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NCBI C++ ToolKit: include/objtools/alnmgr/sparse_ci.hpp Source File

1 #ifndef __OBJTOOLS_ALNMGR___SPARSE_CI__HPP 2 #define __OBJTOOLS_ALNMGR___SPARSE_CI__HPP 46 virtual operator bool

(

void

)

const

;

57

m_AlnRange.Set(aln_from, aln_to);

58

m_RowRange.Set(from, to);

100 virtual operator bool

(

void

)

const

;

109 virtual const value_type

* operator->(

void

)

const

;

115 void

x_InitIterator(

void

);

116 void

x_InitSegment(

void

);

117 void

x_CheckSegment(

void

);

118 void

x_NextSegment(

void

);

119 bool

x_Equals(

const CSparse_CI

& other)

const

;

CPairwiseAln iterator. Iterates over aligned ranges and gaps.

CAnchoredAln::TDim TDim

Synonym of TNumrow.

Implementation of IAlnSegment for CSparseAln.

void Init(TSignedSeqPos aln_from, TSignedSeqPos aln_to, TSignedSeqPos from, TSignedSeqPos to, TSegTypeFlags type)

Implementation of IAlnSegmentIterator for CSparseAln.

TSignedRange m_TotalRange

CConstRef< CAnchoredAln > m_Aln

bool IsAnchorDirect(void) const

Check if the anchor row coordinates are on plus strand.

CPairwise_CI::TSignedRange TSignedRange

TSignedRange m_NextAnchorRg

Alignment segment iterator interface.

Alignment segment interface.

virtual const TSignedRange & GetRange(void) const =0

Get the selected row range.

virtual TSegTypeFlags GetType(void) const =0

Get current segment type.

virtual const TSignedRange & GetAlnRange(void) const =0

Get alignment range for the segment.

bool operator==(const CEquivRange &A, const CEquivRange &B)

int TSignedSeqPos

Type for signed sequence position.

CVect2< NCBI_PROMOTE(int,U) > operator*(int v1, const CVect2< U > &v2)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

bool operator!=(const CNCBI_IPAddr &lhs, unsigned int rhs)

#define NCBI_XALNMGR_EXPORT

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

Miscellaneous common-use basic types and functionality.

#define row(bind, expected)

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