vg::ZipCode Class Reference

#include <zip_code.hpp>

Classes
struct	chain_code_t
struct	decoder_t
struct	node_code_t
struct	snarl_code_t

Public Types
enum	code_type_t {   NODE = 1, CHAIN, REGULAR_SNARL, IRREGULAR_SNARL,   CYCLIC_SNARL, ROOT_SNARL, ROOT_CHAIN, ROOT_NODE,   EMPTY }
typedef std::uint64_t	code_type

Public Member Functions
void	fill_in_zipcode (const SnarlDistanceIndex &distance_index, const vg::pos_t &pos, bool fill_in_decoder=true)
void	fill_in_zipcode_from_payload (const gbwtgraph::Payload &payload)
gbwtgraph::Payload	get_payload_from_zip () const
size_t	byte_count () const
	How many bytes were used to store this zipcode? More...
bool	operator== (const ZipCode &other) const
	Equality operator. More...
std::vector< size_t >	to_vector () const
	Dump to a normal vector. More...
void	from_vector (const std::vector< size_t > &values)
	Load from a normal vector. More...
node_code_t	unpack_node_code (size_t zipcode_level) const
chain_code_t	unpack_chain_code (size_t zipcode_level) const
snarl_code_t	unpack_snarl_code (size_t zipcode_level) const
void	fill_in_full_decoder ()
	Go through the entire zipcode and fill in the decoder. More...
bool	fill_in_next_decoder ()
size_t	max_depth () const
	What is the maximum depth of this zipcode? More...
size_t	decoder_length () const
	How many codes in the zipcode have been decoded? More...
ZipCode::code_type_t	get_code_type (const size_t &depth) const
	What type of snarl tree node is at the given depth (index into the zipcode) More...
size_t	get_length (const size_t &depth, bool get_chain_component_length=false) const
size_t	get_rank_in_snarl (const size_t &depth) const
	Get the rank of a node/snarl in a snarl. Throw an exception if it isn't the child of a snarl. More...
size_t	get_snarl_child_count (const size_t &depth, const SnarlDistanceIndex *distance_index=nullptr) const
	Get the number of children in a snarl. Throw an exception if it isn't a snarl. More...
size_t	get_offset_in_chain (const size_t &depth, const SnarlDistanceIndex *distance_index=nullptr) const
size_t	get_chain_component (const size_t &depth) const
size_t	get_last_chain_component (const size_t &depth, bool get_end=false) const
bool	get_is_looping_chain (const size_t &depth) const
bool	get_is_reversed_in_parent (const size_t &depth) const
	Is the snarl tree node backwards relative to its parent. More...
net_handle_t	get_net_handle (const size_t &depth, const SnarlDistanceIndex *distance_index) const
net_handle_t	get_net_handle_slow (nid_t id, const size_t &depth, const SnarlDistanceIndex *distance_index, const net_handle_t *child_handle=nullptr) const
size_t	get_distance_index_address (const size_t &depth) const
size_t	get_distance_to_snarl_bound (const size_t &depth, bool snarl_start, bool left_side) const
	The minimum distance from start or end of the snarl to the left or right side of the child. More...
bool	is_externally_start_end_connected (const size_t &depth) const
bool	is_externally_start_start_connected (const size_t &depth) const
bool	is_externally_end_end_connected (const size_t &depth) const
void	dump (std::ostream &out) const
MIPayload	get_payload_from_zipcode (nid_t id, const SnarlDistanceIndex &distance_index, hash_map< size_t, net_handle_t > *component_to_net_handle=nullptr) const
net_identifier_t	get_identifier (size_t depth) const

Static Public Member Functions
static size_t	minimum_distance_between (ZipCode &zip1, const pos_t &pos1, ZipCode &zip2, const pos_t &pos2, const SnarlDistanceIndex &distance_index, size_t distance_limit=std::numeric_limits< size_t >::max(), bool undirected_distance=false, const HandleGraph *graph=nullptr)
static bool	is_farther_than (const ZipCode &zip1, const ZipCode &zip2, const size_t &limit)
static tuple< size_t, size_t, size_t >	get_top_level_chain_offset ()
const static bool	is_equal (const ZipCode &zip1, const ZipCode &zip2, const size_t &depth)
const static net_identifier_t	get_parent_identifier (const net_identifier_t &child)

Public Attributes
varint_vector_t	zipcode
std::vector< decoder_t >	decoder
bool	finished_decoding = false

