Class Specialization
Score Manhattan
Scoring scheme for chaining that computes gap scores using manhattan distance.
Score
Score Manhattan
Score<TValue, Manhattan>
Parameters
TValue
Type of the score values.
Remarks
The manhattan distance between two n-dimensional points is defined is the sum of the (absolute) differences of their coordinates.
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)
SeqAn - Sequence Analysis Library - www.seqan.de
 

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