Class
Score
A scoring scheme.
Score
 EditDistance Score ChainSoP Score Manhattan Score Matrix Score Zero Simple Score
Score<TValue, TSpec>
Include Headers
seqan/score.h
Parameters
 TValue The value type.Default: int TSpec The specializing type.Default: Simple
Specializations
 EditDistance Edit distance scoring scheme. Score ChainSoP Scoring scheme for chaining that uses a special method for scoring the gaps between two fragments. Score Manhattan Scoring scheme for chaining that computes gap scores using manhattan distance. Score Matrix A general scoring matrix. Score Zero Scoring scheme for chaining that set gap scores to 0 Simple Score Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.
Metafunctions
 DefaultFindBeginPatternSpec Type of the default findBegin pattern specialization, given a score. Value Type of the items in the container.
Member Functions
 Score Constructor
Functions
 alignmentEvaluation Given a multiple alignment, this function calculates all kinds of alignment statistics. globalAlignment Computes the best global alignment of the two sequences. globalMsaAlignment Computes a global multiple alignment. localAlignment Computes the best local alignment of two sequences. matchRefinement Refines (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. multiLocalAlignment Computes multiple local alignments of two sequences. score Returns the score for aligning the characters seq1[pos1] and seq2[pos2]. This function allows to define a position-dependent scoring scheme. score Returns the score for aligning the characters seq1[pos1] and seq2[pos2]. This function allows to define a position-dependent scoring scheme. sumOfPairsScore Given a multiple alignment, this function calculates the sum-of-pairs score.
Example Programs
SeqAn - Sequence Analysis Library - www.seqan.de

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