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NCBI C++ ToolKit: src/objtools/alnmgr/sparse_ci.cpp Source File

CSparseSegment::operator

(

)

!IsInvalidType();

anchor_gap = anchor_gap ||

anchor_gap = anchor_gap ||

(left_offset, right_offset);

(left_offset > row_rg.

()) {

(right_offset > row_rg.

() - left_offset) {

right_offset = row_rg.

() - left_offset;

( aln_rg.

() ) {

( !*

)

;

: m_Flags(eAllSegments),

m_AnchorDirect(

),

m_AnchorDirect(

),

m_AnchorDirect(

),

CSparse_CI::operator

(

)

m_Aln && (m_AnchorIt || m_RowIt);

(

(*

) ==

(it)) {

(

(*

) ==

(it)) {

@ fMixedDir

contains at least one reversed range

const TPairwiseAlnVector & GetPairwiseAlns(void) const

The vector of pairwise alns.

TDim GetAnchorRow(void) const

Which is the anchor row?

A pairwise aln is a collection of ranges for a pair of rows.

CPairwiseAln iterator. Iterates over aligned ranges and gaps.

bool IsDirect(void) const

Direction of the second sequence relative to the first one.

@ eGap

Gap or unaligned range.

bool IsFirstDirect(void) const

Absolute direction of the first sequence.

ESegType GetSegType(void) const

Get current segment type.

const TSignedRange & GetSecondRange(void) const

Current range on the second sequence. May be empty when in a gap.

const TSignedRange & GetFirstRange(void) const

Current range on the first sequence.

virtual const TSignedRange & GetAlnRange(void) const

Get alignment range for the segment.

virtual TSegTypeFlags GetType(void) const

Get current segment type.

virtual const TSignedRange & GetRange(void) const

Get the selected row range.

CSparseSegment(void)

CSparseSegment - IAlnSegment implementation for CAlnMap::CAlnChunk.

Implementation of IAlnSegmentIterator for CSparseAln.

virtual const value_type & operator*(void) const

TSignedRange m_TotalRange

void x_InitSegment(void)

CSparse_CI.

virtual ~CSparse_CI(void)

virtual IAlnSegmentIterator * Clone(void) const

Create a copy of the iterator.

CConstRef< CAnchoredAln > m_Aln

void x_CheckSegment(void)

virtual const value_type * operator->(void) const

virtual bool operator==(const IAlnSegmentIterator &it) const

Compare iterators.

virtual bool operator!=(const IAlnSegmentIterator &it) const

void x_InitIterator(void)

CSparse_CI(void)

Create 'empty' iterator.

virtual IAlnSegmentIterator & operator++(void)

Advance to the next segment.

TSignedRange m_NextAnchorRg

bool x_Equals(const CSparse_CI &other) const

Alignment segment iterator interface.

@ eSkipInserts

Iterate segments where at least some rows are aligned (including gap segments)

@ eInsertsOnly

Iterate only ranges not participating in the alignment (unaligned segments)

@ eAllSegments

Iterate all segments.

@ eSkipGaps

Skip gap segments (show only aligned ranges)

Alignment segment interface.

@ fAligned

Aligned segment.

@ fInvalid

The iterator is in bad state.

@ fIndel

Either anchor or the selected row is not present in the segment.

@ fUnaligned

The range on the selected sequence does not participate in the alignment (the alignment range of the ...

@ fReversed

The selected row is reversed (relative to the anchor).

@ fGap

Both anchor row and the selected row are not included in the segment (some other row is present and t...

bool IsAligned(void) const

int TSignedSeqPos

Type for signed sequence position.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

void Reset(void)

Reset reference object.

position_type GetLength(void) const

TThisType & SetToOpen(position_type toOpen)

position_type GetToOpen(void) const

static TThisType GetEmpty(void)

TThisType & SetOpen(position_type from, position_type toOpen)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

void SetFrom(TFrom value)

Assign a value to From data member.

TFrom GetFrom(void) const

Get the From member data.

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

USING_SCOPE(ncbi::objects)

#define row(bind, expected)

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