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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/equiv__range_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/align/mergetree/equiv_range.cpp Source File

55 template

typename

57 typedef

list<T> TypeList;

58 size_t

Count = List.size();

61 ITERATE

(

typename

TypeList, Iter, List) {

68 template

typename

70 typedef

list<T> TypeList;

71 size_t

Count = List.size();

73 double

RunningTotal = 0;

74 ITERATE

(

typename

TypeList, Iter, List) {

75

RunningTotal += ((*Iter - Mean) * (*Iter - Mean))/

double

(Count);

78 return

sqrt(RunningTotal);

81 template

typename

82 void s_CalcDevs

(

const

list<T>& Values,

Mean,

double

StdDev, list<double>& Devs) {

83 typedef

list<T> TypeList;

85 ITERATE

(

typename

TypeList, Iter, Values) {

86 double

Dist =

fabs

(

double

(*Iter) -

double

(Mean));

87 double

Dev = (Dist/StdDev);

100

" to "

<< range.

Subjt

"+" 103

","

<< range.

SplitId

")"

;

132 return

(

.Query ==

.Query &&

.Subjt ==

.Subjt);

136 if

(

.Query.GetFrom() !=

.Query.GetFrom())

137 return

(

.Query.GetFrom() <

.Query.GetFrom());

138 else if

(

.Query.GetTo() !=

.Query.GetTo())

139 return

(

.Query.GetTo() <

.Query.GetTo());

140 else if

(

.Subjt.GetFrom() !=

.Subjt.GetFrom())

141 return

(

.Subjt.GetFrom() <

.Subjt.GetFrom());

142 else if

(

.Subjt.GetTo() !=

.Subjt.GetTo())

143 return

(

.Subjt.GetTo() <

.Subjt.GetTo());

145 return A

.Strand <

.Strand;

151 if

(

.Subjt.GetFrom() !=

.Subjt.GetFrom())

152 return

(

.Subjt.GetFrom() <

.Subjt.GetFrom());

153 else if

(

.Subjt.GetTo() !=

.Subjt.GetTo())

154 return

(

.Subjt.GetTo() <

.Subjt.GetTo());

155 else if

(

.Query.GetFrom() !=

.Query.GetFrom())

156 return

(

.Query.GetFrom() <

.Query.GetFrom());

157 else if

(

.Query.GetTo() !=

.Query.GetTo())

158 return

(

.Query.GetTo() <

.Query.GetTo());

160 return A

.Strand <

.Strand;

231 if

(Result ==

eWtf

) {

232 ERR_POST

(

Info

"CEquivRange::CalcRelative:: Got a eWTF (" 233

<< *

this

") vs ("

Check

")"

);

332 TSeqRange

QI =

.Query.IntersectionWith(

.Query);

333 TSeqRange

SI =

.Subjt.IntersectionWith(

.Subjt);

337 if

(

.Query.GetFrom() >=

.Query.GetTo() ) {

338

QD =

.Query.GetFrom() -

.Query.GetTo();

340

QD =

.Query.GetFrom() -

.Query.GetTo();

344 if

(

.Subjt.GetFrom() >=

.Subjt.GetTo() ) {

345 SD

.Subjt.GetFrom() -

.Subjt.GetTo();

347 SD

.Subjt.GetFrom() -

.Subjt.GetTo();

356 return max

(

, DeltaInt);

363

AQR += EquivIter->Query;

364

ASR += EquivIter->Subjt;

367

BQR += EquivIter->Query;

368 BSR

+= EquivIter->Subjt;

395 return max

(

, DeltaInt);

401

: x_GAlignId(0), x_GSegmtId(0), x_GSplitId(0)

412 bool

MadeCuts =

false

;

416 if

(Equivs.empty()) {

419

Sources.push_back(*OrigIter);

421

TEquivList::iterator NE;

422 sort

(Sources.begin(), Sources.end());

423

NE = unique(Sources.begin(), Sources.end());

424

Sources.erase(NE, Sources.end());

428

Equivs.swap(Sources);

433 typedef

vector<TSeqPos> TPointContainer;

435

TPointContainer QueryPoints, SubjtPoints;

436

QueryPoints.reserve(Sources.size()*2);

437

SubjtPoints.reserve(Sources.size()*2);

439 ITERATE

(vector<CEquivRange>, SourceIter, Sources) {

440

QueryPoints.push_back(SourceIter->Query.GetFrom());

441

QueryPoints.push_back(SourceIter->Query.GetTo()+1);

442

SubjtPoints.push_back(SourceIter->Subjt.GetFrom());

443

SubjtPoints.push_back(SourceIter->Subjt.GetTo()+1);

447

vector<TSeqPos>::iterator NE;

448 sort

(QueryPoints.begin(), QueryPoints.end());

449

NE = unique(QueryPoints.begin(), QueryPoints.end());

450

QueryPoints.erase(NE, QueryPoints.end());

451 sort

(SubjtPoints.begin(), SubjtPoints.end());

452

NE = unique(SubjtPoints.begin(), SubjtPoints.end());

453

SubjtPoints.erase(NE, SubjtPoints.end());

462 size_t F

= 0,

= QueryPoints.size()-1;

469

I = (

+((

)/2));

485 for

(TPointContainer::const_iterator StartIter = QueryPoints.begin()+JumpTo;

486

StartIter != QueryPoints.end(); ++StartIter) {

488

TPointContainer::const_iterator Next = StartIter;

490 if

(Next == QueryPoints.end())

496

Range.

SetTo

(*Next-1);

501 if

(Range == Equiv.

