Contain all the information for the mapping of a k-mer or a sequence to a unitig of a Compacted de Bruijn graph. More...

Public Member Functions
	UnitigMap (size_t length=1, CompactedDBG_ptr_t cdbg_=nullptr)
	UnitigMap constructor. More...

	UnitigMap (const size_t start, const size_t length, const size_t unitig_sz, const bool strand)
	UnitigMap constructor. More...

bool	operator== (const UnitigMap &o) const
	Equality operator: check if two UnitigMap are the same. More...

bool	operator!= (const UnitigMap &o) const
	Inequality operator: check if two UnitigMap are different. More...

bool	isSameReferenceUnitig (const UnitigMap &o) const
	check if two UnitigMap have the same unitig as reference. More...

string	mappedSequenceToString () const
	Create a string containing the sequence corresponding to the mapping. More...

string	referenceUnitigToString () const
	Create a string containing the sequence of the reference unitig used the mapping. More...

size_t	lcp (const char *s, const size_t pos_s=0, const size_t pos_um_seq=0, const bool um_reversed=false) const
	Compute the length of the longest common prefix between a given sequence and the reference unitig used in the mapping. More...

Kmer	getUnitigHead () const
	Get the head k-mer of the reference unitig used for the mapping. More...

Kmer	getUnitigTail () const
	Get the tail k-mer of the reference unitig used for the mapping. More...

Kmer	getUnitigKmer (const size_t pos) const
	Get the k-mer starting at position pos in the reference unitig used for the mapping. More...

Kmer	getMappedHead () const
	Get the head k-mer of the mapped sequence. More...

Kmer	getMappedTail () const
	Get the tail k-mer of the mapped sequence. More...

Kmer	getMappedKmer (const size_t pos) const
	Get the k-mer starting at position pos in the mapped sequence. More...

UnitigMap< U, G, is_const >	getKmerMapping (const size_t pos) const
	Create a new UnitigMap object which is the mapping of a k-mer on a reference unitig. More...

Unitig_data_ptr_t	getData () const
	Get a pointer to the data associated with the reference unitig used in the mapping. More...

UnitigMap_BW	getPredecessors () const
	Create a UnitigMap_BW object that can create iterators (through UnitigMap_BW::begin() and UnitigMap_BW::end()) over the predecessors of the reference unitig used in the mapping. More...

UnitigMap_FW	getSuccessors () const
	Create a UnitigMap_FW object that can create iterators (through UnitigMap_FW::begin() and UnitigMap_FW::end()) over the successors of the reference unitig used in the mapping. More...

CompactedDBG_ptr_t	getGraph () const
	Get a pointer to the CompactedDBG containing the reference unitig used in the mapping. More...

Detailed Description

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>
class UnitigMap< Unitig_data_t, Graph_data_t, is_const >

Contain all the information for the mapping of a k-mer or a sequence to a unitig of a Compacted de Bruijn graph.

A UnitigMap object has 3 template parameters: the type of data associated with the unitigs of the graph, the type of data associated with the graph and a boolean indicating if this is a constant UnitigMap (const_UnitigMap) or not. A const_UnitigMap can be modified but you can't modify the CompactedDBG you can access using UnitigMap::getCompactedDBG. The unitig data and graph data types should be the same as the ones used for the CompactedDBG.

UnitigMap<> um_1; // No unitig data, no graph data, NOT constant and its content IS NOT constant
UnitigMap<void, void, false> um_2; // Equivalent to previous notation
const UnitigMap<> um_3; // No unitig data, no graph data, constant BUT its content IS NOT constant
UnitigMap<void, void, true> um_4; // No unitig data, no graph data, NOT constant BUT its content IS constant
const UnitigMap<void, void, true> um_5; // No unitig data, no graph data, constant AND its content IS constant
UnitigMap<myUnitigData, myGraphData> um_6; // Unitig data of type myUnitigData for each unitig, graph data of type myGraphData, not constant
 
CompactedDBG<>* cdbg_ptr_1 = um_1.getGraph(); // Associated CompactedDBG can be modified from the UnitigMap
CompactedDBG<>* cdbg_ptr_2 = um_2.getGraph(); // Associated CompactedDBG can be modified from the UnitigMap
CompactedDBG<>* cdbg_ptr_3 = um_3.getGraph(); // Associated CompactedDBG can be modified from the UnitigMap
const CompactedDBG<>* cdbg_ptr_4 = um_4.getGraph(); // Associated CompactedDBG cannot be modified from the UnitigMap
const CompactedDBG<>* cdbg_ptr_5 = um_5.getGraph(); // Associated CompactedDBG cannot be modified from the UnitigMap
CompactedDBG<myUnitigData, myGraphData>* cdbg_ptr_6 = um_6.getGraph(); // Associated CompactedDBG can be modified from the UnitigMap

Constructor & Destructor Documentation

◆ UnitigMap() [1/2]

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

UnitigMap< Unitig_data_t, Graph_data_t, is_const >::UnitigMap	(	size_t	length = `1`,
		CompactedDBG_ptr_t	cdbg_ = `nullptr`
	)

UnitigMap constructor.

