Class AlignConfig
Indication of whether begin/end gaps are free for DP alignment algorithms.

Defined in <seqan/align.h>
Signature template <bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TSpec> struct AlignConfig;

Template Parameters

TOP Whether or not the begin gaps in the vertical sequence are free.
LEFT Whether or not the begin gaps in the horizontal sequence are free.
RIGHT Whether or not the end gaps in the horizontal sequence are free.
BOTTOM Whether or not the end gap sin the vertical sequence are free.
TSpec Tag for specializing the AlignConfig object (default: Default).

Detailed Description

Used in the DP alignment algorithms to configure the begin/end gap free-nes.

Specialization List

The following gives an (incomplete) list of useful AlignConfig specializations.

AlignConfig<false, false, false, false>
ordinary global alignment
AlignConfig<true, false, false, true>
semiglobal alignment, free begin and end gaps in second/vertical sequence
AlignConfig<false, true, true, false>
semiglobal alignment, free begin and end gaps in first/horizontal sequence
AlignConfig<false, true, false, true>
overlap alignment with second/vertical sequence overhanging to the left of first/horizontal
AlignConfig<true, false, true, false>
overlap alignment with first/horizontal sequence overhanging to the left of second/vertical
AlignConfig<false, true, false, false>
free begin gaps in second/vertical sequence only
AlignConfig<false, false, true, false>
free end gaps in second/vertical sequence only

See Also