Class Specialization
Simple Score
Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.
Score
Simple Score
Score<TValue, Simple>
Include Headers
seqan/score.h
Parameters
TValue
The value type.
Default: int
Specialization of
Score
Metafunctions
DefaultFindBeginPatternSpecType of the default findBegin pattern specialization, given a score. (Score)
ValueType of the items in the container. (Score)
Member Functions
ScoreConstructor (Score)
Functions
alignmentEvaluationGiven a multiple alignment, this function calculates all kinds of alignment statistics. (Score)
bandedAlignmentCalculates a banded alignment around a Seed.
bandedChainAlignment Calculates a banded alignment around a chain of seeds.
extendSeedExtends a seed.
extendSeeds Extension of seeds.
extendSeedScoreExtends a seed and increases the score.
extendSeedsScore Extension of seeds with score calculation.
getAlignment Constructs a alignment from a ChainedSeed.
globalAlignmentComputes the best global alignment of the two sequences. (Score)
globalMsaAlignmentComputes a global multiple alignment. (Score)
localAlignmentComputes the best local alignment of two sequences. (Score)
matchRefinementRefines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the segments partly overlap. They are either identical (fully overlapping) or non-overlapping. (Score)
multiLocalAlignmentComputes multiple local alignments of two sequences. (Score)
scoreReturns the score for aligning the characters seq1[pos1] and seq2[pos2]. This function allows to define a position-dependent scoring scheme. (Score)
scoreReturns the score for aligning the characters seq1[pos1] and seq2[pos2]. This function allows to define a position-dependent scoring scheme. (Score)
scoreGapScore for gaps.
scoreGapExtendScore for extending gaps.
scoreGapOpenScore for opening a gap.
scoreMatchMatch score.
scoreMismatchMismatch score.
scoreSeed Calculates the score of a seed.
setScoreGapSet gap opening and extension score.
setScoreGapExtendSet gap extension score.
setScoreGapOpenSet gap opening score.
setScoreMatchSet match score.
setScoreMismatchSet mismatch score.
sumOfPairsScoreGiven a multiple alignment, this function calculates the sum-of-pairs score. (Score)
Shortcuts
SimpleScoreSimple scoring scheme.
See Also
SimpleScore
SeqAn - Sequence Analysis Library - www.seqan.de
 

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