Parameters

length	is the length of the mapping in k-mers (default is 1 k-mer).
cdbg_	is a pointer to the CompactedDBG containing the reference unitig used for the mapping (default is nullptr).

Returns: an empty UnitigMap.

◆ UnitigMap() [2/2]

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

UnitigMap< Unitig_data_t, Graph_data_t, is_const >::UnitigMap	(	const size_t	start,
		const size_t	length,
		const size_t	unitig_sz,
		const bool	strand
	)

UnitigMap constructor.

This constructor is used to create temporary mappings and must not be used to extract information from the graph.

Parameters

start	is the start position of the mapping (0-based distance) from the start of the reference unitig.
length	is the length of the mapping in k-mers.
unitig_sz	is the length of the reference unitig used for the mapping.
strand	indicates if the mapped k-mer or sequence matches the forward strand (true) or the reverse-complement (false).

Returns: a UnitigMap.

Member Function Documentation

◆ getData()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

Unitig_data_ptr_t UnitigMap< Unitig_data_t, Graph_data_t, is_const >::getData ( ) const

Get a pointer to the data associated with the reference unitig used in the mapping.

Returns

a pointer to the data associated with the reference unitig used in the mapping or a nullptr pointer if:

there is no mapping (UnitigMap::isEmpty = true)
there is no data associated with the unitigs (U = void). The returned pointer is constant if the UnitigMap is constant (UnitigMap<U, G, true>).

◆ getGraph()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

CompactedDBG_ptr_t UnitigMap< Unitig_data_t, Graph_data_t, is_const >::getGraph ( ) const

inline

Get a pointer to the CompactedDBG containing the reference unitig used in the mapping.

Returns: a pointer to the CompactedDBG containing the reference unitig used in the mapping. If the mapping is empty, a nullptr pointer is returned. The pointer is a constant pointer if the UnitigMap is constant (UnitigMap<U, G, true>).

◆ getKmerMapping()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

UnitigMap<U, G, is_const> UnitigMap< Unitig_data_t, Graph_data_t, is_const >::getKmerMapping ( const size_t pos ) const

Create a new UnitigMap object which is the mapping of a k-mer on a reference unitig.

Parameters

pos	is the start position of the k-mer to map in the reference unitig used for the current mapping.

Returns: a UnitigMap object which is the mapping.

◆ getMappedHead()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

Kmer UnitigMap< Unitig_data_t, Graph_data_t, is_const >::getMappedHead ( ) const

Get the head k-mer of the mapped sequence.

Returns: a Kmer object which is either the head k-mer of the mapped sequence or an empty k-mer if there is no mapping (UnitigMap::isEmpty = true).

◆ getMappedKmer()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

Kmer UnitigMap< Unitig_data_t, Graph_data_t, is_const >::getMappedKmer ( const size_t pos ) const

Get the k-mer starting at position pos in the mapped sequence.

Parameters

pos	is the start position of the k-mer to extract within the mapped sequence.

Returns: a Kmer object which is either the k-mer starting at position pos in the mapped sequence or an empty k-mer if there is either no mapping (UnitigMap::isEmpty = true) or the position is greater than length(unitig)-k.

◆ getMappedTail()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

Kmer UnitigMap< Unitig_data_t, Graph_data_t, is_const >::getMappedTail ( ) const

Get the tail k-mer of the mapped sequence.

Returns: a Kmer object which is either the tail k-mer of the mapped sequence or an empty k-mer if there is no mapping (UnitigMap::isEmpty = true).

◆ getPredecessors()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

UnitigMap_BW UnitigMap< Unitig_data_t, Graph_data_t, is_const >::getPredecessors ( ) const

Create a UnitigMap_BW object that can create iterators (through UnitigMap_BW::begin() and UnitigMap_BW::end()) over the predecessors of the reference unitig used in the mapping.

Returns: a UnitigMap_BW object that can create iterators (through UnitigMap_BW::begin() and UnitigMap_BW::end()) over the predecessors of the reference unitig used in the mapping.

◆ getSuccessors()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

UnitigMap_FW UnitigMap< Unitig_data_t, Graph_data_t, is_const >::getSuccessors ( ) const

Create a UnitigMap_FW object that can create iterators (through UnitigMap_FW::begin() and UnitigMap_FW::end()) over the successors of the reference unitig used in the mapping.

