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NCBI C++ ToolKit: src/gui/objutils/sparse_iterator.cpp Source File

( ! (

)*

) {

.IntersectWith(clip);

.IntersectWith(clip);

first_gap =

, last_gap =

;

pair<TAlignColl::const_iterator, bool> res =

->

(from);

(res.first->FirstContains(from));

(res.first->FirstContains(to));

: m_Coll(

.m_Coll),

m_Flag(

.m_Flag),

m_It_1(

.m_It_1),

m_It_2(

.m_It_2)

CSparseIterator::operator

()

(m_Coll && m_It_1 >= m_Coll->begin()) {

(m_It_1 <= m_Clip->m_Last_It_1) && (m_It_2 <= m_Clip->m_Last_It_2);

}

((

)*

&&

->GetFirstFrom() !=

->GetFirstToOpen());

(

->GetFirstFrom() ==

->GetFirstTo()) {

(

(*

) ==

(it)) {

(

(*

) ==

(it)) {

const_iterator end() const

pair< const_iterator, bool > find_2(position_type pos) const

returns an iterator pointing to a range containing "pos"; if such a range does not exists an iterator...

const_iterator begin() const

CAlignRange Represents an element of pairwise alignment of two sequences.

CSparseIterator - IAlnSegmentIterator implementation for CAlnMap::CAlnChunkVec.

void x_InitSegment()

CSparseIterator.

TAlignColl::const_iterator m_It_1

SClip * m_Clip

iterating mode

virtual const value_type * operator->() const

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

TAlignColl::const_iterator m_It_2

virtual IAlnSegmentIterator * Clone() const

Create a copy of the iterator.

virtual const value_type & operator*() const

virtual IAlnSegmentIterator & operator++()

postfix operators are not defined to avoid performance overhead

const TAlignColl * m_Coll

bool x_Equals(const CSparseIterator &it) const

CSparseSegment m_Segment

if m_It1 != m_It2 then the iterator points to a gap between m_It1 and m_It2

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

Compare iterators.

virtual ~CSparseIterator()

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

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.

@ 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...

int TSignedSeqPos

Type for signed sequence position.

position_type GetToOpen(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

USING_SCOPE(ncbi::objects)

const_iterator m_Last_It_1

const_iterator m_Last_It_2

const_iterator m_First_It

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