Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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< TSequenceTStringSet
 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...


 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)


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
SeqanSequenceConverterConverter 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.
FreeEndsAlignmentSeqan parameter (true by default) (see Simon)
ScoreTypeReturned score type (int by default)
SeqanUnitTypeUnit type in Seqan, that could be amino acid or nucleotid (AminoAcid by default)
SeqanCustomMatrixSeqan matrix defined in this header file for adapting the seqan matrix notation to this engine matrix notation (default is custom for amino acids)
SeqanAlgorithmSeqan 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.