Returns: a UnitigMap_FW object that can create iterators (through UnitigMap_FW::begin() and UnitigMap_FW::end()) over the successors of the reference unitig used in the mapping.

◆ getUnitigHead()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

Kmer UnitigMap< Unitig_data_t, Graph_data_t, is_const >::getUnitigHead ( ) const

Get the head k-mer of the reference unitig used for the mapping.

Returns: a Kmer object which is either the head k-mer of the mapped unitig or an empty k-mer if there is no mapping (UnitigMap::isEmpty = true).

◆ getUnitigKmer()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

Kmer UnitigMap< Unitig_data_t, Graph_data_t, is_const >::getUnitigKmer ( const size_t pos ) const

Get the k-mer starting at position pos in the reference unitig used for the mapping.

Parameters

pos	is the start position of the k-mer to extract.

Returns: a Kmer object which is either the k-mer starting at position pos in the mapped unitig or an empty k-mer if there is either no mapping (UnitigMap::isEmpty = true) or the position is greater than length(unitig)-k.

◆ getUnitigTail()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

Kmer UnitigMap< Unitig_data_t, Graph_data_t, is_const >::getUnitigTail ( ) const

Get the tail k-mer of the reference unitig used for the mapping.

Returns: a Kmer object which is either the tail k-mer of the mapped unitig or an empty k-mer if there is no mapping (UnitigMap::isEmpty = true).

◆ isSameReferenceUnitig()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

bool UnitigMap< Unitig_data_t, Graph_data_t, is_const >::isSameReferenceUnitig ( const UnitigMap< Unitig_data_t, Graph_data_t, is_const > & o ) const

check if two UnitigMap have the same unitig as reference.

Returns: a boolean indicating if two UnitigMap have the same unitig as reference.

◆ lcp()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

size_t UnitigMap< Unitig_data_t, Graph_data_t, is_const >::lcp	(	const char *	s,
		const size_t	pos_s = `0`,
		const size_t	pos_um_seq = `0`,
		const bool	um_reversed = `false`
	)		const

Compute the length of the longest common prefix between a given sequence and the reference unitig used in the mapping.

Parameters

s	is a pointer to an array of characters representing the sequence from which the length of the longest common prefix must be computed.
pos_s	is the start position in s from which the longest common prefix must be computed.
pos_um_seq	is the start position in the reference unitig of the mapping from which the longest common prefix must be computed.
um_reversed	indicates if the longest common prefix must be computed from the reverse-complement of the reference unitig used in the mapping (true) or not (false).

Returns: the length of the longest common prefix

◆ mappedSequenceToString()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

string UnitigMap< Unitig_data_t, Graph_data_t, is_const >::mappedSequenceToString ( ) const

Create a string containing the sequence corresponding to the mapping.

Returns: a string containing the sequence corresponding to the mapping or an empty string if there is no mapping (UnitigMap::isEmpty = true).

◆ operator!=()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

bool UnitigMap< Unitig_data_t, Graph_data_t, is_const >::operator!= ( const UnitigMap< Unitig_data_t, Graph_data_t, is_const > & o ) const

Inequality operator: check if two UnitigMap are different.

Returns: a boolean indicating if the two UnitigMap are different.

◆ operator==()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

bool UnitigMap< Unitig_data_t, Graph_data_t, is_const >::operator== ( const UnitigMap< Unitig_data_t, Graph_data_t, is_const > & o ) const

Equality operator: check if two UnitigMap are the same.

Returns: a boolean indicating if two UnitigMap are the same.

◆ referenceUnitigToString()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>

string UnitigMap< Unitig_data_t, Graph_data_t, is_const >::referenceUnitigToString ( ) const

Create a string containing the sequence of the reference unitig used the mapping.

Returns: a string containing the sequence of the reference unitig used the mapping or an empty string if there is no mapping (UnitigMap::isEmpty = true).

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

src/NeighborIterator.hpp
src/UnitigMap.hpp

Public Member Functions

Detailed Description

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false> class UnitigMap< Unitig_data_t, Graph_data_t, is_const >

Constructor & Destructor Documentation

◆ UnitigMap() [1/2]

◆ UnitigMap() [2/2]

Member Function Documentation

◆ getData()

◆ getGraph()

◆ getKmerMapping()

◆ getMappedHead()

◆ getMappedKmer()

◆ getMappedTail()

◆ getPredecessors()

◆ getSuccessors()

◆ getUnitigHead()

◆ getUnitigKmer()

◆ getUnitigTail()

◆ isSameReferenceUnitig()

◆ lcp()

◆ mappedSequenceToString()

◆ operator!=()

◆ operator==()

◆ referenceUnitigToString()

template<typename Unitig_data_t = void, typename Graph_data_t = void, bool is_const = false>
class UnitigMap< Unitig_data_t, Graph_data_t, is_const >