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
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
ColType of a column in an alignment.
ColsType of column container of an alignment.
GetValueType for reading values.
ReferenceReference type.
RowType of a row in an alignment.
RowsType of row container of an alignment.
SourceReturn underlying sequence of Gaps/Alignments.
ValueType of the items in the container or behind an iterator.
Functions
bamRecordToAlignmentConvert BamAlignmentRecord to an Align object.
bandedAlignmentCalculates a banded alignment around a Seed.
bandedChainAlignment Calculates a banded alignment around a chain of seeds.
colA column in an alignment.
colsThe container of columns in an alignment.
detachMakes an object independent from other objects.
getAlignment Constructs a alignment from a ChainedSeed.
globalAlignmentComputes the best global pairwise alignment.
integrateAlignIntegrates an alignment into another by copying the gaps.
localAlignmentComputes the best pairwise local alignment using the Smith-Waterman algorithm.
matchRefinementRefines (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.
nextLocalAlignmentCompute next suboptimal local alignment.
rowA row in an alignment.
rowsThe container of rows in an alignment.
setStringsLoads the sequences of a stringset into an alignment.
stringSetGets the string set of an alignment graph.
See Also
SeqAn - Sequence Analysis Library - www.seqan.de
 

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