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

skip_unsupported)

Curr->

(

,

(AlignLen)/

(AlignedLen) );

WeightedIdent;

NumIdent, Matches, QueryLen;

WeightedIdent = (NumIdent + (Matches *

)) / (Matches + (QueryLen *

));

QueryId.

(QueryIter->first);

TargetId.

(SubjectIter->first);

!

.GetInst_Ext().IsDelta()) {

list<TSeqRange> Gaps;

( (*DeltaIter)->IsLiteral() ) {

= (*DeltaIter)->GetLiteral().GetLength();

}

( (*DeltaIter)->IsLoc() ) {

= (*DeltaIter)->GetLoc().GetInt().GetLength();

CurrStart = CurrStop + 1;

(TargetRange.

() == QueryLen) {

(TargetRange.

() > 0)

(list<TSeqRange>, GapIter, Gaps) {

(GapIter->IntersectingWith(TargetRange)) {

(TargetRange.

() == 0)

(TargetRange.

() >= (TargetLen-1))

vector<pair<TSeqPos, TSeqPos> > Tails;

(

Row = 0; Row < Curr->

().GetDenseg().GetDim(); ++Row) {

pair<TSeqPos, TSeqPos> Pair;

Pair.second = SeqLen - Stop - 1;

Pair.first = SeqLen - Stop - 1;

Tails.push_back(Pair);

Full = (Tails[0].second <=

&& Tails[1].first <=

)

Forewards = (Tails[0].first > Tails[0].second)

&& (Tails[1].

< Tails[1].second);

Half = Tails[0].second <=

|| Tails[1].first <=

;

TailLen =

(Tails[0].second, Tails[1].

);

Half = Tails[0].first <=

|| Tails[1].second <=

;

TailLen =

(Tails[0].

, Tails[1].second);

AnnotIter->

() ==

) {

( (*AnnotIter)->GetData().IsLocs() ) {

LocIter, (*AnnotIter)->GetData().GetLocs()) {

( (*LocIter)->IsInt() &&

(*LocIter)->GetInt().GetId().Equals(EndId))

ClipLoc.

(**LocIter);

ClipBioseq->

().push_back(ClipId);

ClipDelta->SetLoc().Assign(ClipLoc);

ClipBioseq->

().SetExt().SetDelta().Set().push_back(ClipDelta);

ClipHandle = Scope.

(*ClipBioseq);

ClipAlign->

(*Curr);

(Intersect.

())

ClipDenseg->

().front()->Assign(*ClipId);

ClipAlign->

().SetDenseg().Assign(*ClipDenseg);

(

);

Curr->

(

, Temp);

ClipAlign->

(

,

(AlignLen)/

(AlignedLen) );

list<CRef<CSeq_id> > QueryIds, SubjectIds;

(!

.CanGetDescr())

(TypeString ==

&& User.

(

)) {

CompIds.push_back(Id);

(!

.CanGetInst_Ext())

(Seg->IsLiteral()) {

SegStart += Seg->GetLiteral().GetLength();

(!

.IsInt()) {

(Start <= (SegStart+Int.

()) && Stop >= SegStart) {

CompIds.push_back(Id);

(!

.CanGetInst_Hist())

component_row = 1;

(AlignIdHandle != HandleId) {

list< CConstRef<CSeq_align> > SplitAligns;

SplitAligns.push_back(*it);

((*SplitIter)->GetSeq_id(component_row));

(Start <= (*SplitIter)->GetSeqStop(query_row) &&

Stop >= (*SplitIter)->GetSeqStart(query_row)) {

CompIds.push_back(Id);

(CompIds.empty()) {

CompIds.push_back(SelfId);

list<CRef<CSeq_id> >::iterator QueryIter, SubjectIter;

(QueryIter = QueryIds.begin(); QueryIter != QueryIds.end(); ++QueryIter) {

(SubjectIter = SubjectIds.begin(); SubjectIter != SubjectIds.end(); ++SubjectIter) {

( (*QueryIter)->Equals(**SubjectIter) )

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static void s_ScoreAlignments(const CSeq_align_set &alignments, CScope &Scope, CScoreBuilder &Scorer, bool skip_unsupported)

static const Int8 kEffectiveSearchSpace

Declares the CBl2Seq (BLAST 2 Sequences) class.

Declares the CBlastNucleotideOptionsHandle class.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

Definitions of special type used in BLAST.