Query

) {

502

Equivs.push_back(Equiv);

507

Equivs.push_back(Temp);

518 size_t F

= 0,

= SubjtPoints.size()-1;

525

I = (

+((

)/2));

539 for

(TPointContainer::const_iterator StartIter = SubjtPoints.begin()+JumpTo;

540

StartIter != SubjtPoints.end(); ++StartIter) {

542

TPointContainer::const_iterator Next = StartIter;

544 if

(Next == SubjtPoints.end())

550

Range.

SetTo

(*Next-1);

556 if

(Range == Equiv.

Subjt

) {

557

Equivs.push_back(Equiv);

562

Equivs.push_back(Temp);

684

TEquivList::iterator NE;

685 sort

(Equivs.begin(), Equivs.end());

686

NE = unique(Equivs.begin(), Equivs.end());

687

Equivs.erase(NE, Equivs.end());

692 ITERATE

(vector<CEquivRange>, EquivIter, Equivs) {

693

Splits.push_back(*EquivIter);

696 return

!Splits.empty();

703 bool

MadeChanges =

false

;

709

Sources.insert(Sources.end(), Originals.begin(), Originals.end());

711

Sources.insert(Sources.end(), Merges.begin(), Merges.end());

713

TEquivList::iterator NE;

715

NE = unique(Sources.begin(), Sources.end());

716

Sources.erase(NE, Sources.end());

719

MadeChanges =

false

;

724 if

(SourceIter->Empty()) {

728 if

(Curr.

Empty

()) {

734

Curr.

AlignId

== SourceIter->AlignId &&

735

Curr.

SegmtId

== SourceIter->SegmtId) {

736

Curr =

Merge

(Curr, *SourceIter);

742

Merges.push_back(Curr);

748

Merges.push_back(Curr);

750

}

while

(MadeChanges);

773 for

(

int

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

774 size_t

StartIndex = (Loop*Denseg.

GetDim

());

776 if

(Denseg.

GetStarts

()[StartIndex] == -1 ||

777

Denseg.

GetStarts

()[StartIndex+1] == -1)

796

SubjtStrand = Denseg.

GetStrands

()[StartIndex+1];

814

Equivs.push_back(Curr);

823

objects::CBioseq_Handle SubjtHandle,

837

QRange += CurrEquiv.

Query

;

838

SRange += CurrEquiv.

Subjt

;

841 string

QueryStr, SubjtStr;

863 for

(

size_t

Loop = 0; Loop < CurrEquiv.

Subjt

GetLength

(); Loop++) {

864 size_t

QLoop = QOffset+Loop;

865 size_t

SLoop = SOffset+Loop;

870 if

(QueryStr[QLoop] == SubjtStr[SLoop]) {

952 if

(Inter.

Empty

()) {

953

Slice.

Query

= Inter;

955

}

else if

(Original.

Query

== Inter) {

959

Slice.

Query

= Inter;

997 if

(Inter.

Empty

()) {

998

Slice.

Subjt

= Inter;

1000

}

else if

(Original.

Subjt

== Inter) {

1004

Slice.

Subjt

= Inter;

1056

cerr << __LINE__ <<

" ERROR"

<< endl;

1058

cerr << __LINE__ <<

" ERROR"

<< endl;

1060

cerr << __LINE__ <<

" ERROR"

<< endl;

void CalcMatches(objects::CBioseq_Handle QueryHandle, objects::CBioseq_Handle SubjtHandle, TEquivList &Equivs)

CEquivRange SliceOnSubjt(const CEquivRange &Original, const CRange< TSeqPos > &pSubjt)

bool MergeAbuttings(const TEquivList &Originals, TEquivList &Merges)

void ExtractRangesFromSeqAlign(const objects::CSeq_align &Alignment, TEquivList &Equivs)

CEquivRange Merge(const CEquivRange &First, const CEquivRange &Second)

CEquivRange SliceOnQuery(const CEquivRange &Original, const CRange< TSeqPos > &pQuery)

bool SplitIntersections(const TEquivList &Originals, TEquivList &Splits)

ERelative CalcRelative(const CEquivRange &Check) const

bool AbuttingWith(const CEquivRange &Other) const

ERelative CalcRelativeDuo(const CEquivRange &Check) const

static TSeqPos Distance(const CEquivRange &A, const CEquivRange &B)

objects::ENa_strand Strand

vector< TSeqPos > MisMatchSubjtPoints

bool IntersectingWith(const CEquivRange &Other) const

void s_CalcDevs(const list< T > &Values, T Mean, double StdDev, list< double > &Devs)

bool s_SortEquivBySubjt(const CEquivRange &A, const CEquivRange &B)

bool operator<(const CEquivRange &A, const CEquivRange &B)

double s_CalcStdDev(const list< T > &List, T Mean)

T s_CalcMean(const list< T > &List)

string s_RelToStr(CEquivRange::ERelative rel)

bool operator==(const CEquivRange &A, const CEquivRange &B)

CNcbiOstream & operator<<(CNcbiOstream &out, const CEquivRange &range)

vector< CEquivRange > TEquivList

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

main entry point for tests

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#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 Info(CExceptionArgs_Base &args)

@ 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).

position_type GetLength(void) const

TThisType & SetLengthDown(position_type length)

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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

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 TDenseg & GetDenseg(void) const

Get the variant data.

const TStarts & GetStarts(void) const

Get the Starts member data.

const TLens & GetLens(void) const

Get the Lens member data.

TDim GetDim(void) const

Get the Dim member data.

bool IsDisc(void) const

Check if variant Disc is selected.

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 TDisc & GetDisc(void) const

Get the variant data.

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.

ENa_strand

strand of nucleic acid

unsigned int

A callback function used to compare two keys in a database.

constexpr auto sort(_Init &&init)

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

#define F(x)

Make a parametrized function appear to have only one variable.

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