Private Member Functions
node_code_t	get_node_code (const net_handle_t &node, const SnarlDistanceIndex &distance_index)
chain_code_t	get_chain_code (const net_handle_t &chain, const SnarlDistanceIndex &distance_index)
snarl_code_t	get_regular_snarl_code (const net_handle_t &snarl, const net_handle_t &snarl_child, const SnarlDistanceIndex &distance_index)
snarl_code_t	get_irregular_snarl_code (const net_handle_t &snarl, const net_handle_t &snarl_child, const SnarlDistanceIndex &distance_index)

Static Private Attributes
const static size_t	ROOT_SNARL_SIZE = 2
const static size_t	ROOT_IS_CHAIN_OFFSET = 0
const static size_t	ROOT_IDENTIFIER_OFFSET = 1
const static size_t	ROOT_CHAIN_SIZE = 4
const static size_t	ROOT_CHAIN_COMPONENT_COUNT_OFFSET = 2
const static size_t	ROOT_NODE_OR_CHAIN_CONNECTIVITY_OR_LENGTH_OFFSET = 3
const static size_t	ROOT_NODE_SIZE = 4
const static size_t	ROOT_NODE_LENGTH_OFFSET = 2
const static size_t	CHAIN_SIZE = 3
	Offsets for chain codes. More...
const static size_t	CHAIN_RANK_IN_SNARL_OFFSET = 0
const static size_t	CHAIN_LENGTH_OFFSET = 1
const static size_t	CHAIN_COMPONENT_COUNT_OFFSET = 2
const static size_t	REGULAR_SNARL_SIZE = 6
	Offsets for snarl codes. More...
const static size_t	IRREGULAR_SNARL_SIZE = 10
const static size_t	SNARL_IS_REGULAR_OFFSET = 0
const static size_t	SNARL_OFFSET_IN_CHAIN_OFFSET = 1
const static size_t	SNARL_LENGTH_OFFSET = 2
const static size_t	SNARL_CHILD_COUNT_OFFSET = 3
const static size_t	SNARL_CHAIN_COMPONENT_OFFSET = 4
const static size_t	REGULAR_SNARL_IS_REVERSED_OFFSET = 5
const static size_t	IRREGULAR_SNARL_RECORD_OFFSET = 5
const static size_t	IRREGULAR_SNARL_DISTANCE_LEFT_START_OFFSET = 6
const static size_t	IRREGULAR_SNARL_DISTANCE_LEFT_END_OFFSET = 7
const static size_t	IRREGULAR_SNARL_DISTANCE_RIGHT_START_OFFSET = 8
const static size_t	IRREGULAR_SNARL_DISTANCE_RIGHT_END_OFFSET = 9
const static size_t	NODE_SIZE = 4
	Offsets for nodes. More...
const static size_t	NODE_OFFSET_OFFSET = 0
const static size_t	NODE_LENGTH_OFFSET = 1
const static size_t	NODE_IS_REVERSED_OFFSET = 2
const static size_t	NODE_CHAIN_COMPONENT_OFFSET = 3

Member Typedef Documentation

code_type

typedef std::uint64_t vg::ZipCode::code_type

Member Enumeration Documentation

code_type_t

enum vg::ZipCode::code_type_t

The type of codes that can be stored in the zipcode Trivial chains that are children of snarls get saved as a chain with no child node EMPTY doesn't actually mean anything, it's used to catch errors Snarls can be regular, irregular, or cyclic. Regular snarls are bubbles. Irregular snarls are snarls that aren't bubbles but are dags Cyclic snarls are non-dags. They are stored the same as irregular snarls. Only the type is different

Enumerator
NODE
CHAIN
REGULAR_SNARL
IRREGULAR_SNARL
CYCLIC_SNARL
ROOT_SNARL
ROOT_CHAIN
ROOT_NODE
EMPTY

Member Function Documentation

byte_count()

size_t vg::ZipCode::byte_count ( ) const

inline

How many bytes were used to store this zipcode?

decoder_length()

size_t vg::ZipCode::decoder_length ( ) const

inline

How many codes in the zipcode have been decoded?

dump()

void vg::ZipCode::dump

(

std::ostream &

out

)

const

Dump a ZipCode to a stream so that it can be reconstructed for a unit test from the resulting information.

fill_in_full_decoder()

void vg::ZipCode::fill_in_full_decoder

(

)

Go through the entire zipcode and fill in the decoder.

fill_in_next_decoder()

bool vg::ZipCode::fill_in_next_decoder

(

)

