A scoring scheme.
Score<TValue, TSpec>
Include Headers
The value type.
Default: int
The specializing type.
Default: Tag.Simple
EditDistanceEdit distance scoring scheme.
Score MatrixA general scoring matrix.
Simple ScoreSimple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.
DefaultFindBeginPatternSpecType of the default findBegin pattern specialization, given a score.
SequenceEntryForScoreReturns representation type for a character of a position in a sequence.
ValueType of the items in the container or behind an iterator.
Member Functions
alignmentEvaluationGiven a multiple alignment, this function calculates all kinds of alignment statistics.
bandedChainAlignmentComputes the best global pairwise alignment between two sequences given a non-empty seed chain.
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 entries entryH and entryV.
scoreGapScore for gaps.
scoreGapExtendScore for extending gaps.
scoreGapExtendHorizontalReturns the score for extending a gap in horizontal direction.
scoreGapExtendVerticalReturns the score for extending a gap in vertical direction.
scoreGapHorizontalReturns the score for a gap in horizontal direction.
scoreGapOpenScore for opening a gap.
scoreGapOpenHorizontalReturns the score for opening a gap in horizontal direction.
scoreGapOpenVerticalReturns the score for opening a gap in vertical direction.
scoreGapVerticalReturns the score for a gap in vertical direction.
scoreMatchMatch score.
scoreMismatchMismatch score.
sequenceEntryForScoreHelper function for element access, depending on score type.
setScoreGapSet gap opening and extension score.
setScoreGapExtendSet gap extension score.
setScoreGapOpenSet gap opening score.
setScoreMatchSet match score.
setScoreMismatchSet mismatch score.
splitAlignmentCompute split alignments.
sumOfPairsScoreGiven a multiple alignment, this function calculates the sum-of-pairs score.
1    Score<int> scoreScheme(5, -6, -2, -11);           // Initialize Score object with affine gap costs.
2    int score = globalAlignment(align, scoreScheme);  // Computes a global alignment usign the defined scoring scheme.
4    std::cout << "Score = " << score << std::endl;
5    std::cout << "Alignment:" << std::endl;
6    std::cout << align << std::endl;
Snippet from "score.cpp"
The output is as follows:
Score = 66
0     .    :    .    :    .
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SeqAn - Sequence Analysis Library -

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