| Class Specialization Simple Score Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.
Score
Simple Score
Score<TValue, Simple> Include Headers seqan/score.h Parameters
TValue | The value type. Default: int
Specialization of Score Metafunctions
DefaultFindBeginPatternSpec | Type of the default findBegin pattern specialization, given a score. (Score)
SequenceEntryForScore | Returns representation type for a character of a position in a sequence. (Score)
Value | Type of the items in the container or behind an iterator. (Score)
Member Functions
Score | Constructor (Score)
Functions
addSeed | Adds a seed to an existing SeedSet using different algorithms for local chaining.
alignmentEvaluation | Given a multiple alignment, this function calculates all kinds of alignment statistics. (Score)
bandedChainAlignment | Computes the best global pairwise alignment between two sequences given a non-empty seed chain. (Score)
buildAlignmentGraph | Builds an Alignment Graph from a set of input alignments. (Score)
extendSeed | Extends a seed.
globalAlignment | Computes the best global pairwise alignment. (Score)
globalAlignmentScore | Computes the best global pairwise alignment score. (Score)
globalMsaAlignment | Computes a global multiple alignment. (Score)
localAlignment | Computes the best pairwise local alignment using the Smith-Waterman algorithm. (Score)
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. (Score)
score | Returns the score for aligning the entries entryH and entryV. (Score)
scoreGap | Score for gaps. (Score)
scoreGapExtend | Score for extending gaps. (Score)
scoreGapExtendHorizontal | Returns the score for extending a gap in horizontal direction. (Score)
scoreGapExtendVertical | Returns the score for extending a gap in vertical direction. (Score)
scoreGapHorizontal | Returns the score for a gap in horizontal direction. (Score)
scoreGapOpen | Score for opening a gap. (Score)
scoreGapOpenHorizontal | Returns the score for opening a gap in horizontal direction. (Score)
scoreGapOpenVertical | Returns the score for opening a gap in vertical direction. (Score)
scoreGapVertical | Returns the score for a gap in vertical direction. (Score)
scoreMatch | Match score. (Score)
scoreMismatch | Mismatch score. (Score)
sequenceEntryForScore | Helper function for element access, depending on score type. (Score)
setScoreGap | Set gap opening and extension score. (Score)
setScoreGapExtend | Set gap extension score. (Score)
setScoreGapOpen | Set gap opening score. (Score)
setScoreMatch | Set match score. (Score)
setScoreMismatch | Set mismatch score. (Score)
splitAlignment | Compute split alignments. (Score)
sumOfPairsScore | Given a multiple alignment, this function calculates the sum-of-pairs score. (Score)
Shortcuts
SimpleScore | Simple scoring scheme.
Example Programs Local Alignments, Global Alignments See Also SimpleScore SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2014/10/13 16:13:00