Class
Score
A scoring scheme.
Score
 EditDistance Pam Score ChainSoP Score Manhattan Score Matrix Score Zero Simple Score
Score<TValue, TSpec>
Parameters
 TValue The value type.Default: int TSpec The specializing type.Default: Simple Score
Specializations
 EditDistance Edit distance scoring scheme. Pam Pam scoring matrices. 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.
Member Functions
 Score Constructor ~Score Destructor
Functions
 alignmentEvaluation Given a multiple alignment, this function calculates all kinds of alignment statistics. globalAlignment Computes the best global alignment of the two sequences. 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. 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 The score for aligning two values according to a scoring scheme. smithWaterman Computes the best local alignment of the (two) sequences given in align. smithWatermanGetNext Computes next best local alignment. sumOfPairsScore Given a multiple alignment, this function calculates the sum-of-pairs score.
Example Programs
SeqAn - Sequence Analysis Library - www.seqan.de