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NCBI C++ ToolKit: src/algo/align/ngalign/banded_aligner.cpp Source File

Dims = Denseg.

();

(

CurrSeg = 0; CurrSeg < SegCount; ++CurrSeg) {

Index = (Dims*CurrSeg)+Row;

CurrStart = Denseg.

()[Index];

( CurrStart != -1) {

CurrLoc->

().SetId().Assign( *Denseg.

()[Row] );

CurrLoc->

().SetFrom() = CurrStart;

CurrLoc->

().SetTo() = CurrStart + Denseg.

()[CurrSeg];

Accum->

().Set().push_back(CurrLoc);

PosCoveredBases = 0, NegCoveredBases = 0;

PosCoveredBases += (*LocIter)->GetInt().GetLength();

NegCoveredBases += (*LocIter)->GetInt().GetLength();

(PosCoveredBases, NegCoveredBases);

AccumResults->Get()) {

BestRank = QueryIter->second->GetBestRank();

(

<< QueryIter->second->GetQueryId()->AsFastaString()

<<

);

<< QueryIter->second->GetQueryId()->AsFastaString()

<<

);

vector<CRef<CInstance> > Instances;

(Instances.empty()) {

(

<<

<< Instances.size());

(

<<

<< Inst.

.GetId().AsFastaString() <<

<< Inst.

.GetId().AsFastaString());

<< Inst.

.GetTo() <<

<<

<< Inst.

.GetFrom() <<

<< Inst.

.GetTo() <<

Inst.

.GetStrand(),

.

(

, Inst.

.GetId().AsFastaString())

.

(

, Inst.

.GetId().AsFastaString())

.

(

, (GlobalDs.

() ?

:

));

Result->

().SetDenseg().Assign(*GlobalDs);

ResultSet->

().push_back(Result);

(!ResultSet->

().empty()) {

PercentRemaining = 1.0-PercentComplete;

Factor = PercentRemaining/PercentComplete;

(

<<

);

TimeEstimated = Span.

() * Factor;

(

<<

<< TimeEstimated

<<

<< (CallbackData->

/60.0)

<<

);

QueryStrandedStart, QueryStrandedStop;

QueryStrandedStart = QueryStart;

QueryStrandedStop = QueryStop;

QueryStrandedStart = ( (QueryVec.

()-1) - QueryStop);

QueryStrandedStop = ( (QueryVec.

()-1) - QueryStart);

QuerySeq, SubjectSeq;

QueryVec.

(QueryStrandedStart, QueryStrandedStop+1, QuerySeq);

SubjectVec.

(SubjectStart, SubjectStop+1, SubjectSeq);

Score = Aligner.

();

ResultDenseg = Aligner.

(ExtractQueryStart, Strand, QueryId,

ResultDenseg->

(0, QueryStart);

ResultDenseg->

(1, SubjectStart);

objects::CScope& Scope)

list<CConstRef<CSeq_align> > In;

& Denseg = (*AlignIter)->SetSegs().SetDenseg();

Pluses->Set().push_back(*AlignIter);

Minuses->

().push_back(*AlignIter);

(!Pluses->Set().empty()) {

(!

.IsNull()) {

Instances.push_back(Inst);

(!Minuses->

().empty()) {

(!

.IsNull()) {

Instances.push_back(Inst);

.SetId().Assign(AlignSet.

().front()->GetSeq_id(0));

.SetId().Assign(AlignSet.

().front()->GetSeq_id(1));

.SetStrand() = AlignSet.

().front()->GetSeqStrand(0);

.SetStrand() = AlignSet.

().front()->GetSeqStrand(1);

.SetFrom(

(

.GetFrom(), (*AlignIter)->GetSeqStart(0)));

.SetTo(

(

.GetTo(), (*AlignIter)->GetSeqStop(0)));

(

.GetLength() /

(

.GetLength()));

.GetLength();

TSubjectCoverage BestCoverage;

MaxCoverage = 0;

IdStr = Set->

().front()->GetSeq_id(1).AsFastaString();

SubjCoverage = 0;

(*AlignIter)->GetNamedScore(

, PctCov);

SubjCoverage =

(SubjCoverage, PctCov);

BestCoverage[IdStr] = SubjCoverage;

MaxCoverage =

(SubjCoverage, MaxCoverage);

vector<CRef<CInstance> > TInstVector;