Fill in one more item in the decoder Returns true if this is the last thing in the zipcode and false if there is more to decode

fill_in_zipcode()

void vg::ZipCode::fill_in_zipcode	(	const SnarlDistanceIndex &	distance_index,
		const vg::pos_t &	pos,
		bool	fill_in_decoder = true
	)

fill_in_zipcode_from_payload()

void vg::ZipCode::fill_in_zipcode_from_payload

(

const gbwtgraph::Payload &

payload

)

from_vector()

void vg::ZipCode::from_vector

(

const std::vector< size_t > &

values

)

Load from a normal vector.

get_chain_code()

ZipCode::chain_code_t vg::ZipCode::get_chain_code ( const net_handle_t &  chain, const SnarlDistanceIndex &  distance_index  )

inlineprivate

get_chain_component()

size_t vg::ZipCode::get_chain_component

(

const size_t &

depth

)

const

Get the chain component of a chain child. For snarls, this will be the component of the start node

get_code_type()

ZipCode::code_type_t vg::ZipCode::get_code_type

(

const size_t &

depth

)

const

What type of snarl tree node is at the given depth (index into the zipcode)

get_distance_index_address()

size_t vg::ZipCode::get_distance_index_address

(

const size_t &

depth

)

const

Get the information that was stored to get the address in the distance index This is the connected component number for a root structure, or the address of an irregular snarl. Throws an error for anything else This is used for checking equality without looking at the distance index. Use get_net_handle for getting the actual handle

get_distance_to_snarl_bound()

size_t vg::ZipCode::get_distance_to_snarl_bound	(	const size_t &	depth,
		bool	snarl_start,
		bool	left_side
	)		const

The minimum distance from start or end of the snarl to the left or right side of the child.

get_identifier()

net_identifier_t vg::ZipCode::get_identifier

(

size_t

depth

)

const

Get an identifier for the snarl tree node at this depth. If the snarl tree node at this depth would be the node, also include the node id

get_irregular_snarl_code()

ZipCode::snarl_code_t vg::ZipCode::get_irregular_snarl_code ( const net_handle_t &  snarl, const net_handle_t &  snarl_child, const SnarlDistanceIndex &  distance_index  )

inlineprivate

get_is_looping_chain()

bool vg::ZipCode::get_is_looping_chain

(

const size_t &

depth

)

const

get_is_reversed_in_parent()

bool vg::ZipCode::get_is_reversed_in_parent

(

const size_t &

depth

)

const

Is the snarl tree node backwards relative to its parent.

get_last_chain_component()

size_t vg::ZipCode::get_last_chain_component	(	const size_t &	depth,
		bool	get_end = false
	)		const

Get the chain component of the last node in the chain This behaves like the distance index get_chain_component- for looping chains it returns the last component if get_end is true, and 0 if it is false

get_length()

size_t vg::ZipCode::get_length	(	const size_t &	depth,
		bool	get_chain_component_length = false
	)		const

Get the length of a snarl tree node given the depth in the snarl tree If get_chain_component_length is true, then return the length of the last component of the multicomponent chain. If get_chain_component_length is false for a multi-cmponent chain, return max()

get_net_handle()

net_handle_t vg::ZipCode::get_net_handle	(	const size_t &	depth,
		const SnarlDistanceIndex *	distance_index
	)		const

Get the handle of the thing at the given depth. This can only be used for Root-level structures or irregular snarls

get_net_handle_slow()

net_handle_t vg::ZipCode::get_net_handle_slow	(	nid_t	id,
		const size_t &	depth,
		const SnarlDistanceIndex *	distance_index,
		const net_handle_t *	child_handle = nullptr
	)		const

Get the handle of the thing at the given depth. This can be used for anything but is slow, even for roots and irregular/cyclic snarls. It's a separate function to make sure I remember that it's slow If the child handle is given, get the net handle as the parent of the child, if the address isn't stored

get_node_code()

ZipCode::node_code_t vg::ZipCode::get_node_code ( const net_handle_t &  node, const SnarlDistanceIndex &  distance_index  )

inlineprivate

get_offset_in_chain()

size_t vg::ZipCode::get_offset_in_chain	(	const size_t &	depth,
		const SnarlDistanceIndex *	distance_index = nullptr
	)		const

Get the prefix sum of a child of a chain This requires the distance index for irregular snarls (except for a top-level snarl) Throws an exception if the distance index is not given when it is needed Doesn't use a given distance index if it isn't needed

get_parent_identifier()

const net_identifier_t vg::ZipCode::get_parent_identifier ( const net_identifier_t &  child )

static

get_payload_from_zip()

gbwtgraph::Payload vg::ZipCode::get_payload_from_zip

(

)

const

get_payload_from_zipcode()

