represents an edge in terms of its endpoints. More...

Enumerations
enum	PathSense { PathSense::GENERIC, PathSense::REFERENCE, PathSense::HAPLOTYPE }
	Represents a sense that a path can have. More...

Functions
bool	operator== (const handle_t &a, const handle_t &b)
	Define equality on handles. More...
bool	operator!= (const handle_t &a, const handle_t &b)
	Define inequality on handles. More...
bool	operator== (const path_handle_t &a, const path_handle_t &b)
	Define equality on path handles. More...
bool	operator!= (const path_handle_t &a, const path_handle_t &b)
	Define inequality on path handles. More...
bool	operator== (const step_handle_t &a, const step_handle_t &b)
	Define equality on step handles. More...
bool	operator!= (const step_handle_t &a, const step_handle_t &b)
	Define inequality on step handles. More...
bool	operator== (const net_handle_t &a, const net_handle_t &b)
	Define equality on net handles. More...
bool	operator!= (const net_handle_t &a, const net_handle_t &b)
	Define inequality on net handles. More...
uint64_t &	as_integer (handle_t &handle)
	View a handle as an integer. More...
const uint64_t &	as_integer (const handle_t &handle)
	View a const handle as a const integer. More...
handle_t &	as_handle (uint64_t &value)
	View an integer as a handle. More...
const handle_t &	as_handle (const uint64_t &value)
	View a const integer as a const handle. More...
bool	operator< (const handle_t &a, const handle_t &b)
	It's convenient to be able to sort handles. More...
uint64_t &	as_integer (path_handle_t &handle)
	View a path handle as an integer. More...
const uint64_t &	as_integer (const path_handle_t &handle)
	View a const path handle as a const integer. More...
path_handle_t &	as_path_handle (uint64_t &value)
	View an integer as a path handle. More...
const path_handle_t &	as_path_handle (const uint64_t &value)
	View a const integer as a const path handle. More...
bool	operator< (const path_handle_t &a, const path_handle_t &b)
	It's convenient to be able to sort path handles. More...
int64_t *	as_integers (step_handle_t &step_handle)
	View a step handle as an integer array. More...
const int64_t *	as_integers (const step_handle_t &step_handle)
	View a const step handle as a const integer array. More...
bool	operator< (const step_handle_t &a, const step_handle_t &b)
	Sort of step handles is based on first then second integers. More...
uint64_t &	as_integer (net_handle_t &handle)
	View a net_handle as an integer. More...
const uint64_t &	as_integer (const net_handle_t &handle)
	View a const net_handle as a const integer. More...
net_handle_t &	as_net_handle (uint64_t &value)
	View an integer as a net handle. More...
const net_handle_t &	as_net_handle (const uint64_t &value)
	View a const integer as a const handle. More...
bool	operator< (const net_handle_t &a, const net_handle_t &b)
	It's convenient to be able to sort handles. More...

Typedef Documentation

edge_t

typedef std::pair<handle_t, handle_t> handlegraph::edge_t

Represents an edge in terms of its endpoints.

id_t

typedef nid_t handlegraph::id_t

nid_t

typedef long long int handlegraph::nid_t

Represents an id. We use "long long int" here so that we resolve to a consistent C-level type across platforms. On Mac, int64_t is "long long" while on Linux it is just "long", and generated code that resolves all typedefs (i.e. Python bindings) is thus not portable between them if we use int64_t.

off_t

typedef offset_t handlegraph::off_t

offset_t

typedef std::size_t handlegraph::offset_t

Represents an offset.

oriented_node_range_t

using handlegraph::oriented_node_range_t = typedef std::tuple<nid_t, bool, size_t, size_t>

Represents a range along an oriented node in a graph. The range is counted on the specified strand of the node, and consists of a start and a length.

pos_t

typedef std::tuple<nid_t, bool, offset_t> handlegraph::pos_t

Represents a position.

subrange_t

typedef std::pair<offset_t, offset_t> handlegraph::subrange_t

Represents a range of offsets, 0-based, end-exclusive.

