LocARNA::AlignmentImpl Class Reference

Implementation of Alignment. More...

#include <alignment_impl.hh>

List of all members.

Public Member Functions
	AlignmentImpl (Alignment *self, const Sequence &seqA, const Sequence &seqB)
	Constructor as empty alignment of two sequences.
void	write_debug (std::ostream &out) const
	Write raw alignment information for debugging.
Static Public Member Functions
static void	write_debug (std::ostream &out, const Alignment::edge_ends_t &ends)
	Write raw alignment information (one sequence) for debugging.
static std::string	dot_bracket_structure (const std::string &str, const Alignment::edge_ends_t &x)
	dot bracket structure
Public Attributes
Alignment *	self_
	self pointer
const Sequence &	seqA_
	sequence A
const Sequence &	seqB_
	sequence B
Alignment::edge_ends_t	a_
	first components of alignment edges
Alignment::edge_ends_t	b_
	second components of alignment edges
std::string	strA_
	structure of A as dot-bracket string
std::string	strB_
	structure of B as dot-bracket string

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Detailed Description

Implementation of Alignment.

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Constructor & Destructor Documentation

LocARNA::AlignmentImpl::AlignmentImpl	(	Alignment *	self,
		const Sequence &	seqA,
		const Sequence &	seqB
	)		[inline]

Constructor as empty alignment of two sequences.

Parameters:

self	self pointer
seqA	sequence A
seqB	sequence B

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Member Function Documentation

std::string LocARNA::AlignmentImpl::dot_bracket_structure	(	const std::string &	str,
		const Alignment::edge_ends_t &	x
	)		[static]

dot bracket structure

Parameters:

str	structure string
x	edge ends array

Returns:

structure string

void LocARNA::AlignmentImpl::write_debug

(

std::ostream &

out

)

const

Write raw alignment information for debugging.

Parameters:

out	output stream

void LocARNA::AlignmentImpl::write_debug	(	std::ostream &	out,
		const Alignment::edge_ends_t &	ends
	)		[static]

Write raw alignment information (one sequence) for debugging.

Parameters:

out	output stream
ends	description of alignment edge ends

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Member Data Documentation

Alignment::edge_ends_t LocARNA::AlignmentImpl::a_

first components of alignment edges

a_[i] is the position of the i-th alignment edge in seq A. Entries are positions of sequence A or -1 for gap.

Edges are sorted in ascending order.

Note:

the contained positions define the aligned subsequence! Not necessarily all sequence positions are contained.

Alignment::edge_ends_t LocARNA::AlignmentImpl::b_

second components of alignment edges

b_[i] is the position of the i-th alignment edge in seq B. Entries are positions of sequence B or -1 for gap.

Edges are sorted in ascending order.

Note:

the contained positions define the aligned subsequence! Not necessarily all sequence positions are contained.

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

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