Class
Score
A scoring scheme.
Include Headers
seqan/score.h
Parameters
The value type. Default: int | |
The specializing type. Default: |
Specializations
| Edit distance scoring scheme. | |
| A general scoring matrix. | |
| Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps. |
Metafunctions
| 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. |
Member Functions
| Constructor |
Functions
| 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 characters | |
| Score for gaps. | |
| Score for extending gaps. | |
| Returns the score for extending a horizontal gap after | |
| Returns the score for extending a vertical gap after | |
| Returns the score for a horizontal gap after | |
| Score for opening a gap. | |
| Returns the score for opening a horizontal gap after | |
| Returns the score for opening a vertical gap after | |
| Returns the score for a vertical gap after | |
| Match score. | |
| Mismatch score. | |
| 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. |
Example Programs
SeqAn - Sequence Analysis Library - www.seqan.de