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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/align__cleanup_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/sequence/align_cleanup.hpp Source File

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1 #ifndef ALGO_SEQ___ALIGN_CLEANUP__HPP 2 #define ALGO_SEQ___ALIGN_CLEANUP__HPP 55  typedef

list< CRef<CSeq_align> >

TAligns

;

67  void

Cleanup(

const

TAligns& aligns_in,

71  void

Cleanup(

const

TConstAligns& aligns_in,

99  static void

CreatePairwiseFromMultiple(

const CSeq_align

& multiple,

108  void

x_Cleanup_AlignVec(

const TConstAligns

& aligns_in,

111  void

x_Cleanup_AnchoredAln(

const TConstAligns

& aligns_in,

class CAlignCleanup implements an alignment cleanup utility based on the C++ alignment manager.

void AllowTranslocations(bool)

Permit off-diagonal high-scoring items (particularly ones on the opposite strand)

list< CConstRef< CSeq_align > > TConstAligns

list< CRef< CSeq_align > > TAligns

void FillUnaligned(bool b)

Fill any unaligned regions with explicit gaps.

void SortInputsByScore(bool b)

flags these primarity affect the CAlnVec implementation

void PreserveRows(bool b)

Assume that the alignments contains alignments of a sequence to itself.

Include a standard set of the NCBI C++ Toolkit most basic headers.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_XALGOSEQ_EXPORT

E_Choice

Choice variants.

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