Class Specialization
Score ChainSoP
Scoring scheme for chaining that uses a special method for scoring the gaps between two fragments.
Score
Score ChainSoP
Score<TValue, ChainSoP>
Parameters
TValue
Type of the score values.
Remarks
This scoring scheme is used to score gaps between to fragments in chaining.
Specialization of
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)
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)
sumOfPairsScoreGiven a multiple alignment, this function calculates the sum-of-pairs score. (Score)
SeqAn - Sequence Analysis Library - www.seqan.de
 

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