An alignment of sequences.
Align<TSource, TSpec>
Include Headers
Type of the ungapped sequences.
Metafunctions: Source
The specializing type.
Metafunctions: Spec
Default: ArrayGaps
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.
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.
StringSetTypeReturn type of stringSet function.
ValueType of the items in the container or behind an iterator.
bamRecordToAlignmentConvert BamAlignmentRecord to an Align object.
bandedChainAlignmentComputes the best global pairwise alignment between two sequences given a non-empty seed chain.
colA column in an alignment.
colsThe container of columns in an alignment.
detachMakes an object independent from other objects.
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.
splitAlignmentCompute split alignments.
stringSetGets the string set of an alignment graph.
See Also
SeqAn - Sequence Analysis Library -

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