MIPayload vg::ZipCode::get_payload_from_zipcode	(	nid_t	id,
		const SnarlDistanceIndex &	distance_index,
		hash_map< size_t, net_handle_t > *	component_to_net_handle = nullptr
	)		const

Fill in a payload with values from the zipcode Remember how to get the net handle from the connected component number.

get_rank_in_snarl()

size_t vg::ZipCode::get_rank_in_snarl

(

const size_t &

depth

)

const

Get the rank of a node/snarl in a snarl. Throw an exception if it isn't the child of a snarl.

get_regular_snarl_code()

ZipCode::snarl_code_t vg::ZipCode::get_regular_snarl_code ( const net_handle_t &  snarl, const net_handle_t &  snarl_child, const SnarlDistanceIndex &  distance_index  )

inlineprivate

get_snarl_child_count()

size_t vg::ZipCode::get_snarl_child_count	(	const size_t &	depth,
		const SnarlDistanceIndex *	distance_index = nullptr
	)		const

Get the number of children in a snarl. Throw an exception if it isn't a snarl.

get_top_level_chain_offset()

static tuple<size_t, size_t, size_t> vg::ZipCode::get_top_level_chain_offset ( )

static

is_equal()

const bool vg::ZipCode::is_equal ( const ZipCode &  zip1, const ZipCode &  zip2, const size_t &  depth  )

static

Are the two decoders pointing to the same snarl tree node at the given depth This only checks if the values in the zipcode are the same at the given depth, so if the preceeding snarl tree nodes are different, then this might actually refer to different things

is_externally_end_end_connected()

bool vg::ZipCode::is_externally_end_end_connected

(

const size_t &

depth

)

const

is_externally_start_end_connected()

bool vg::ZipCode::is_externally_start_end_connected

(

const size_t &

depth

)

const

is_externally_start_start_connected()

bool vg::ZipCode::is_externally_start_start_connected

(

const size_t &

depth

)

const

is_farther_than()

bool vg::ZipCode::is_farther_than ( const ZipCode &  zip1, const ZipCode &  zip2, const size_t &  limit  )

static

max_depth()

size_t vg::ZipCode::max_depth

(

)

const

What is the maximum depth of this zipcode?

minimum_distance_between()

size_t vg::ZipCode::minimum_distance_between ( ZipCode &  zip1, const pos_t &  pos1, ZipCode &  zip2, const pos_t &  pos2, const SnarlDistanceIndex &  distance_index, size_t  distance_limit = std::numeric_limits<size_t>::max(), bool  undirected_distance = false, const HandleGraph *  graph = nullptr  )

static

operator==()

bool vg::ZipCode::operator== ( const ZipCode &  other ) const

inline

Equality operator.

to_vector()

std::vector< size_t > vg::ZipCode::to_vector

(

)

const

Dump to a normal vector.

unpack_chain_code()

ZipCode::chain_code_t vg::ZipCode::unpack_chain_code

(

size_t

zipcode_level

)

const

unpack_node_code()

ZipCode::node_code_t vg::ZipCode::unpack_node_code

(

size_t

zipcode_level

)

const

unpack_snarl_code()

ZipCode::snarl_code_t vg::ZipCode::unpack_snarl_code

(

size_t

zipcode_level

)

const

Member Data Documentation

CHAIN_COMPONENT_COUNT_OFFSET

const static size_t vg::ZipCode::CHAIN_COMPONENT_COUNT_OFFSET = 2

staticprivate

CHAIN_LENGTH_OFFSET

const static size_t vg::ZipCode::CHAIN_LENGTH_OFFSET = 1

staticprivate

CHAIN_RANK_IN_SNARL_OFFSET

const static size_t vg::ZipCode::CHAIN_RANK_IN_SNARL_OFFSET = 0

staticprivate

CHAIN_SIZE

const static size_t vg::ZipCode::CHAIN_SIZE = 3

staticprivate

Offsets for chain codes.

decoder

std::vector<decoder_t> vg::ZipCode::decoder

finished_decoding

bool vg::ZipCode::finished_decoding = false

Did we fill in the entire decoder TODO: I'm making it fill in the decoder automatically because it seems to be faster that way, instead of waiting to see which parts are actually needed

