Class
Score
A scoring scheme.

Score

EditDistance | ProfileSeq Score | ProfileSeqFrac Score | Score Matrix | Simple Score

Score<TValue, TSpec>
Include Headers
seqan/score.h
Parameters

TValue | The value type. Default: int
TSpec | The specializing type. Default: Tag.Simple

Specializations

EditDistance | Edit distance scoring scheme.
ProfileSeq Score | Score for profile-to-sequence alignments.
ProfileSeqFrac Score | Score for profile-to-sequence alignments.
Score Matrix | A general scoring matrix.
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.
SequenceEntryForScore | Returns representation type for a character of a position in a sequence.
Value | Type of the items in the container or behind an iterator.

Member Functions

Score | Constructor

Functions

alignmentEvaluation | Given a multiple alignment, this function calculates all kinds of alignment statistics.
bandedChainAlignment | Computes the best global pairwise alignment between two sequences given a non-empty seed chain.
buildAlignmentGraph | Builds an Alignment Graph from a set of input alignments.
globalAlignment | Computes the best global pairwise alignment.
globalAlignmentScore | Computes the best global pairwise alignment score.
globalMsaAlignment | Computes a global multiple alignment.
localAlignment | Computes the best pairwise local alignment using the Smith-Waterman algorithm.
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 | Returns the score for aligning the entries entryH and entryV.
scoreGap | Score for gaps.
scoreGapExtend | Score for extending gaps.
scoreGapExtendHorizontal | Returns the score for extending a gap in horizontal direction.
scoreGapExtendVertical | Returns the score for extending a gap in vertical direction.
scoreGapHorizontal | Returns the score for a gap in horizontal direction.
scoreGapOpen | Score for opening a gap.
scoreGapOpenHorizontal | Returns the score for opening a gap in horizontal direction.
scoreGapOpenVertical | Returns the score for opening a gap in vertical direction.
scoreGapVertical | Returns the score for a gap in vertical direction.
scoreMatch | Match score.
scoreMismatch | Mismatch score.
sequenceEntryForScore | Helper function for element access, depending on score type.
setScoreGap | Set gap opening and extension score.
setScoreGapExtend | Set gap extension score.
setScoreGapOpen | Set gap opening score.
setScoreMatch | Set match score.
setScoreMismatch | Set mismatch score.
splitAlignment | Compute split alignments.
sumOfPairsScore | Given a multiple alignment, this function calculates the sum-of-pairs score.

Examples

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.
3 |
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
Alignment:
0 . : . : .
ACGTG--GATCGGTGACTTACGGACTG
||||| || |||| ||||||||||
ACGTGTTGA---GTGA-TTACGGACTG
Example Programs
Local Alignments, Global Alignments
SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2014/10/13 16:12:56