A scoring scheme.
The value type.
The specializing type.
|Edit distance scoring scheme.|
|A general scoring matrix.|
|Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.|
|Type of the default findBegin pattern specialization, given a score.|
|Returns representation type for a character of a position in a sequence.|
|Type of the items in the container or behind an iterator.|
|Given a multiple alignment, this function calculates all kinds of alignment statistics.|
|Computes the best global pairwise alignment between two sequences given a non-empty seed chain.|
|Builds an Alignment Graph from a set of input alignments.|
|Computes the best global pairwise alignment.|
|Computes the best global pairwise alignment score.|
|Computes a global multiple alignment.|
|Computes the best pairwise local alignment using the Smith-Waterman algorithm.|
|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.|
|Returns the score for aligning the entries |
|Score for gaps.|
|Score for extending gaps.|
|Returns the score for extending a gap in horizontal direction.|
|Returns the score for extending a gap in vertical direction.|
|Returns the score for a gap in horizontal direction.|
|Score for opening a gap.|
|Returns the score for opening a gap in horizontal direction.|
|Returns the score for opening a gap in vertical direction.|
|Returns the score for a gap in vertical direction.|
|Helper function for element access, depending on score type.|
|Set gap opening and extension score.|
|Set gap extension score.|
|Set gap opening score.|
|Set match score.|
|Set mismatch score.|
|Compute split alignments.|
|Given a multiple alignment, this function calculates the sum-of-pairs score.|
Snippet from "score.cpp"
The output is as follows:
0 . : . : .
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