Class
AlignConfigIndication of whether begin/end gaps are free for DP alignment algorithms.
Indication of whether begin/end gaps are free for DP alignment algorithms.
Defined in | <seqan/align.h> |
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Signature |
template <bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TSpec>
struct AlignConfig;
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Template Parameters
TOP |
Whether or not the begin gaps in the vertical sequence are free. |
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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