Class
Align
An alignment of sequences.
Align<TSource, TSpec>
Include Headers
seqan/align.h
Parameters

TSource | Type of the ungapped sequences. Metafunctions: Source
TSpec | The specializing type. Metafunctions: Spec

Remarks
The default implementation of Align stores the alignment in a set of TSpec> objects. Hence, the default implementation is row-based, so it will be faster to access the alignment row-wise than column-wise.
Metafunctions

Col | Type of a column in an alignment.
Cols | Type of column container of an alignment.
Cols | Type of column container of an alignment.
GetValue | Type for reading values.
Reference | Reference type.
Row | Type of a row in an alignment.
Rows | Type of row container of an alignment.
Rows | Type of row container of an alignment.
Source | The underlying sequence for alignments or gaps data structures.
Value | Type of the items in the container.

Functions

bandedAlignment | Calculates a banded alignment around a Seed.
bandedChainAlignment | Calculates a banded alignment around a chain of seeds.
col | A column in an alignment.
cols | The container of columns in an alignment.
detach | Makes an object independent from other objects.
getAlignment | Turns a HSP from a Blast search into an Alignment object.
getAlignment | Constructs a alignment from a ChainedSeed.
globalAlignment | Computes the best global alignment of the two sequences.
integrateAlign | Integrates an alignment into another by copying the gaps.
integrateAlign | Integrates an alignment into another by copying the gaps.
localAlignment | Computes the best local alignment of two sequences.
matchRefinement | 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.
row | A row in an alignment.
rows | The container of rows in an alignment.
setStrings | Loads the sequences of a stringset into an alignment.
stringSet | Gets the string set of an alignment graph.

Example Programs
Local Alignments, Global Alignments
See Also
AlignCols
SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2012/03/14 16:34:45