Class Specialization
EditDistance
Edit distance scoring scheme.
Score
EditDistance
Score<TValue, EditDistance>
Include Headers
seqan/score.h
Parameters
TValue
The value type.
Default: int
Remarks
Semantically equivalent to a default contructed Score<int, Simple>.
EditDistance is a synonym for LevenshteinDistance.
Specialization of
Metafunctions
DefaultFindBeginPatternSpecType of the default findBegin pattern specialization, given a score. (Score)
ValueType of the items in the container or behind an iterator. (Score)
Member Functions
ScoreConstructor (Score)
Functions
alignmentEvaluationGiven a multiple alignment, this function calculates all kinds of alignment statistics. (Score)
buildAlignmentGraphBuilds an Alignment Graph from a set of input alignments. (Score)
globalAlignmentComputes the best global pairwise alignment. (Score)
globalAlignmentScoreComputes the best global pairwise alignment score. (Score)
globalMsaAlignmentComputes a global multiple alignment. (Score)
localAlignmentComputes the best pairwise local alignment using the Smith-Waterman algorithm. (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)
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. (Score)
scoreGapExtendScore for extending gaps. (Score)
scoreGapOpenScore for opening a gap. (Score)
scoreMatchMatch score. (Score)
scoreMismatchMismatch score. (Score)
setScoreGapSet gap opening and extension score. (Score)
setScoreGapExtendSet gap extension score. (Score)
setScoreGapOpenSet gap opening score. (Score)
setScoreMatchSet match score. (Score)
setScoreMismatchSet mismatch score. (Score)
sumOfPairsScoreGiven a multiple alignment, this function calculates the sum-of-pairs score. (Score)
Shortcuts
EditDistanceScoreEdit distance scoring scheme.
SeqAn - Sequence Analysis Library - www.seqan.de
 

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