Class
Align
An alignment of sequences.
Include Headers
seqan/align.h
Parameters
Type of the ungapped sequences. Metafunctions: Source | |
The specializing type. Metafunctions: Spec Default: ArrayGaps |
Remarks
The default implementation of Align stores the alignment in a set of Gaps<TSource,TSpec> objects.
Hence, the default implementation is row-based, so it will be faster to access the alignment row-wise than column-wise.
Metafunctions
| Type of a column in an alignment. | |
| Type of column container of an alignment. | |
| Type for reading values. | |
| Reference type. | |
| Type of a row in an alignment. | |
| Type of row container of an alignment. | |
| Return underlying sequence of Gaps/Alignments. | |
| Return type of stringSet function. | |
| Type of the items in the container or behind an iterator. |
Functions
| Convert BamAlignmentRecord to an Align object. | |
| Computes the best global pairwise alignment between two sequences given a non-empty seed chain. | |
| A column in an alignment. | |
| The container of columns in an alignment. | |
| Makes an object independent from other objects. | |
| Computes the best global pairwise alignment. | |
| Integrates an alignment into another by copying the gaps. | |
| 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. | |
| Compute next suboptimal local alignment. | |
| A row in an alignment. | |
| The container of rows in an alignment. | |
| Loads the sequences of a stringset into an alignment. | |
| Compute split alignments. | |
| Gets the string set of an alignment graph. |
Examples
File "align.cpp"
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The output is as follows:
align
0 . :
AGTTTAATCA
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AGTAT-ACGA
Example Programs
See Also
SeqAn - Sequence Analysis Library - www.seqan.de