LocARNA::Alignment Class Reference

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

#include <alignment.hh>

List of all members.

Public Types
typedef EdgeEnd	edge_end_t
	edge end
typedef Alignment__edge_ends_t	edge_ends_t
	edge ends
typedef AlignmentEdges	edges_t
	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.
	Alignment (const Alignment &alignment)
	copy constructor
Alignment &	operator= (const Alignment &alignment)
	assignment operator
void	swap (Alignment &a1, Alignment &a2)
	swap two alignments
void	set_consensus_structure (const RnaStructure &structure)
	Set consensus structure of the alignment.
void	set_structures (const RnaStructure &structureA, const RnaStructure &structureB)
	Set structures of the alignment.
void	clear ()
void	append (edge_end_t i, edge_end_t j)
	Append an alignment edge.
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.
size_type	local_startA () const
	get first position of A that is locally aligned to something
size_type	local_endA () const
	get last position of A that is locally aligned to something
size_type	local_startB () const
	get first position of B that is locally aligned to something
size_type	local_endB () const
	get last position of B that is locally aligned to something
std::string	dot_bracket_structureA (bool only_local) const
	Structure A.
std::string	dot_bracket_structureB (bool only_local) const
	Structure B.
const Sequence &	seqA () const
	read access seqA
const Sequence &	seqB () const
	read access seqB
Static Public Member Functions
static edge_ends_t	alistr_to_edge_ends (const std::string &alistr)
	convert alignemnt string to edge end vector

---

Detailed Description

Represents a structure-annotated sequence alignment.

Supports construction of the alignment during traceback.

---

Constructor & Destructor Documentation

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

Construct empty alignment from sequences

Parameters:

seqA	First sequence
seqB	Second sequence

LocARNA::Alignment::~Alignment

(

)

Destructor

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

LocARNA::Alignment::Alignment

(

const Alignment &

alignment

)

copy constructor

Parameters:

alignment

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

---

Member Function Documentation

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:

pair of vectors 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).

Alignment::edge_ends_t LocARNA::Alignment::alistr_to_edge_ends

(

const std::string &

alistr

)

[static]

convert alignemnt string to edge end vector

Parameters:

alistr

alignment string

Returns:

vector of edge ends corresponding to alistr

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

void LocARNA::Alignment::clear

(

)

Delete the alignment edges and reset structure

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

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

Alignment & LocARNA::Alignment::operator=

(

const Alignment &

alignment

)

assignment operator

Parameters:

alignment

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

const Sequence & LocARNA::Alignment::seqA

(

)

const

read access seqA

Returns:

sequence A

const Sequence & LocARNA::Alignment::seqB

(

)

const

read access seqB

Returns:

sequence B

void LocARNA::Alignment::set_consensus_structure

(

const RnaStructure &

structure

)

Set consensus structure of the alignment.

Parameters:

structure

consensus structure

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

Set structures of the alignment.

Parameters:

structureA	structure A
structureB	structure B

void LocARNA::Alignment::swap	(	Alignment &	a1,
		Alignment &	a2
	)

swap two alignments

Parameters:

a1	first alignment
a2	second alignment Swaps implementation objects (not only pointer)

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

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