LocARNA-1.9.2
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Public Member Functions | Static Public Member Functions | Public Attributes
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

Alignmentself_
 self pointer
const SequenceseqA_
 sequence A
const SequenceseqB_
 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

Detailed Description

Implementation of Alignment.


Constructor & Destructor Documentation

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

Constructor as empty alignment of two sequences.

Parameters:
selfself pointer
seqAsequence A
seqBsequence B

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:
strstructure string
xedge ends array
Returns:
structure string
void LocARNA::AlignmentImpl::write_debug ( std::ostream &  out) const

Write raw alignment information for debugging.

Parameters:
outoutput 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:
outoutput stream
endsdescription of alignment edge ends

Member Data Documentation

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.

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.

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