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

m_QueryId->Assign(*Results.GetSeqId());

Insert(*Results.GetSeqAlign());

(Results.Get().empty()) {

cerr << __FILE__<<

<<__LINE__<<

<<

<<endl;

->Assign(Results.Get().front()->GetSeq_id(0));

(Alignment.

()) {

cerr << __FILE__<<

<<__LINE__<<

<<

<<endl;

(Results.Get().empty()) {

cerr << __FILE__<<

<<__LINE__<<

<<

<<endl;

->Assign(Results.Get().front()->GetSeq_id(0));

(Alignment.

()) {

cerr << __FILE__<<

<<__LINE__<<

<<

<<endl;

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

(!

->IsSet() ||

->Get().empty())

(

<< BestRank

<<

<< AssemIter->first

<<

<<

->GetSeqIdString(

)

<<

<< AssemIter->second.size());

(BestRank == -1) {

(CurrRank == BestRank) {

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

(!

->IsSet() ||

->Get().empty())

(*SubjectIter->second);

<<

(!SeqList.empty())

Seq = SeqList.front();

Unit = Seq->GetAssemblyUnit();

AssemblyAcc = Unit->GetAccession();

(CurrSubjectSet.find(IdString) == CurrSubjectSet.end()) {

CurrSubjectSet[IdString] = AlignSet;

CurrSubjectSet[IdString]->

().push_back(Alignment);

NeverRanked =

;

(!AssemblyAcc.empty() && AssemIter->first != AssemblyAcc) {

BestRank =

(BestRank, CurrRank);

NeverRanked =

;

( (*AlignIter)->GetSeqStart(0) == New.

(0) &&

(*AlignIter)->GetSeqStop(0) == New.

(0) &&

(*AlignIter)->GetSeqStart(1) == New.

(1) &&

(*AlignIter)->GetSeqStop(1) == New.

(1) &&

(*AlignIter)->GetSegs().Which() == New.

().

() &&

(*AlignIter)->Equals(New) ) {

}

( (*AlignIter)->GetSegs().Equals(New.

()) ) {

Source.

().reverse();

CSeq_align_set::Tdata::iterator Outer, Inner;

(Outer = Source.

().begin(); Outer != Source.

().end(); ++Outer) {

& OuterSubjId = (*Outer)->GetSeq_id(1);

(Inner = Outer, ++Inner; Inner != Source.

().end(); ) {

& InnerSubjId = (*Inner)->GetSeq_id(1);

(!OuterSubjId.

(InnerSubjId)) {

(IsInnerContained) {

Inner = Source.

().erase(Inner);

AccumResults =

;

AccumResults =

;

OuterSegIdx, InnerSegIdx;

AllMatch =

;

(InnerSegIdx = 0; InnerSegIdx < InnerSeg.

(); InnerSegIdx++) {

InnerMatched =

;

(OuterSegIdx = 0; OuterSegIdx < OuterSeg.

(); OuterSegIdx++) {

InnerMatched =

;

Found->second;

Found->second;

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

CurrSet = QueryIter->second->ToBestSeqAlignSet();

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

IdString = QuerySet->

()->AsFastaString();

!Alignments->

().empty()) {

(QueryIter->second);

IdString = (*Iter)->GetSeqId()->AsFastaString();

(!AlignSet.

() || AlignSet.

().empty())

Definition of classes which constitute the results of running a BLAST search.

void Insert(CRef< CQuerySet > QuerySet)

void DropQuery(const objects::CSeq_id &Id)

TQueryToSubjectSet m_QueryMap

CRef< CQuerySet > GetQuerySet(const objects::CSeq_id &Id)

bool QueryExists(const objects::CSeq_id &Id) const

CRef< objects::CSeq_align_set > ToBestSeqAlignSet() const

CRef< objects::CGC_Assembly > m_GenColl

CRef< objects::CSeq_align_set > ToSeqAlignSet() const

list< CConstRef< CGC_Sequence > > TSequenceList

bool x_ContainsAlignment(const objects::CSeq_align &Outer, const objects::CSeq_align &Inner) const

int GetBestRank(const string AssemblyAcc="") const

TAssemblyToSubjectSet m_AssemblyMap

CRef< objects::CSeq_align_set > ToSeqAlignSet() const

CRef< objects::CSeq_align_set > ToBestSeqAlignSet() const

bool x_AlreadyContains(const objects::CSeq_align_set &Set, const objects::CSeq_align &New) const

TAssemblyToSubjectSet & Get()

void Insert(CRef< CQuerySet > QuerySet)

CRef< objects::CGC_Assembly > m_GenColl

map< string, CRef< objects::CSeq_align_set > > TSubjectToAlignSet

void x_FilterStrictSubAligns(objects::CSeq_align_set &Source) const

CRef< objects::CSeq_id > m_QueryId

CQuerySet(const blast::CSearchResults &Results)

CConstRef< objects::CSeq_id > GetQueryId() const

Search Results for All Queries.

Search Results for One Query.

CRange< TSeqPos > GetSeqRange(TDim row) const

GetSeqRange NB: On a Spliced-seg, in case the product-type is protein, these only return the amin par...

TSeqPos GetSeqStop(TDim row) const

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).

static const char * KFILTER_SCORE

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

CConstRef< objects::CSeq_align_set > GetSeqAlign() const

Accessor for the Seq-align results.

CConstRef< objects::CSeq_id > GetSeqId() const

Accessor for the query's sequence identifier.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST(message)

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

void Error(CExceptionArgs_Base &args)

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

const string AsFastaString(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

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

bool IntersectingWith(const TThisType &r) const

TThisType IntersectionWith(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.

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.

const TLens & GetLens(void) const

Get the Lens member data.

bool IsDisc(void) const

Check if variant Disc is selected.

TNumseg GetNumseg(void) const

Get the Numseg member data.

list< CRef< CSeq_align > > Tdata

const TDisc & GetDisc(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

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

Defines NCBI C++ exception handling.

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

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