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

m_TreeAlignMerger.SetScope(&Scope);

QueryIter, AccumResults->Get()) {

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

(BestRank > m_Threshold || BestRank == -1) {

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

<<

);

Results = x_MergeAlignments(*QueryIter->second, Scope);

(!Results->

().empty()) {

(

<<

<< Results->

().size() <<

);

QueryAligns.

()) {

(

= 0;

< 1;

++) {

list< CRef<CSeq_align_set> > compartments;

(

&& !

->Set().empty() ) {

Merged->

().push_back(*AlignIter);

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

Minuses->

().push_back(*AlignIter);

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

(!Minuses->

().empty()) {

Merged->

().push_back(*AlignIter);

Merged->

().push_back(*AlignIter);

list<CRef<CSeq_align> > In;

(

->Set().empty())

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

Scores[2] = {0, 0};

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

vector<CRef<CSeq_align> > TempVec;

TempVec.reserve(AlignSet.

().size());

(AlignSet.

().begin(), AlignSet.

().end(),

AlignSet.

().clear();

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

insert_iterator<CSeq_align_set::Tdata>(AlignSet.

(), AlignSet.

().end()));

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.

ENa_strand GetSeqStrand(TDim row) const

void Reverse(void)

Reverse the segments' orientation.

CRef< CDense_seg > FillUnaligned() const

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

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

overloaded Assign()

@ eAlignCleanup

Use the older (CAlignCleanup) merge algorithm.

@ eTreeAlignMerger

Use the new (CTreeAlignMerger) merge algorithm.

void x_SortAlignSet(objects::CSeq_align_set &AlignSet, int CompartFlags=0)

CRef< objects::CSeq_align_set > x_MergeAlignments(CQuerySet &QueryAligns, objects::CScope &Scope)

CTreeAlignMerger m_TreeAlignMerger

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

TAssemblyToSubjectSet & Get()

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

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

void SetNamedScore(const string &id, int score)

void Merge(const list< CRef< objects::CSeq_align > > &Input, list< CRef< objects::CSeq_align > > &Output)

Declares the CDiscNucleotideOptionsHandle class.

std::ofstream out("events_result.xml")

main entry point for tests

void FindCompartments(const list< CRef< CSeq_align > > &aligns, list< CRef< CSeq_align_set > > &align_sets, TCompartOptions options=fCompart_Defaults, float diff_len_filter=3.0f)

@ fCompart_AllowIntersections

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.

#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.

void Info(CExceptionArgs_Base &args)

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.

Tdata & Set(void)

Assign a value to data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

TDim GetDim(void) const

Get the Dim member data.

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.

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

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

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

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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