Enumeration Type Documentation

PathSense

enum handlegraph::PathSense

strong

Represents a sense that a path can have.

Enumerator
GENERIC
REFERENCE
HAPLOTYPE

Function Documentation

as_handle() [1/2]

const handle_t& handlegraph::as_handle ( const uint64_t &  value )

inline

View a const integer as a const handle.

as_handle() [2/2]

handle_t& handlegraph::as_handle ( uint64_t &  value )

inline

View an integer as a handle.

as_integer() [1/6]

const uint64_t& handlegraph::as_integer ( const handle_t &  handle )

inline

View a const handle as a const integer.

as_integer() [2/6]

const uint64_t& handlegraph::as_integer ( const net_handle_t &  handle )

inline

View a const net_handle as a const integer.

as_integer() [3/6]

const uint64_t& handlegraph::as_integer ( const path_handle_t &  handle )

inline

View a const path handle as a const integer.

as_integer() [4/6]

uint64_t& handlegraph::as_integer ( handle_t &  handle )

inline

View a handle as an integer.

as_integer() [5/6]

uint64_t& handlegraph::as_integer ( net_handle_t &  handle )

inline

View a net_handle as an integer.

as_integer() [6/6]

uint64_t& handlegraph::as_integer ( path_handle_t &  handle )

inline

View a path handle as an integer.

as_integers() [1/2]

const int64_t* handlegraph::as_integers ( const step_handle_t &  step_handle )

inline

View a const step handle as a const integer array.

as_integers() [2/2]

int64_t* handlegraph::as_integers ( step_handle_t &  step_handle )

inline

View a step handle as an integer array.

as_net_handle() [1/2]

const net_handle_t& handlegraph::as_net_handle ( const uint64_t &  value )

inline

View a const integer as a const handle.

as_net_handle() [2/2]

net_handle_t& handlegraph::as_net_handle ( uint64_t &  value )

inline

View an integer as a net handle.

as_path_handle() [1/2]

const path_handle_t& handlegraph::as_path_handle ( const uint64_t &  value )

inline

View a const integer as a const path handle.

as_path_handle() [2/2]

path_handle_t& handlegraph::as_path_handle ( uint64_t &  value )

inline

View an integer as a path handle.

operator!=() [1/4]

bool handlegraph::operator!=	(	const handle_t &	a,
		const handle_t &	b
	)

Define inequality on handles.

operator!=() [2/4]

bool handlegraph::operator!=	(	const net_handle_t &	a,
		const net_handle_t &	b
	)

Define inequality on net handles.

operator!=() [3/4]

bool handlegraph::operator!=	(	const path_handle_t &	a,
		const path_handle_t &	b
	)

Define inequality on path handles.

operator!=() [4/4]

bool handlegraph::operator!=	(	const step_handle_t &	a,
		const step_handle_t &	b
	)

Define inequality on step handles.

operator<() [1/4]

bool handlegraph::operator< ( const handle_t &  a, const handle_t &  b  )

inline

It's convenient to be able to sort handles.

operator<() [2/4]

bool handlegraph::operator< ( const net_handle_t &  a, const net_handle_t &  b  )

inline

It's convenient to be able to sort handles.

operator<() [3/4]

bool handlegraph::operator< ( const path_handle_t &  a, const path_handle_t &  b  )

inline

It's convenient to be able to sort path handles.

operator<() [4/4]

bool handlegraph::operator< ( const step_handle_t &  a, const step_handle_t &  b  )

inline

Sort of step handles is based on first then second integers.

operator==() [1/4]

bool handlegraph::operator==	(	const handle_t &	a,
		const handle_t &	b
	)

Define equality on handles.

operator==() [2/4]

bool handlegraph::operator==	(	const net_handle_t &	a,
		const net_handle_t &	b
	)

Define equality on net handles.

operator==() [3/4]

bool handlegraph::operator==	(	const path_handle_t &	a,
		const path_handle_t &	b
	)

Define equality on path handles.

operator==() [4/4]

bool handlegraph::operator==	(	const step_handle_t &	a,
		const step_handle_t &	b
	)

Define equality on step handles.