TInstVector SubjInstances;

SubjIdStr = Set->

().front()->GetSeq_id(1).AsFastaString();

(BestCoverage[SubjIdStr] < (MaxCoverage*0.10)) {

Inserted =

;

Contained =

;

(TInstVector, InstIter, SubjInstances) {

CurrContained = (*InstIter)->IsAlignmentContained(**AlignIter);

Contained |= CurrContained;

GapDist = (*InstIter)->GapDistance(**AlignIter);

(GapDist < 20000) {

(*InstIter)->MergeIn(*AlignIter);

SubjInstances.push_back(Inst);

TInstVector CleanedInstances;

(TInstVector, InstIter, SubjInstances) {

((*InstIter)->Alignments.Get().size() <= 1)

Cleaned =

((*InstIter)->Alignments, Scope);

(!Cleaned.

()) {

DupeFound =

;

( (*AlignIter)->GetSeqStart(0) == (*SourceIter)->GetSeqStart(0) &&

(*AlignIter)->GetSeqStart(1) == (*SourceIter)->GetSeqStart(1) &&

(*AlignIter)->GetSeqStop(0) == (*SourceIter)->GetSeqStop(0) &&

(*AlignIter)->GetSeqStop(1) == (*SourceIter)->GetSeqStop(1)) {

Contained =

;

(TInstVector, CleanIter, CleanedInstances) {

Curr = (*CleanIter)->IsAlignmentContained(**AlignIter);

Dupe |= ((*OldInstIter)->Query.Equals(Inst->Query)

&& (*OldInstIter)->Subject.Equals(Inst->Subject));

CleanedInstances.push_back(Inst);

(CleanedInstances.begin(), CleanedInstances.end(),

insert_iterator<TInstVector>(Instances, Instances.end()));

vector<CRef<CInstance> >::iterator Curr;

Curr = Instances.begin();

(Curr = Instances.begin(); Curr != Instances.end(); ) {

( (*Curr)->SubjToQueryRatio() > MaxRatio ||

(*Curr)->SubjToQueryRatio() < 0.10 )

Curr = Instances.erase(Curr);

(Curr = Instances.begin(); Curr != Instances.end(); ++Curr) {

CurrLength = (*Curr)->QueryLength();

LongestInstance =

(CurrLength, LongestInstance);

(Curr = Instances.begin(); Curr != Instances.end(); ) {

( (*Curr)->QueryLength() <= (LongestInstance*0.05))

Curr = Instances.erase(Curr);

vector<CRef<CInstance> >::iterator Outer, Inner;

(Outer = Instances.begin(); Outer != Instances.end(); ++Outer) {

(Inner = Outer+1; Inner != Instances.end(); ) {

( (*Outer)->Query.Equals((*Inner)->Query) &&

(*Outer)->Subject.Equals((*Inner)->Subject) ) {

Inner = Instances.erase(Inner);

BestPctCoverage = -1.0;

PctCoverage = -1.0;

(*AlignIter)->GetNamedScore(

, PctCoverage);

BestPctCoverage =

(BestPctCoverage, PctCoverage);

TSeqPos s_CalcCoverageCount(TAlignSetRef Alignments, int Row, CScope &Scope)

bool s_ProgressCallback(CNWAligner::SProgressInfo *ProgressInfo)

CRef< CSeq_loc > s_CoverageSeqLoc(TAlignSetRef Alignments, int Row, CScope &Scope)

Declares the CBl2Seq (BLAST 2 Sequences) class.

Declares the CBlastNucleotideOptionsHandle class.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

Definitions of special type used in BLAST.

Main argument class for BLASTN application.

class CAlignCleanup implements an alignment cleanup utility based on the C++ alignment manager.

void Cleanup(const TAligns &aligns_in, TAligns &aligns_out, EMode mode=eDefault, CSeq_align::TSegs::E_Choice output_seg_type=CSeq_align::TSegs::e_Denseg)

void TrimEndGaps()

Trim leading/training gaps if possible.

