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

m_It != m_Aln->end() &&

m_GapIt != m_Aln->end() &&

m_GapIt->GetFirstFrom() < m_Range.GetToOpen() &&

m_It->GetFirstToOpen() > m_Range.GetFrom();

m_It == m_GapIt ? eAligned :

;

m_It->IsDirect();

m_Direct(force_direct),

x_Init(force_direct);

x_Init(

force_direct =

);

: m_AnchorRow(kInvalidAnchorRow),

m_AnchorRow(c.m_AnchorRow),

m_PairwiseAlns.resize(c.

());

m_PairwiseAlns[

].Reset(pairwise_aln);

(

)m_PairwiseAlns.size();

GetPairwiseAlns()[

]->GetSecondId();

m_PairwiseAlns;

(m_AnchorRow != kInvalidAnchorRow);

(m_AnchorRow < GetDim());

(m_AnchorRow);

(m_AnchorRow == kInvalidAnchorRow);

m_PairwiseAlns.resize(dim);

m_PairwiseAlns;

m_AnchorRow = anchor_row;

SplitStrands(

);

kInvalidAnchorRow = -1;

c_1->GetScore() > c_2->GetScore();

class CAlignRangeCollectionList<TAlignRange> represent a sorted collection of TAlignRange.

@ fDefaultPolicy

do not store insertions

void x_MultiplyCoordsBy3()

class CAlignRangeCollection<TAlignRange> represent a sorted collection of TAlignRange.

void Assign(const CAlignRangeCollectionList< TAlignRange > &src)

CAlignRange Represents an element of pairwise alignment of two sequences.

Query-anchored alignment can be 2 or multi-dimentional.

const TPairwiseAlnVector & GetPairwiseAlns(void) const

The vector of pairwise alns.

int & SetScore(void)

Non-const access to the total score.

vector< CRef< CPairwiseAln > > TPairwiseAlnVector

CAnchoredAln(void)

Default constructor.

const TAlnSeqIdIRef & GetId(TDim row) const

Seq ids of the rows.

TPairwiseAlnVector m_PairwiseAlns

TDim GetDim(void) const

How many rows.

void SetAnchorRow(TDim anchor_row)

Modify anchor row (never do this unless you are creating a new alignment and know what you're doing).

TPairwiseAlnVector & SetPairwiseAlns(void)

Modify pairwise alns.

void SetScore(int score)

Set the total score.

TDim GetAnchorRow(void) const

Which is the anchor row?

CAnchoredAln & operator=(const CAnchoredAln &c)

NB: Assignment operator is deep on pairwise_alns so that pairwise_alns can be modified.

int GetScore(void) const

What is the total score?

CAnchoredAln(const CAnchoredAln &c)

NB: Copy constructor is deep on pairwise_alns so that pairwise_alns can be modified.

const TAlnSeqIdIRef & GetAnchorId(void) const

What is the seq id of the anchor?

void SetDim(TDim dim)

Modify the number of rows.

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

CAlignRangeCollectionList< TAlnRng > TAlnRngColl

CAlignRange< TPos > TAlnRng

int GetSecondBaseWidth(void) const

Base width of the second row.

void ForceGenomicCoords(void)

If both sequences are proteins, convert coordinates to genomic anyway.

const TAlnSeqIdIRef & GetFirstId(void) const

Get first sequence id.

CPairwiseAln(const TAlnSeqIdIRef &first_id, const TAlnSeqIdIRef &second_id, int flags=fDefaultPolicy)

Constructor - creates an empty pairwise alignment.

int GetFirstBaseWidth(void) const

Base width of the first row.

void SetUsingGenomic(void)

Tell the pairwise alignment that the coordinates are already tranlated to genomic.

const TAlnSeqIdIRef & GetSecondId(void) const

Get second sequence id.

CPairwiseAln iterator. Iterates over aligned ranges and gaps.

bool IsDirect(void) const

Direction of the second sequence relative to the first one.

CPairwiseAln::const_iterator TIterator

@ eAligned

Aligned range.

bool IsFirstDirect(void) const

Absolute direction of the first sequence.

ESegType GetSegType(void) const

Get current segment type.

pair< TIterator, bool > TCheckedIterator

const TSignedRange & GetSecondRange(void) const

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

CPairwise_CI(const CPairwiseAln &pairwise)

Iterate the whole pairwise alignment.

const TSignedRange & GetFirstRange(void) const

Current range on the first sequence.

CPairwiseAln::TAlnRng TAlnRange

CRange< TSignedSeqPos > TSignedRange

CConstRef< CPairwiseAln > m_Aln

CPairwise_CI(const CPairwiseAln &pairwise, const TSignedRange &range, bool force_direct)

CPairwise_CI(const CPairwiseAln &pairwise, const TSignedRange &range)

Iterate the selected range on the first sequence.

Implementation of IAlnSegmentIterator for CSparseAln.

void x_InitSegment(void)

CSparse_CI.

CConstRef< CAnchoredAln > m_Aln

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

int TSignedSeqPos

Type for signed sequence position.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_XALNMGR_EXPORT

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

vector< CRef< CAnchoredAln > > TAnchoredAlnVec

Collection of anchored alignments.

#define row(bind, expected)

Compare alignments by score.

bool operator()(const C *const c_1, const C *const c_2) const

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