fn() globalAlignmentScoreComputes the best global pairwise alignment score.
Computes the best global pairwise alignment score.
Defined in | <seqan/align.h> |
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Signature |
TScoreVal globalAlignmentScore(seqH, seqV, scoringScheme[, alignConfig][, lowerDiag, upperDiag][, algorithmTag]);
TScoreVal globalAlignmentScore(strings, scoringScheme[, alignConfig][, lowerDiag, upperDiag][, algorithmTag]);
TScoreVal globalAlignmentScore(seqH, seqV, {MyersBitVector | MyersHirschberg});
TScoreVal globalAlignmentScore(strings, {MyersBitVector | MyersHirschberg});
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Parameters
seqH
|
Horizontal gapped sequence in alignment matrix. Types: String |
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seqV
|
Vertical gapped sequence in alignment matrix. Types: String |
strings
|
A StringSet containing two sequences. Type: StringSet. |
alignConfig
|
The AlignConfig to use for the alignment. Type: AlignConfig |
scoringScheme
|
The scoring scheme to use for the alignment. Note that the user is responsible for ensuring that the scoring scheme is compatible with algorithmTag. Type: Score. |
lowerDiag
|
Optional lower diagonal. Types: int |
upperDiag
|
Optional upper diagonal. Types: int |
algorithmTag
|
The Tag for picking the alignment algorithm. Types: PairwiseLocalAlignmentAlgorithms. |
Return Values
TScoreVal |
Score value of the resulting alignment (Metafunction: Value of the type of scoringScheme). |
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Detailed Description
This function does not perform the (linear time) traceback step after the (mostly quadratic time) dynamic programming step. Note that Myers' bit-vector algorithm does not compute an alignment (only in the Myers-Hirschberg variant) but scores can be computed using globalAlignmentScore.
The same limitations to algorithms as in globalAlignment apply. Furthermore, the MyersBitVector and MyersHirschberg variants can only be used without any other parameter.
Data Races
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