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

<< __LINE__ << endl

AccumResults->Get()) {

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

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

<<

);

(Scope, *QueryIter->second, NewResults);

PctCovExists[0] =

->GetNamedScore(

, PctCovs[0]);

PctCovExists[1] =

->GetNamedScore(

, PctCovs[1]);

(PctCovExists[0] != PctCovExists[1])

PctCovExists[0];

(!PctCovExists[0])

( PctCovs[0] > PctCovs[1] );

(Pluses->Set().empty() || Minuses->

().empty()) {

PctCovs[2] = { 0.0, 0.0 };

Expands[2] = { 0.0, 0.0 };

NumIdts[2] = { 0.0, 0.0 };

Pluses->Get().front()->GetNamedScore(

, PctCovs[0]);

Minuses->

().front()->GetNamedScore(

, PctCovs[1]);

(PctCovs[0] >= PctCovs[1]) {

NonDominant = Minuses;

NonDominant = Pluses;

(*DomIter)->GetNamedScore(

, PctCovs[0]);

(*NonIter)->GetNamedScore(

, PctCovs[1]);

(*DomIter)->GetNamedScore(

, Expands[0]);

(*NonIter)->GetNamedScore(

, Expands[1]);

(*DomIter)->GetNamedScore(

, NumIdts[0]);

(*NonIter)->GetNamedScore(

, NumIdts[1]);

(DomSubjRange.

() > NonSubjRange.

())

Dist = DomSubjRange.

() - NonSubjRange.

();

Dist = NonSubjRange.

() - DomSubjRange.

();

( (PctCovs[0]/PctCovs[1]) <= 1000.0 &&

(PctCovs[0]/PctCovs[1]) >= 1.0 &&

Expands[0] <= 3.0 && Expands[1] <= 3.0 ) {

cerr <<

<< NumIdts[0] <<

<< Expands[0] <<

<<

<< NumIdts[1] <<

<< Expands[1] <<

<< endl;

ResultSet->

().push_back(Disc);

(!ResultSet->

().empty()) {

vector<CRef<CSeq_align> > TempVec;

TempVec.reserve(AlignSet.

().size());

TempVec.resize(AlignSet.

().size());

(AlignSet.

().begin(), AlignSet.

().end(), TempVec.begin());

AlignSet.

().clear();

(TempVec.begin(), TempVec.end(),

insert_iterator<CSeq_align_set::Tdata>(AlignSet.

(), AlignSet.

().end()));

Pluses.

().push_back(*AlignIter);

Minuses.

().push_back(*AlignIter);

(Source.

() && !Source.

().empty()) {

(!

.IsNull() &&

->CanGet() && !

->Get().empty()) {

AlignLen = (*MergedIter)->GetSeqRange(1).GetLength();

(*MergedIter)->SetNamedScore(

,

(AlignLen)/

(AlignedLen) );

Source.

().push_back(*MergedIter);

Results.

().push_back(*MergedIter);

DomSlice = DomRef->GetSegs().GetDenseg().

(0, SwitchSpot, DomRef->GetSeqStop(0));

DomRef->SetSegs().SetDenseg().

(*DomSlice);

NonRef->

().SetDenseg().Assign(*NonSlice);

Source->

().push_back(DomRef);

Source->Set().push_back(NonRef);

(Cleaned.

() || Cleaned->

().size() != 2) {

DomRef = Cleaned->

().front();

NonRef = *( ++(Cleaned->

().begin()) );

(DomRef, NonRef);

& DomSeg = DomRef->SetSegs().SetDenseg();

DomIndex = 0, NonIndex = 0;

(DomIndex = 0; DomIndex < DomSeg.

(); DomIndex++) {

(NonIndex = 0; NonIndex < NonSeg.

(); NonIndex++) {

NonSeg.

()[NonIndex]-1);

(!FillUnaligned.

()) {

NonSeg.

(*FillUnaligned);

Disc->

().SetDisc().Set().push_back(DomRef);

Disc->

().SetDisc().Set().push_back(NonRef);

list<CConstRef<CSeq_align> > In;

(

->Set().empty())

(

Index = 0; Index < Denseg.

(); Index++) {

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 FillUnaligned(bool b)

Fill any unaligned regions with explicit gaps.

void SortInputsByScore(bool b)

flags these primarity affect the CAlnVec implementation

void TrimEndGaps()

Trim leading/training gaps if possible.

ENa_strand GetSeqStrand(TDim row) const

void Reverse(void)

Reverse the segments' orientation.

void RemovePureGapSegs()

Remove any segments in which every row has a gap (these can arise when ExtractRows is used)

CRef< CDense_seg > ExtractSlice(TDim row, TSeqPos from, TSeqPos to) const

Extract a slice of the alignment that includes the specified range.

CRef< CDense_seg > FillUnaligned() const

Create a new dense-seg with added all unaligned pieces (implicit inserts), if any,...

void Compact()

Join adjacent mergeable segments to create a more compact alignment.

CRange< TSeqPos > GetSeqRange(TDim row) const

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

overloaded Assign()

void x_SplitAlignmentsByStrand(const objects::CSeq_align_set &Source, objects::CSeq_align_set &Pluses, objects::CSeq_align_set &Minuses)

void x_HandleSingleStrandMerging(objects::CSeq_align_set &Source, objects::CSeq_align_set &Results, objects::CScope &Scope)

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

void x_SortAlignSet(objects::CSeq_align_set &AlignSet)

CRef< objects::CSeq_align > x_CreateDiscAlignment(const objects::CSeq_align &Dom, const objects::CSeq_align &Non, objects::CScope &Scope)

CRef< objects::CSeq_align_set > x_MergeSeqAlignSet(const objects::CSeq_align_set &InAligns, objects::CScope &Scope)

static bool s_SortByPctCoverage(const CRef< objects::CSeq_align > &A, const CRef< objects::CSeq_align > &B)

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

bool x_IsAllGap(const objects::CDense_seg &Denseg)

TAssemblyToSubjectSet & Get()

TSeqPos GetAlignLength(const CSeq_align &align, bool ungapped=false)

Compute the length of the alignment (= length of all segments, gaps + aligned)

void AddScore(CScope &scope, CSeq_align &align, EScoreType score)

deprecated: use CSeq_align::EScoreType directly

@ eScore_PercentIdentity_Ungapped

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.

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.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define ERR_POST(message)

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

void Error(CExceptionArgs_Base &args)

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

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

Set object to copy of another one.

bool IsNull(void) const THROWS_NONE

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

position_type GetLength(void) const

bool IntersectingWith(const TThisType &r) const

TThisType & SetLength(position_type length)

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

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.

const TStr & GetStr(void) const

Get the variant data.

const TDenseg & GetDenseg(void) const

Get the variant data.

Tdata & Set(void)

Assign a value to data member.

bool CanGet(void) const

Check if it is safe to call Get method.

E_Choice Which(void) const

Which variant is currently selected.

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.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

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_disc

discontinuous alignment

const TLocal & GetLocal(void) const

Get the variant data.

bool IsLocal(void) const

Check if variant Local is selected.

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

constexpr auto sort(_Init &&init)

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

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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