IRREGULAR_SNARL_DISTANCE_LEFT_END_OFFSET

const static size_t vg::ZipCode::IRREGULAR_SNARL_DISTANCE_LEFT_END_OFFSET = 7

staticprivate

IRREGULAR_SNARL_DISTANCE_LEFT_START_OFFSET

const static size_t vg::ZipCode::IRREGULAR_SNARL_DISTANCE_LEFT_START_OFFSET = 6

staticprivate

IRREGULAR_SNARL_DISTANCE_RIGHT_END_OFFSET

const static size_t vg::ZipCode::IRREGULAR_SNARL_DISTANCE_RIGHT_END_OFFSET = 9

staticprivate

IRREGULAR_SNARL_DISTANCE_RIGHT_START_OFFSET

const static size_t vg::ZipCode::IRREGULAR_SNARL_DISTANCE_RIGHT_START_OFFSET = 8

staticprivate

IRREGULAR_SNARL_RECORD_OFFSET

const static size_t vg::ZipCode::IRREGULAR_SNARL_RECORD_OFFSET = 5

staticprivate

IRREGULAR_SNARL_SIZE

const static size_t vg::ZipCode::IRREGULAR_SNARL_SIZE = 10

staticprivate

NODE_CHAIN_COMPONENT_OFFSET

const static size_t vg::ZipCode::NODE_CHAIN_COMPONENT_OFFSET = 3

staticprivate

NODE_IS_REVERSED_OFFSET

const static size_t vg::ZipCode::NODE_IS_REVERSED_OFFSET = 2

staticprivate

NODE_LENGTH_OFFSET

const static size_t vg::ZipCode::NODE_LENGTH_OFFSET = 1

staticprivate

NODE_OFFSET_OFFSET

const static size_t vg::ZipCode::NODE_OFFSET_OFFSET = 0

staticprivate

NODE_SIZE

const static size_t vg::ZipCode::NODE_SIZE = 4

staticprivate

Offsets for nodes.

REGULAR_SNARL_IS_REVERSED_OFFSET

const static size_t vg::ZipCode::REGULAR_SNARL_IS_REVERSED_OFFSET = 5

staticprivate

REGULAR_SNARL_SIZE

const static size_t vg::ZipCode::REGULAR_SNARL_SIZE = 6

staticprivate

Offsets for snarl codes.

ROOT_CHAIN_COMPONENT_COUNT_OFFSET

const static size_t vg::ZipCode::ROOT_CHAIN_COMPONENT_COUNT_OFFSET = 2

staticprivate

ROOT_CHAIN_SIZE

const static size_t vg::ZipCode::ROOT_CHAIN_SIZE = 4

staticprivate

ROOT_IDENTIFIER_OFFSET

const static size_t vg::ZipCode::ROOT_IDENTIFIER_OFFSET = 1

staticprivate

ROOT_IS_CHAIN_OFFSET

const static size_t vg::ZipCode::ROOT_IS_CHAIN_OFFSET = 0

staticprivate

ROOT_NODE_LENGTH_OFFSET

const static size_t vg::ZipCode::ROOT_NODE_LENGTH_OFFSET = 2

staticprivate

ROOT_NODE_OR_CHAIN_CONNECTIVITY_OR_LENGTH_OFFSET

const static size_t vg::ZipCode::ROOT_NODE_OR_CHAIN_CONNECTIVITY_OR_LENGTH_OFFSET = 3

staticprivate

ROOT_NODE_SIZE

const static size_t vg::ZipCode::ROOT_NODE_SIZE = 4

staticprivate

ROOT_SNARL_SIZE

const static size_t vg::ZipCode::ROOT_SNARL_SIZE = 2

staticprivate

Offsets of values in a root chain or snarl code Roots have a bool for is_chain and an identifier, which is the connected component number from the distance index

SNARL_CHAIN_COMPONENT_OFFSET

const static size_t vg::ZipCode::SNARL_CHAIN_COMPONENT_OFFSET = 4

staticprivate

SNARL_CHILD_COUNT_OFFSET

const static size_t vg::ZipCode::SNARL_CHILD_COUNT_OFFSET = 3

staticprivate

SNARL_IS_REGULAR_OFFSET

const static size_t vg::ZipCode::SNARL_IS_REGULAR_OFFSET = 0

staticprivate

SNARL_LENGTH_OFFSET

const static size_t vg::ZipCode::SNARL_LENGTH_OFFSET = 2

staticprivate

SNARL_OFFSET_IN_CHAIN_OFFSET

const static size_t vg::ZipCode::SNARL_OFFSET_IN_CHAIN_OFFSET = 1

staticprivate

zipcode

varint_vector_t vg::ZipCode::zipcode

---

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

• src/zip_code.hpp
• src/zip_code.cpp