T_Aligner_sequence_seqan_wrapper< SeqanSequenceConverter, FreeEndsAlignment, ScoreType, SeqanUnitType, SeqanCustomMatrix, SeqanAlgorithm > Class Template Reference

Wrapper of the Seqan algorithm for aligning pairwise sequences. More...

#include <Alignment_engine_sequences_seqan.hpp>

Public Types
typedef seqan::Score< ScoreType, seqan::ScoreMatrix< SeqanUnitType, SeqanCustomMatrix > >	Scoring_matrix
	Scoring matrix in Seqan. More...
typedef seqan::String< char >	TSequence
	Sequence type. More...
typedef seqan::StringSet< TSequence >	TStringSet
	Container for strings. More...
typedef seqan::StringSet< TSequence, seqan::Dependent<> >	TDepStringSet
	Dependent string set. More...
typedef seqan::Graph< seqan::Alignment< TDepStringSet > >	TAlignGraph
	Alignment graph. More...
typedef std::pair< std::string, std::string >	AlignedSequences
	Return type independent of seqan's objects. More...

Constructors
	T_Aligner_sequence_seqan_wrapper (Score_type gap_open_score=-10, Score_type gap_extend_score=-1)

Accessors / Modifiers
char	get_gap_symbol (void) const
void	set_gap_symbol (char gap_symbol)
const Score_type &	get_gap_open_score (void) const
void	set_gap_open_score (const Score_type &gap_open_score)
const Score_type &	get_gap_extend_score (void) const
void	set_gap_extend_score (const Score_type &gap_extend_score)
void	set_substitution_score (char x, char y, const Score_type &score)

Functor
template<class SequenceType , class OutputIterator >
Score_type	operator() (const SequenceType &seq_1, const SequenceType &seq_2, OutputIterator out)

Detailed Description

template<class SeqanSequenceConverter = T_Default_amino_acid_seqan_sequence_converter<>, bool FreeEndsAlignment = true, class ScoreType = int, class SeqanUnitType = seqan::AminoAcid, class SeqanCustomMatrix = seqan::CustomAminoAcidMatrix, class SeqanAlgorithm = seqan::Gotoh>
class SBL::CSB::T_Aligner_sequence_seqan_wrapper< SeqanSequenceConverter, FreeEndsAlignment, ScoreType, SeqanUnitType, SeqanCustomMatrix, SeqanAlgorithm >

Wrapper of the Seqan algorithm for aligning pairwise sequences.

It is specialized by default for amino acids with a custom score matrix filled with integers.

Template Parameters

SeqanSequenceConverter	Converter between unit names in a sequence defined in the SBL and a unit of a Seqan sequence. It defines the two methods to_seqan_sequence and to_unit_name.
FreeEndsAlignment	Seqan parameter (true by default) (see Simon)
ScoreType	Returned score type (int by default)
SeqanUnitType	Unit type in Seqan, that could be amino acid or nucleotid (AminoAcid by default)
SeqanCustomMatrix	Seqan matrix defined in this header file for adapting the seqan matrix notation to this engine matrix notation (default is custom for amino acids)
SeqanAlgorithm	Seqan algorithm used to solve the alignments (default is Gotoh)

Member Typedef Documentation

AlignedSequences

typedef std::pair<std::string, std::string> AlignedSequences

Return type independent of seqan's objects.

Scoring_matrix

typedef seqan::Score<ScoreType, seqan::ScoreMatrix<SeqanUnitType, SeqanCustomMatrix> > Scoring_matrix

Scoring matrix in Seqan.

TAlignGraph

typedef seqan::Graph<seqan::Alignment<TDepStringSet> > TAlignGraph

Alignment graph.

TDepStringSet

typedef seqan::StringSet<TSequence, seqan::Dependent<> > TDepStringSet

Dependent string set.

TSequence

typedef seqan::String<char> TSequence

Sequence type.

TStringSet

typedef seqan::StringSet<TSequence> TStringSet

Container for strings.