ppALIGN API documentation

AlignOverlap::AlignSegment Class Reference

#include <alignoverlap.hpp>

List of all members.

Public Member Functions

result retrieval.



void StreamOutQuery (std::ostream &ost)
void StreamOutSubject (std::ostream &ost)
void GetAlign (Align &a) const
alternative_iterator BeginAlternatives (const std::string &generator)
alternative_iterator EndAlternatives (const std::string &generator)

Public Attributes

Pair start_pos
bool overlap
long n_matches
long n_insertions
long n_deletions

Friends

class AlignOverlap
class AlternativeSegment

Detailed Description

Segments in the original alignment.

Definition at line 198 of file alignoverlap.hpp.

Member Function Documentation

AlignOverlap::alternative_iterator AlignOverlap::AlignSegment::BeginAlternatives ( const std::string &  generator  )  [inline]

begin iterator for the map AlterantiveAlign -> number of occurencies.

Definition at line 367 of file alignoverlap.hpp.

AlignOverlap::alternative_iterator AlignOverlap::AlignSegment::EndAlternatives ( const std::string &  generator  )  [inline]

end iterator for the map AlterantiveAlign -> number of occurencies.

Definition at line 382 of file alignoverlap.hpp.

void AlignOverlap::AlignSegment::GetAlign ( Align &  a  )  const

create an alignment with poster probs from the segment.

Parameters:
a alignment that is generated
void AlignOverlap::AlignSegment::StreamOutQuery ( std::ostream &  ost  ) 

Stream out formated query sequence of the alignment segment.

Parameters:
ost outstream object
seq1 sequence
void AlignOverlap::AlignSegment::StreamOutSubject ( std::ostream &  ost  ) 

Stream out formated subject sequence of the alignment segment.

Parameters:
ost outstream object
seq2 sequence

Member Data Documentation

long AlignOverlap::AlignSegment::n_matches

number of matches/mismatches, insertions and deletions in this region

Definition at line 213 of file alignoverlap.hpp.

bool AlignOverlap::AlignSegment::overlap

is an overlap region. If it is true, this is a common segment to all alignments, the reference and all alternative alignments.

Definition at line 210 of file alignoverlap.hpp.

Pair AlignOverlap::AlignSegment::start_pos

first pair of letter indices

Definition at line 204 of file alignoverlap.hpp.

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