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

: m_AlignedSeq(

),

m_BioseqHandle(

)

m_BioseqHandle;

vector<SAlignedSeq*>& aln_seqs,

objects::CScope& scope)

( ! aln_seqs.empty()) {

aln_n = aln_seqs.size();

.reserve(aln_n + 1);

(

= 0;

< aln_n;

++ ) {

(

.size() == 1) {

*(

[

]->m_AlignedSeq->m_AlignColl);

[

]->m_AlignedSeq->m_SeqId.GetObject();

[

]->m_AlignedSeq->m_AlignColl->GetFirstRange();

[

]->m_AlignedSeq->m_SecondRange.GetFrom();

[

]->m_AlignedSeq->m_SecondRange.GetTo();

!

[

]->m_AlignedSeq->m_NegativeStrand;

[

]->m_AlignedSeq->m_NegativeStrand;

T::eBackwards;

try_reverse_dir)

try_reverse_dir)

(seq_to >= seq_from) {

= seq_to - seq_from + 1;

seq_vector.

(vec_size - seq_to - 1, vec_size - seq_from,

);

seq_vector.

(

.GetFrom(),

.GetTo() + 1, s);

vec_size -

.GetFrom(), s);

(prev_to_open != string::npos) {

gap_size = (

)(off - prev_to_open);

prev_to_open = off +

;

fill_len = (

)(

- prev_to_open);

(prev_to_open != string::npos && fill_len > 0 && coll.

() > aln_range.

()) {

User-defined methods of the data storage class.

position_type GetFirstTo() const

TSignedSeqPos GetFirstPosBySecondPos(position_type pos, ESearchDirection dir=eNone) const

CRange< position_type > GetFirstRange() const

position_type GetFirstFrom() const

const_iterator insert(const TAlignRange &r)

TSignedSeqPos GetSecondPosByFirstPos(position_type pos, ESearchDirection dir=eNone) const

ESearchDirection

adding empty ranges is considered valid, they are simply ignored

CAlignRange Represents an element of pairwise alignment of two sequences.

TARange GetAlnRange() const

returns number of rows in the alignment

CConstRef< objects::CSeq_id > m_MasterId

void x_AssertRowValid(TNumrow row) const

TNumrow GetAnchor() const

TSignedSeqPos GetSeqAlnStop(TNumrow row) const

CRef< objects::CScope > GetScope()

bool IsNegativeStrand(TNumrow row) const

TSignedSeqPos GetSeqAlnStart(TNumrow row) const

TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const

vector< SRowRec * > TRows

TSeqPos GetSeqStop(TNumrow row) const

CRef< objects::CScope > m_Scope

bool IsPositiveStrand(TNumrow row) const

TSignedSeqPos GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const

TSeqPos GetSeqStart(TNumrow row) const

const TAlignColl & GetAlignCollection(TNumrow row)

CSparseAlignment()

CSparseAlignment.

string & GetAlnSeqString(TNumrow row, string &buffer, const TSignedRange &aln_rng) const

SAlignTools::TAlignColl TAlignColl

IAlnExplorer::TNumrow TNumrow

const objects::CBioseq_Handle & GetBioseqHandle(TNumrow row) const

IAlnExplorer::TRange GetSeqRange(TNumrow row) const

virtual IAlnSegmentIterator * CreateSegmentIterator(TNumrow row, const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flags) const

TResidue m_GapChar

the extent of all segments in alignment coords

void SetGapChar(TResidue gap_char)

const objects::CSeq_id & GetSeqId(TNumrow row) const

void Init(const objects::CSeq_id &master_id, vector< SAlignedSeq * > &aln_seqs, objects::CScope &scope)

string & GetSeqString(TNumrow row, string &buffer, TSeqPos seq_from, TSeqPos seq_to) const

TSignedRange GetSeqAlnRange(TNumrow row) const

IAlnExplorer::TResidue TResidue

TNumrow GetNumRows() const

virtual ~CSparseAlignment()

CSparseIterator - IAlnSegmentIterator implementation for CAlnMap::CAlnChunkVec.

ESearchDirection

Position search options.

@ eRight

Towards higher aln coord (always to the right)

@ eLeft

Towards lower aln coord (always to the left)

@ eBackwards

Towards lower seq coord (to the left if plus strand, right if minus)

@ eForward

Towards higher seq coord (to the right if plus strand, left if minus)

Alignment segment iterator interface.

@ eSkipGaps

Skip gap segments (show only aligned ranges)

virtual const TSignedRange & GetRange(void) const =0

Get the selected row range.

virtual const TSignedRange & GetAlnRange(void) const =0

Get alignment range for the segment.

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eStrand_Plus

Plus strand.

@ eStrand_Minus

Minus strand.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

position_type GetLength(void) const

TThisType & CombineWith(const TThisType &r)

TThisType & Set(position_type from, position_type to)

#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.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

unsigned int

A callback function used to compare two keys in a database.

const struct ncbi::grid::netcache::search::fields::SIZE size

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

CSparseAlignment::TAlignColl::ESearchDirection GetCollectionSearchDirection(IAlnExplorer::ESearchDirection dir)

USING_SCOPE(ncbi::objects)

#define row(bind, expected)

describes a sequence in the alignment

SAlignedSeq * m_AlignedSeq

SRowRec()

CSparseAlignment::SRowRec.

objects::CBioseq_Handle * m_BioseqHandle

This is a building block for a Builder represents a Sequence aligned to an Anchor (pairwise alignment...

TSignedRange m_SecondRange

CConstRef< objects::CSeq_id > m_SeqId

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