Class
Score
A scoring scheme.
Score<TValue, TSpec>
Include Headers
seqan/score.h
Parameters
TValue
The value type.
Default: int
TSpec
The specializing type.
Default: Tag.Simple
Specializations
EditDistanceEdit distance scoring scheme.
Score ChainSoPScoring scheme for chaining that uses a special method for scoring the gaps between two fragments.
Score ManhattanScoring scheme for chaining that computes gap scores using manhattan distance.
Score MatrixA general scoring matrix.
Score ZeroScoring scheme for chaining that set gap scores to 0
Simple ScoreSimple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.
Metafunctions
DefaultFindBeginPatternSpecType of the default findBegin pattern specialization, given a score.
ValueType of the items in the container or behind an iterator.
Member Functions
ScoreConstructor
Functions
alignmentEvaluationGiven a multiple alignment, this function calculates all kinds of alignment statistics.
buildAlignmentGraphBuilds an Alignment Graph from a set of input alignments.
globalAlignmentComputes the best global pairwise alignment.
globalAlignmentScoreComputes the best global pairwise alignment score.
globalMsaAlignmentComputes a global multiple alignment.
localAlignmentComputes the best pairwise local alignment using the Smith-Waterman algorithm.
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.
scoreReturns the score for aligning the characters seq1[pos1] and seq2[pos2]. This function allows to define a position-dependent scoring scheme.
scoreGapScore for gaps.
scoreGapExtendScore for extending gaps.
scoreGapOpenScore for opening a gap.
scoreMatchMatch score.
scoreMismatchMismatch score.
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.
SeqAn - Sequence Analysis Library - www.seqan.de
 

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