ENa_strand GetSeqStrand(TDim row) const

void Reverse(void)

Reverse the segments' orientation.

void OffsetRow(TDim row, TSignedSeqPos offset)

Offset row's coords.

double SubjToQueryRatio() const

int GapDistance(const objects::CSeq_align &Align) const

objects::CSeq_interval Subject

void MergeIn(CRef< objects::CSeq_align > Align)

objects::CSeq_align_set Alignments

TSeqPos QueryLength() const

bool IsAlignmentContained(const objects::CSeq_align &Align) const

CInstance(const CRef< objects::CSeq_align > Align)

objects::CSeq_interval Query

TAlignResultsRef GenerateAlignments(objects::CScope &Scope, ISequenceSet *QuerySet, ISequenceSet *SubjectSet, TAlignResultsRef AccumResults)

void x_FilterInstances(vector< CRef< CInstance > > &Instances, double MaxRatio)

CRef< objects::CSeq_align_set > x_RunCleanup(const objects::CSeq_align_set &AlignSet, objects::CScope &Scope)

void x_RunAligner(objects::CScope &Scope, CQuerySet &QueryAligns, TAlignResultsRef Results)

void x_GetDistanceInstances(CQuerySet &QueryAligns, objects::CScope &Scope, vector< CRef< CInstance > > &Instances)

void x_GetCleanupInstances(CQuerySet &QueryAligns, objects::CScope &Scope, vector< CRef< CInstance > > &Instances)

CRef< objects::CDense_seg > x_RunMMGlobal(const objects::CSeq_id &QueryId, const objects::CSeq_id &SubjectId, objects::ENa_strand Strand, TSeqPos QueryStart, TSeqPos QueryStop, TSeqPos SubjectStart, TSeqPos SubjectStop, objects::CScope &Scope)

bool x_MinCoverageCheck(const CQuerySet &QueryAligns)

TAssemblyToSubjectSet & Get()

CConstRef< objects::CSeq_id > GetQueryId() const

TSeqPos GetSeqStop(TDim row) const

void SetNamedScore(const string &id, int score)

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

TSeqPos GetSeqStart(TDim row) const

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

Declares the CDiscNucleotideOptionsHandle class.

void SetProgressCallback(FProgressCallback prg_callback, void *data)

void SetScoreMatrix(const SNCBIPackedScoreMatrix *scoremat)

void SetWms(TScore value)

CRef< objects::CDense_seg > GetDense_seg(TSeqPos query_start, objects::ENa_strand query_strand, TSeqPos subj_start, objects::ENa_strand subj_strand, bool trim_end_gaps=false) const

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

CDiagContext_Extra & Print(const string &name, const string &value)

The method does not print the argument, but adds it to the string.

CDiagContext & GetDiagContext(void)

Get diag context instance.

CDiagContext_Extra Extra(void) const

Create a temporary CDiagContext_Extra object.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

void Info(CExceptionArgs_Base &args)

CRef< CSeq_loc > Seq_loc_Merge(const CSeq_loc &loc, CSeq_loc::TOpFlags flags, CScope *scope)

Merge ranges in the seq-loc.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

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).

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

double GetAsDouble(void) const

Return time span as number of seconds.

long GetCompleteSeconds(void) const

Get number of complete seconds.

@ eCurrent

Use current time. See also CCurrentTime.

static bool IsSignaled(TSignalMask signals=eSignal_Any)

Check that any of specified signals is received.

const TDenseg & GetDenseg(void) const

Get the variant data.

Tdata & Set(void)

Assign a value to data member.

const TStarts & GetStarts(void) const

Get the Starts member data.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

const TLens & GetLens(void) const

Get the Lens member data.

void SetType(TType value)

Assign a value to Type data member.

TDim GetDim(void) const

Get the Dim member data.

TStrands & SetStrands(void)

Assign a value to Strands data member.

const TIds & GetIds(void) const

Get the Ids member data.

bool CanGetStrands(void) const

Check if it is safe to call GetStrands method.

TNumseg GetNumseg(void) const

Get the Numseg member data.

list< CRef< CSeq_align > > Tdata

const TStrands & GetStrands(void) const

Get the Strands member data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

@ eType_partial

mapping pieces together

ENa_strand

strand of nucleic acid

list< CRef< CSeq_loc > > Tdata

const Tdata & Get(void) const

Get the member data.

const TMix & GetMix(void) const

Get the variant data.

Main class to perform a BLAST search on the local machine.

Magic spell ;-) needed for some weird compilers... very empiric.

Setup interrupt signal handling.

Defines NCBI C++ exception handling.

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

void Out(T t, int w, CNcbiOstream &to=cout)

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