Class
LocalAlignmentEnumeratorEnumeration of local alignments.
Enumeration of local alignments.
All Subcl's | BandedLocalAlignmentEnumerator, UnbandedLocalAlignmentEnumerator |
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Defined in | <seqan/align.h> |
Signature |
template <typename TScore, typename TSpec>
class LocalAlignmentEnumerator;
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Template Parameters
TScore |
The type of the Score to use for the local alignment. |
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TSpec |
The tag to use for specializing the enumerator. |
Interface Function Overview
-
TScoreVal getScore(enumerator);
Get current alignment score. -
bool nextLocalAlignment(align, enumerator);, bool nextLocalAlignment(gapsH, gapsV, enumerator);
Compute next suboptimal local alignment.
Detailed Description
This is an abstract class that will only be instantiated through its subclasses. See the documentation of the specializations for examples.
References
- Waterman MS, Eggert M: A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. J Mol Biol 1987, 197(4):723-728.
Interface Functions Detail
TScoreVal getScore(enumerator);
Get current alignment score.
Parameters
enumerator
|
The LocalAlignmentEnumerator to query. |
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Returns
TScoreVal |
The current alignment score (Value of TScore). |
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Data Races
Thread safety unknown!
bool nextLocalAlignment(align, enumerator);
bool nextLocalAlignment(gapsH, gapsV, enumerator);
Compute next suboptimal local alignment.
Parameters
align
|
Align object to use for the alignment representation. |
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gapsH
|
Gaps object to use for the first/horizontal sequence in the alignment matrix. |
gapsV
|
Gaps object to use for the second/vertical sequence in the alignment matrix. |
enumerator
|
The LocalAlignmentEnumerator to advance. |
Returns
bool |
true if another suboptimal alignment above the given threshold was found and false otherwise. |
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Data Races
Thread safety unknown!