LocARNA::Alignment Class Reference

Represents a structure-annotated sequence alignment. More...

#include <alignment.hh>

Public Types
typedef EdgeEnd	edge_end_t
	edge end
using	edge_ends_t = std::vector< EdgeEnd >
	edge ends
using	edge_end_pair_t = std::pair< EdgeEnd, EdgeEnd >
using	pos_pair_t = std::pair< pos_type, pos_type >
using	edges_t = AlignmentEdges
	description of alignment edges

Public Member Functions
	Alignment (const Sequence &seqA, const Sequence &seqB)
	~Alignment ()
	Alignment (const Sequence &seqA, const Sequence &seqB, const edges_t &edges)
	Construct alignment from sequences and alignment strings. More...
	Alignment (const Alignment &alignment)
	copy constructor More...
Alignment &	operator= (const Alignment &alignment)
	assignment operator More...
void	set_consensus_structure (const RnaStructure &structure)
	Set consensus structure of the alignment. More...
void	set_structures (const RnaStructure &structureA, const RnaStructure &structureB)
	Set structures of the alignment. More...
void	clear ()
void	append (edge_end_t i, edge_end_t j)
	Append an alignment edge. More...
void	add_basepairA (int i, int j)
	Add a basepair to the structure of A.
void	add_basepairB (int i, int j)
	Add a basepair to the structure of B.
void	add_deleted_basepairA (int i, int j)
	Add a basepair to the structure of A.
void	add_deleted_basepairB (int i, int j)
	Add a basepair to the structure of B.
const edges_t	alignment_edges (bool only_local) const
	All alignment edges. More...
pos_pair_t	start_positions () const
pos_pair_t	end_positions () const
std::string	dot_bracket_structureA (bool only_local) const
	Structure A. More...
std::string	dot_bracket_structureB (bool only_local) const
	Structure B. More...
const Sequence &	seqA () const
	read access seqA More...
const Sequence &	seqB () const
	read access seqB More...
bool	empty () const

Static Public Member Functions
static edges_t	alistrs_to_edges (const std::string &alistrA, const std::string &alistrB)
	convert alignemnt string to edge end vector More...

Detailed Description

Represents a structure-annotated sequence alignment.

Supports construction of the alignment during traceback.

Constructor & Destructor Documentation

Alignment() [1/3]

LocARNA::Alignment::Alignment	(	const Sequence &	seqA,
		const Sequence &	seqB
	)

Construct empty alignment from sequences

Parameters

seqA	First sequence
seqB	Second sequence

~Alignment()

LocARNA::Alignment::~Alignment

(

)

Destructor

Alignment() [2/3]

LocARNA::Alignment::Alignment	(	const Sequence &	seqA,
		const Sequence &	seqB,
		const edges_t &	edges
	)

Construct alignment from sequences and alignment strings.

Parameters

seqA	First sequence
seqB	Second sequence
edges	alignment edges

Alignment() [3/3]

LocARNA::Alignment::Alignment

(

const Alignment &

alignment

)

copy constructor

Parameters

alignment

object to be copied Copies implementation object (not only pointer)

Member Function Documentation

alignment_edges()

const Alignment::edges_t LocARNA::Alignment::alignment_edges

(

bool

only_local

)

const

All alignment edges.

Parameters

only_local

if true, return only local edges

Returns

vector of alignment edges

If !only_local, the returned vector contains all positions of the sequence. We distinguish different gaps, in particular locality gaps, which are paired with positions that are not aligned at all (i.e. they are not part of the local alignment).

If only_local, the vector does not contain non-local edges, i.e. edges with locality gaps.

Edges are sorted (ascendingly).

alistrs_to_edges()

Alignment::edges_t LocARNA::Alignment::alistrs_to_edges ( const std::string &  alistrA, const std::string &  alistrB  )

static

convert alignemnt string to edge end vector

Parameters

alistr

alignment string

Returns

vector of edge ends corresponding to alistr

append()

void LocARNA::Alignment::append	(	edge_end_t	i,
		edge_end_t	j
	)

Append an alignment edge.

Parameters

i	first position of edge (or -1 for gap)
j	second position of edge (or -1 for gap) Edges have to be appended in ascending order

clear()

void LocARNA::Alignment::clear

(

)

Delete the alignment edges and reset structure

dot_bracket_structureA()

std::string LocARNA::Alignment::dot_bracket_structureA

(

bool

only_local

)

const

Structure A.

Parameters

only_local

if true, construct string only for aligned subsequence

Returns

dot bracket string for structure A with gaps

dot_bracket_structureB()

std::string LocARNA::Alignment::dot_bracket_structureB

(

bool

only_local

)

const

Structure B.

Parameters

only_local

if true, construct string only for aligned subsequence

Returns

dot bracket string for structure B with gaps

empty()

bool LocARNA::Alignment::empty

(

)

const

check for empty alignment

Returns

whether alignment is empty

end_positions()

Alignment::pos_pair_t LocARNA::Alignment::end_positions

(

)

const

get pair of last positions in the alignment

See also

local_start()

operator=()

Alignment & LocARNA::Alignment::operator=

(

const Alignment &

alignment

)

assignment operator

Parameters

alignment

object to be assigned Assigns implementation object (not only pointer)

seqA()

const Sequence & LocARNA::Alignment::seqA

(

)

const

read access seqA

Returns

sequence A

seqB()

const Sequence & LocARNA::Alignment::seqB

(

)

const

read access seqB

Returns

sequence B

set_consensus_structure()

void LocARNA::Alignment::set_consensus_structure

(

const RnaStructure &

structure

)

Set consensus structure of the alignment.

Parameters

structure

consensus structure

set_structures()

void LocARNA::Alignment::set_structures	(	const RnaStructure &	structureA,
		const RnaStructure &	structureB
	)

Set structures of the alignment.

Parameters

structureA	structure A
structureB	structure B

start_positions()

Alignment::pos_pair_t LocARNA::Alignment::start_positions

(

)

const

get pair of first positions in the alignment

Note

if the alignment starts with a gap, this does not return an edge of the alignment!

---

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

• src/LocARNA/alignment.hh
• src/LocARNA/alignment.cc