gatb.core-API-0.0.0: GraphUnitigsTemplate< span

Class representing a De Bruijn graph based on unitigs. More...

#include <GraphUnitigs.hpp>

Inheritance diagram for GraphUnitigsTemplate< span >:

Public Member Functions
GraphUnitigsTemplate &	operator= (GraphUnitigsTemplate const &graph)

GraphIterator< NodeGU >	iterator () const

GraphVector< NodeGU >	neighbors (NodeGU &node, Direction dir=DIR_END) const

GraphVector< NodeGU >	successors (NodeGU &node) const

int	simplePathAvance (const NodeGU &node, Direction dir, EdgeGU &output) const

bool	isBranching (const NodeGU &node) const

bool	isSimple (EdgeGU &edge) const

void	remove ()

	GraphUnitigsTemplate (size_t kmerSize)

	GraphUnitigsTemplate (const std::string &uri)

Public Member Functions inherited from GraphTemplate< NodeFast< span >, EdgeFast< span >, GraphDataVariantFast< span > >
	GraphTemplate (size_t kmerSize)

	GraphTemplate (bank::IBank bank, tools::misc::IProperties params)

	GraphTemplate (tools::misc::IProperties *params)

	GraphTemplate (const std::string &uri)

GraphTemplate &	operator= (const GraphTemplate &graph)

GraphIterator< NodeFast< span > >	iterator () const

GraphVector< NodeFast< span > >	neighbors (NodeFast< span > &node, Direction dir=DIR_END) const

GraphVector< NodeFast< span > >	neighbors (const typename NodeFast< span >::Value &kmer) const

std::set< BranchingNode_t< NodeFast< span > > >	neighbors (typename std::set< BranchingNode_t< NodeFast< span > > >::iterator first, typename std::set< BranchingNode_t< NodeFast< span > > >::iterator last) const

GraphVector< NodeFast< span > >	successors (NodeFast< span > &node) const

GraphVector< NodeFast< span > >	predecessors (NodeFast< span > &node) const

GraphVector< std::pair< EdgeFast< span >, EdgeFast< span > > >	successorsEdge (const NodeFast< span > &node1, const NodeFast< span > &node2) const

GraphVector< std::pair< EdgeFast< span >, EdgeFast< span > > >	predecessorsEdge (const NodeFast< span > &node1, const NodeFast< span > &node2) const

NodeFast< span >	neighbor (NodeFast< span > &source, Direction dir, kmer::Nucleotide nt) const

NodeFast< span >	neighbor (NodeFast< span > &source, Direction dir, kmer::Nucleotide nt, bool &exists) const

NodeFast< span >	successor (NodeFast< span > &source, kmer::Nucleotide nt) const

NodeFast< span >	predecessor (NodeFast< span > &source, kmer::Nucleotide nt) const

size_t	indegree (NodeFast< span > &node) const

size_t	outdegree (NodeFast< span > &node) const

size_t	degree (NodeFast< span > &node, Direction dir) const

int	simplePathAvance (NodeFast< span > &node, Direction dir, EdgeFast< span > &output) const

bool	contains (const NodeFast< span > &item) const

std::string	toString (const NodeFast< span > &node) const

std::string	toString (const EdgeFast< span > &edge) const

std::string	toString (const BranchingEdge_t< NodeFast< span >, EdgeFast< span > > &edge) const

bool	isBranching (NodeFast< span > &node) const

NodeFast< span >	buildNode (const tools::misc::Data &data, size_t offset=0) const

NodeFast< span >	buildNode (const char *sequence) const

NodeFast< span >	reverse (const NodeFast< span > &node) const

BranchingNode_t< NodeFast< span > >	reverse (const BranchingNode_t< NodeFast< span > > &node) const

EdgeFast< span >	reverse (const EdgeFast< span > &edge) const

GraphVector< NodeFast< span > >	mutate (const NodeFast< span > &node, size_t idx, int mode=0) const

kmer::Nucleotide	getNT (const NodeFast< span > &node, size_t idx) const

int	queryAbundance (NodeFast< span > &node) const

int	queryNodeState (NodeFast< span > &node) const

bool	isSimple (EdgeFast< span > &edge) const

std::string	getName () const

size_t	getKmerSize () const

tools::misc::IProperties &	getInfo () const

void	remove ()

void	precomputeAdjacency (unsigned int nbCores=1, bool verbose=true)

Static Public Member Functions
static GraphUnitigsTemplate	create (size_t kmerSize)

static GraphUnitigsTemplate	create (bank::IBank bank, const char fmt,...)

static GraphUnitigsTemplate	create (const char *fmt,...)

static GraphUnitigsTemplate	create (tools::misc::IProperties *options, bool load_unitigs_after=true)

static GraphUnitigsTemplate	load (const std::string &uri)