@ eMegablast

Nucl-Nucl (traditional megablast)

Main argument class for BLASTN application.

void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)

@ eSkipUnsupportedAlignments

void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)

void x_GetCompList(const objects::CSeq_id &Id, TSeqPos Start, TSeqPos Stop, list< CRef< objects::CSeq_id > > &CompIds, objects::CScope &Scope)

void x_GetSeqHistCompList(CBioseq_Handle Handle, TSeqPos Start, TSeqPos Stop, list< CRef< objects::CSeq_id > > &CompIds)

void x_GetDeltaExtCompList(CBioseq_Handle Handle, TSeqPos Start, TSeqPos Stop, list< CRef< objects::CSeq_id > > &CompIds)

void x_GetUserCompList(CBioseq_Handle Handle, list< CRef< objects::CSeq_id > > &CompIds)

void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)

bool x_CompareCompLists(list< CRef< objects::CSeq_id > > &QueryIds, list< CRef< objects::CSeq_id > > &SubjectIds)

void OffsetRow(TDim row, TSignedSeqPos offset)

Offset row's coords.

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

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

void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)

void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)

void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)

void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)

void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)

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

void SetEffectiveSearchSpace(Int8 searchsp)

@ eScore_PercentIdentity_GapOpeningOnly

@ eScore_PercentIdentity_Gapped

@ eScore_PercentIdentity_Ungapped

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

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).

bool GetNamedScore(const string &id, int &score) const

Get score.

TSeqPos GetSeqStart(TDim row) const

ENa_strand GetSeqStrand(TDim row) const

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

TSeqPos GetAlignLength(bool include_gaps=true) const

Get the length of this alignment.

@Seq_descr.hpp User-defined methods of the data storage class.

TSeqPos GetLength(void) const

bool HasField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Verify that a named field exists.

const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Access a named field in this user object.

void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)

Declares the CDiscNucleotideOptionsHandle class.

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

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.

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

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

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

CConstRef< CSeq_id > GetSeqId(void) const

CSeq_id & Set(const CTempString &the_id, TParseFlags flags=fParse_AnyRaw)

Reassign based on flat specifications; arguments interpreted as with constructors.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

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

Override Assign() to incorporate cache invalidation.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

bool IsFtable(void) const

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

Complete and return const reference to the current seq-annot.

bool HasAnnots(void) const

TInst_Length GetInst_Length(void) const

const string & GetName(void) const

void Reset(void)

Reset reference object.

int64_t Int8

8-byte (64-bit) signed integer

position_type GetLength(void) const

TThisType IntersectionWith(const TThisType &r) const

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

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.

void SetTo(TTo value)

Assign a value to To data member.

const TStr & GetStr(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

bool CanGetType(void) const

Check if it is safe to call GetType method.

const TData & GetData(void) const

Get the Data member data.

const TFields & GetFields(void) const

Get the variant data.

vector< CRef< CUser_field > > TFields

bool IsInt(void) const

Check if variant Int is selected.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

TInt GetInt(void) const

Get the variant data.

TStr & SetStr(void)

Select the variant.

const TType & GetType(void) const

Get the Type member data.

const TDenseg & GetDenseg(void) const

Get the variant data.

TScore & SetScore(void)

Assign a value to Score data member.

E_Choice Which(void) const

Which variant is currently selected.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

TDim GetDim(void) const

Get the Dim member data.

bool IsDisc(void) const

Check if variant Disc is selected.

list< CRef< CSeq_align > > Tdata

TIds & SetIds(void)

Assign a value to Ids data member.

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.

bool IsDenseg(void) const

Check if variant Denseg is selected.

const TRegion & GetRegion(void) const

Get the variant data.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

bool CanGetData(void) const

Check if it is safe to call GetData method.

bool CanGetLocation(void) const

Check if it is safe to call GetLocation method.

bool IsRegion(void) const

Check if variant Region is selected.

@ e_Region

named region (globin locus)

bool IsEmpty(void) const

Check if variant Empty is selected.

const TId & GetId(void) const

Get the Id member data.

TFrom GetFrom(void) const

Get the From member data.

TLocal & SetLocal(void)

Select the variant.

TTo GetTo(void) const

Get the To member data.

const TInt & GetInt(void) const

Get the variant data.

list< CRef< CSeqdesc > > Tdata

TId & SetId(void)

Assign a value to Id data member.

list< CRef< CSeq_align > > TAssembly

const TUser & GetUser(void) const

Get the variant data.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

const Tdata & Get(void) const

Get the member data.

const TAssembly & GetAssembly(void) const

Get the Assembly member data.

bool IsDelta(void) const

Check if variant Delta is selected.

void SetInst(TInst &value)

Assign a value to Inst data member.

list< CRef< CSeq_loc > > TLocs

const TDelta & GetDelta(void) const

Get the variant data.

const TFtable & GetFtable(void) const

Get the variant data.

list< CRef< CSeq_feat > > TFtable

const Tdata & Get(void) const

Get the member data.

const TData & GetData(void) const

Get the Data member data.

list< CRef< CSeq_annot > > TAnnot

list< CRef< CDelta_seq > > Tdata

bool IsUser(void) const

Check if variant User is selected.

bool CanGetAssembly(void) const

Check if it is safe to call GetAssembly method.

@ eRepr_virtual

no seq data

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

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

#define NCBI_CONST_INT8(v)

64-bit integers

Defines NCBI C++ exception handling.

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