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1 #ifndef OBJTOOLS_ALNMGR___ALN_USER_OPTIONS__HPP 2 #define OBJTOOLS_ALNMGR___ALN_USER_OPTIONS__HPPOptions for different alignment manager operations.
objects::CBioseq_Handle m_Anchor
Anchor bioseq - if null then a multiple alignment shall be built.
void SetAnchorId(const TAlnSeqIdIRef &anchor_id)
Set anchor id.
const TAlnSeqIdIRef & GetAnchorId(void) const
Get anchor id.
EMergeAlgo
Alignment merging algorithm.
@ eMergeAllSeqs
Merge all sequences (greedy algo).
@ ePreserveRows
Preserve all rows as they were in the input (e.g.
@ eQuerySeqMergeOnly
Only put the query seq on same row (input order is not significant).
EDirection
Row direction flags.
@ eBothDirections
No filtering: use both direct and reverse sequences.
@ eDefaultDirection
By default don't filter by direction.
@ eDirect
Use only sequences whose strand is the same as that of the anchor.
@ eReverse
Use only sequences whose strand is opposite to that of the anchor.
void SetMergeFlags(TMergeFlags flags, bool set)
Set/clear merge flags.
EMergeFlags
Additional merge flags.
@ fUseAnchorAsAlnSeq
Use the anchor sequence as the alignment sequence.
@ fAllowTranslocation
Allow translocations on the same row.
@ fSkipSortByScore
In greedy algos, skip sorting input alignments by score thus allowing for user-defined sort order.
@ fAnchorRowFirst
Store anchor row in the first pairwise alignment (by default it's stored in the last one).
@ fTruncateOverlaps
Truncate overlapping ranges.
@ fIgnoreInsertions
Do not collect and store insertions (gaps on the anchor).
@ fAllowMixedStrand
Allow mixed strands on the same row.
objects::CBioseq_Handle m_ClipSeq
EShowUnalignedOption m_UnalignedOption
Include a standard set of the NCBI C++ Toolkit most basic headers.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.
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