Static Public Member Functions inherited from GraphTemplate< NodeFast< span >, EdgeFast< span >, GraphDataVariantFast< span > >
static GraphTemplate	create (size_t kmerSize)

static GraphTemplate	create (bank::IBank bank, const char fmt,...)

static GraphTemplate	create (const char *fmt,...)

static GraphTemplate	create (tools::misc::IProperties *options)

static GraphTemplate	load (const std::string &uri)

static tools::misc::IOptionsParser *	getOptionsParser (bool includeMandatory=true)

Additional Inherited Members
Public Attributes inherited from GraphTemplate< NodeFast< span >, EdgeFast< span >, GraphDataVariantFast< span > >
tools::storage::impl::StorageMode_e	_storageMode

tools::storage::impl::Storage *	_storage

void *	_variant

size_t	_kmerSize

size_t	_nbSolidKmers

tools::misc::impl::Properties	_info

Static Public Attributes inherited from GraphTemplate< NodeFast< span >, EdgeFast< span >, GraphDataVariantFast< span > >
static const tools::storage::impl::StorageMode_e	PRODUCT_MODE_DEFAULT

Detailed Description

template<size_t span>
class gatb::core::debruijn::impl::GraphUnitigsTemplate< span >

Class representing a De Bruijn graph based on unitigs.

Nodes are k-mer extremities of unitigs. They're represented implicitly internally. Edges are (k-1) overlaps between nodes in different unitigs

Constructor & Destructor Documentation

GraphUnitigsTemplate ( size_t kmerSize )

Constructor for empty graph.

GraphUnitigsTemplate ( const std::string & uri )

Constructor. Use for reading from filesystem.

Member Function Documentation

static GraphUnitigsTemplate create ( size_t kmerSize )

inlinestatic

Build an empty graph.

Parameters

[in] kmerSize kmer size

Returns: the created graph.

GraphUnitigsTemplate< span > create	(	bank::IBank *	bank,
		const char *	fmt,
			...
	)

static

Build a graph from a given bank.

Parameters

[in]	bank	: bank to get the reads from
[in]	fmt	: printf-like format for the command line string

Returns: the created graph.

GraphUnitigsTemplate< span > create	(	const char *	fmt,
			...
	)

static

Build a graph from user options.

Parameters

[in] fmt printf-like format

Returns: the created graph.

static GraphUnitigsTemplate create	(	tools::misc::IProperties *	options,
		bool	load_unitigs_after = `true`
	)

inlinestatic

so, hm, what's the point of a create() function that just calls a constructor? I really don't get the factory pattern yet

bool isBranching ( const NodeGU & node ) const

REMARKS : it's a bit of a misnomer, but in GATB language, Branching means "anything not simple". I.e. simple means outdegree=indegree=1 and branching is every other degree combination, including 0's

bool isSimple ( EdgeGU & edge ) const

Tells whether the provided edge is simple: outdegree(from)==1 and indegree(to)==1

Parameters

[in] edge : the edge to be asked

Returns: true if the edge is simple, false otherwise.

GraphIterator<NodeGU> iterator ( ) const

inline

Creates an iterator over nodes of the graph.

Returns: the nodes iterator.

static GraphUnitigsTemplate load ( const std::string & uri )

inlinestatic

Load a graph from some URI.

Parameters

[in] uri : the uri to get the graph from

Returns: the loaded graph.

GraphVector<NodeGU> neighbors	(	NodeGU &	node,
		Direction	dir = `DIR_END`
	)		const

inline

Returns a vector of neighbors of the provided node.

Parameters

[in]	node	: the node whose neighbors are wanted
[in]	direction	: the direction of the neighbors. If not set, out and in neighbors are computed.

Returns: a vector of the node neighbors (may be empty). Warning: be sure to check if edge.from (or node.from) is actually your input node, or its reverse complement.

GraphUnitigsTemplate& operator= ( GraphUnitigsTemplate< span > const & graph )

Affectation overload.

void remove ( )

Remove physically a graph.

int simplePathAvance	(	const NodeGU &	node,
		Direction	dir,
		EdgeGU &	output
	)		const

Simple paths traversal invariant: the input kmer has no in-branching.

Returns: 1 if a good extension is found 0 if a deadend was reached -1 if out-branching was detected -2 if no out-branching but next kmer has in-branching

GraphVector<NodeGU> successors ( NodeGU & node ) const

inline

Shortcut for 'neighbors' method

Parameters

[in] node : the node whose neighbors are wanted

Returns: a vector of the node neighbors (may be empty).

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

/builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp
/builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

template<size_t span> class gatb::core::debruijn::impl::GraphUnitigsTemplate< span >

Constructor & Destructor Documentation

Member Function Documentation

template<size_t span>
class gatb::core::debruijn::impl::GraphUnitigsTemplate< span >