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

unique_ptr<SAlignedSeq> aln_seq(

());

aln_seq->m_SeqId.Reset(master_first ? &align.

()

range.

(0).SetLength(0);

aln_from = master_first ? starts_1[

] : starts_2[

];

from = master_first ? starts_2[

] : starts_1[

];

(coll->

()) {

aln_seq->m_AlignColl = coll;

aln_seq->m_NegativeStrand =

;

aln_seq.release();

vector<SAlignedSeq*>& aln_seqs)

TSegs& segs = align.

();

(segs.Which()) {

TSegs::e_Denseg: {

& dense_seg = segs.GetDenseg();

vector<SAlignedSeq*>& aln_seqs)

(

= 0;

< aligns.size();

++ ) {

(

<< 1000 * timer.

() <<

);

TRows& rows = sparse_seg.

();

TRows::const_iterator it = rows.begin();

( ; it != rows.end(); ++it ) {

master_index = -1;

(master_index != -1) {

aln_seqs.push_back(aln_seq);

<<

);

vector<SAlignedSeq*>& aln_seqs)

(

!= anchor_row) {

aln_seqs.push_back(aln_seq);

vector<SAlignedSeq*>& aln_seqs,

objects::CScope& scope)

(! aln_seqs.empty()) {

aln->

(master_id, aln_seqs, scope);

vector<SAlignedSeq*>& aln_seqs,

objects::CScope& scope)

(! aln_seqs.empty()) {

unique_ptr<SAlignedSeq> aln_seq(

());

aln_seq->m_SeqId.Reset(dense_seg.

()[row_2]);

( TNum

= 0;

< n_seg;

++ ) {

from_1 = starts[row_1 +

];

from_2 = starts[row_2 +

];

(from_1 != -1 && from_2 != -1) {

direct = (! minus_1 && ! minus_2) || (minus_1 == minus_2);

(coll.

()) {

aln_seq.release();

= (index == 0);

TNumseg n_seg = sparse_align.

();

( TNumseg

= 0;

< n_seg;

++ ) {

from_1 =

? starts_1[

] : starts_2[

];

from_2 =

? starts_2[

] : starts_1[

];

align->SetFirst_id(*rid_1);

align->SetSecond_id(*rid_2);

TNumseg n_seg = (TNumseg)coll.

();

align->SetNumseg(n_seg);

starts_1.resize(n_seg);

starts_2.resize(n_seg);

strands = &align->SetSecond_strands();

strands->resize(n_seg);

starts_1[

] =

.GetFirstFrom();

starts_2[

] =

.GetSecondFrom();

lens[

] =

.GetLength();

User-defined methods of the data storage class.

@ fMixedDir

contains at least one reversed range

@ fInvalid

collection was modified and not validated

@ fReversed

contains at least one direct range

const_iterator insert(const TAlignRange &r)

CAlignRange Represents an element of pairwise alignment of two sequences.

CSparseAlignment - an alignment based on CSparse_seg and CAlingRangeCollection classes rather than on...

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

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

E_SIC Compare(const CSeq_id &sid2) const

Compare() - more general.

@ e_YES

SeqIds compared, but are different.

TThisType & SetToOpen(position_type toOpen)

position_type GetToOpen(void) const

TThisType & SetLength(position_type length)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Start(void)

Start the timer.

void SetFrom(TFrom value)

Assign a value to From data member.

TFrom GetFrom(void) const

Get the From member data.

vector< CRef< CSparse_align > > TRows

bool IsSetStrands(void) const

Check if a value has been assigned to Strands data member.

const TStarts & GetStarts(void) const

Get the Starts member data.

vector< ENa_strand > TStrands

const TLens & GetLens(void) const

Get the Lens member data.

const TFirst_id & GetFirst_id(void) const

Get the First_id member data.

vector< TSignedSeqPos > TStarts

const TMaster_id & GetMaster_id(void) const

Get the Master_id member data.

vector< CRef< CSeq_id > > TIds

TDim GetDim(void) const

Get the Dim member data.

const TSecond_starts & GetSecond_starts(void) const

Get the Second_starts member data.

const TLens & GetLens(void) const

Get the Lens member data.

bool IsSetSecond_strands(void) const

Check if a value has been assigned to Second_strands data member.

vector< int > TSecond_starts

const TFirst_starts & GetFirst_starts(void) const

Get the First_starts member data.

TNumseg GetNumseg(void) const

Get the Numseg member data.

const TIds & GetIds(void) const

Get the Ids member data.

const TSecond_strands & GetSecond_strands(void) const

Get the Second_strands member data.

const TSecond_id & GetSecond_id(void) const

Get the Second_id member data.

vector< int > TFirst_starts

TNumseg GetNumseg(void) const

Get the Numseg member data.

const TRows & GetRows(void) const

Get the Rows member data.

vector< ENa_strand > TSecond_strands

const TStrands & GetStrands(void) const

Get the Strands member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

static bool Equals(const CVariation::TPlacements &p1, const CVariation::TPlacements &p2)

Defines: CTimeFormat - storage class for time format.

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

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

Builder function.

bool ConvertToPairwise(const CSeq_align &align, const CSeq_id &master_id, vector< SAlignedSeq * > &aln_seqs)

Converter.

USING_SCOPE(ncbi::objects)

SAlignedSeq * CreateAlignRow(const CSparse_align &align, bool master_first)

CRef< CSparse_align > CreateSparseAlign(const CSeq_id &id_1, const CSeq_id &id_2, const SAlignTools::TAlignColl &coll)

Reverse Converter Converts Align Collection into a CSparse_align.

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

Builder function.

void GetAlignColl(const CSparse_align &sparse_align, const CSeq_id &master_id, SAlignTools::TAlignColl &coll)

Creates Align Collection from a CSparse_seg.

#define row(bind, expected)

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

SAlignTools::TAlignColl TAlignColl

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