LocARNA::AlignmentImpl Class Reference

Implementation of Alignment. More...

#include <alignment_impl.hh>

Collaboration diagram for LocARNA::AlignmentImpl:

Public Member Functions
	AlignmentImpl (const Sequence &seqA, const Sequence &seqB)
	Constructor as empty alignment of two sequences. More...
bool	empty () const

Public Attributes
const Sequence	seqA_
	sequence A
const Sequence	seqB_
	sequence B
Alignment::edges_t	edges_
	alignment edges More...
std::string	strA_
	structure of A as dot-bracket string
std::string	strB_
	structure of B as dot-bracket string

Detailed Description

Implementation of Alignment.

Constructor & Destructor Documentation

AlignmentImpl()

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

inline

Constructor as empty alignment of two sequences.

Parameters

seqA	sequence A
seqB	sequence B

Member Function Documentation

empty()

bool LocARNA::AlignmentImpl::empty ( ) const

inline

check for empty alignment

Returns

whether alignment is empty

Member Data Documentation

edges_

Alignment::edges_t LocARNA::AlignmentImpl::edges_

alignment edges

edges_[i] is the pair of positions (in seq A and B) of the i-th alignment edge. edge ends are sequence positions 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 file:

• src/LocARNA/alignment_impl.hh