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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuAlign_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/structure/cd_utils/cuAlign.cpp Source File

63

CDense_diag::TIds::iterator

i

;

65  if

(seqAlign.NotEmpty()) {

67

IdsSet = DenDiag->GetIds();

68

}

else if

(seqAlign->GetSegs().IsDenseg()) {

69

IdsSet = seqAlign->GetSegs().GetDenseg().GetIds();

87  unsigned int

index = (onMaster) ? 0 : 1;

91

ddIt = sa->

SetSegs

().SetDendiag().begin();

92

ddEnd = sa->

SetSegs

().SetDendiag().end();

93  for

(; ddIt != ddEnd; ++ddIt) {

94  if

((*ddIt)->GetDim() != 2 || (*ddIt)->GetIds().size() != 2) {

102

ddIt = sa->

SetSegs

().SetDendiag().begin();

103

ddEnd = sa->

SetSegs

().SetDendiag().end();

105  for

(; ddIt != ddEnd; ++ddIt) {

106

ids = (*ddIt)->SetIds();

107

ids[index]->Assign(*newSeqId);

137

CDense_diag::TStarts::const_iterator k;

138  int

Start,

Len

, OtherStart;

143

ddend = ddlist->end();

144  for

(

i

=ddlist->begin();

i

!=ddend;

i

++) {

145

k = (*i)->GetStarts().begin();

146  Len

= (*i)->GetLen();

149

k = (*i)->GetStarts().begin();

152  if

((Position >= Start) && (Position < (Start+

Len

))) {

153  return

(OtherStart + (Position-Start));

190

iend = pDenDiagSet->end();

191  for

(

i

=pDenDiagSet->begin();

i

!=iend;

i

++) {

192

start = (onMaster) ? (*i)->GetStarts().front() : (*i)->GetStarts().back();

193

stop = start + (*i)->GetLen() - 1;

194  if

(Position >= start && Position <= stop) {

206  int

nBlocks, position;

208

vector<int> align1Blocks, align1Starts;

210

alignedPositions.clear();

215  if

(

GetSeqID

(align1, align1Id, !onMaster) &&

GetSeqID

(align2, align2Id, !onMaster) &&

222

nBlocks = align1Blocks.size();

223  for

(

int i

= 0;

i

< nBlocks; ++

i

) {

224

position = align1Starts[

i

];

225  for

(

int

j = 0; j < align1Blocks[

i

]; ++j) {

227

alignedPositions.push_back(position);

234  return

alignedPositions.size();

243  if

(seqAlign.

Empty

()) {

250  for

(

i

=pDenDiagSet->begin();

i

!=pDenDiagSet->end();

i

++) {

251  Len

+= (*i)->GetLen();

261  if

(seqAlign.

Empty

()) {

267

lowerBound = (onMaster) ? pDenDiagSet->front()->GetStarts().front() : pDenDiagSet->front()->GetStarts().back();

275  if

(seqAlign.

Empty

()) {

281

upperBound = (onMaster) ? pDenDiagSet->back()->GetStarts().front() : pDenDiagSet->back()->GetStarts().back();

282

upperBound += pDenDiagSet->back()->GetLen() - 1;

293  int

alignedResCtr = 0;

294  int

start = -1, stop = -1;

297  if

(align.

Empty

() || sequenceString.size() < 1) {

302  if

(length < 1 || (

int

) sequenceString.size() < length) {

307

pAlignedRes =

new char

[length];

308  if

(!pAlignedRes)

return

;

314

start = (isMaster) ? ddFirst->GetStarts().front() : ddFirst->GetStarts().back();

315

stop = (isMaster) ? ddLast->GetStarts().front() : ddLast->GetStarts().back();

316

stop += ddLast->GetLen() - 1;

324  if

(start >=0 && start <= stop && stop < (

int

) sequenceString.size()) {

325  for

(

int i

= start;

i

<= stop; ++

i

) {

328

pAlignedRes[alignedResCtr] = sequenceString[

i

];

336  if

(alignedResCtr != length) {

337  delete

[] pAlignedRes;

351

vector<int>* starts, vector<int>* lengths) {

354

vector<int> vstarts, vlengths;

357  if

(vlengths.size() == vstarts.size()) {

358

nBlocks = vstarts.size();

359  while

(

i

< nBlocks &&

result

< 0) {

360  if

(residue >= vstarts[

i

] && residue < vstarts[

i

] + vlengths[

i

]) {

365  if

(starts !=

NULL

) {

366

starts->insert(starts->begin(), vstarts.begin(), vstarts.end());

368  if

(lengths !=

NULL

) {

369

lengths->insert(lengths->begin(), vlengths.begin(), vlengths.end());

380  if

(seqAlign.

Empty

()) {

397  if

(seqAlign.

NotEmpty

() && nBlocks > 0) {

400  for

(cit = pDenDiagSet->begin(); cit != pDenDiagSet->end(); ++cit) {

401

lengths.push_back((*cit)->GetLen());

425  if

(seqAlign.

NotEmpty

() && nBlocks > 0) {

428  for

(cit = pDenDiagSet->begin(); cit != pDenDiagSet->end(); ++cit) {

429

start = (onMaster) ? (*cit)->GetStarts().front() : (*cit)->GetStarts().back();

430

starts.push_back(start);

449  if

(align.

SetSegs

().IsDendiag()) {

450

dd = &(align.

SetSegs

().SetDendiag());

467

k = pDenDiagSet->begin();

470

k = pDenDiagSet->end();

485

CDense_diag::TIds::iterator

i

;

490

k = pDenDiagSet->begin();

491

IdsSet = (*k)->GetIds();

497  for

(; k != pDenDiagSet->end(); k++, iii++)

499

IdsSet = (*k)->GetIds();

526  if

(pDD && pAl->

IsInt

()) {

530

to=interval.

SetTo

();

532

RefID = &interval.

SetId

();

536

CPacked_seqint::Tdata::iterator s;

539

from=(*s)->GetFrom();

542

RefID = &((*s)->SetId());

552

CDense_diag::TStarts::const_iterator pos;

553

vector < CRef< CSeq_id > >::const_iterator pid;

555  for

(iDst=0,pp=pDD->begin(); pp!=pDD->end(); pp++,iDst++){

556

pos=(*pp)->GetStarts().begin();

559

pid=(*pp)->GetIds().begin();

564

pAl->

SetInt

().SetFrom(posStart);

566

pAl->

SetInt

().SetId(*SeqID);

573

intrvl->

SetId

(*SeqID);

583

idMaster.

Reset

(seqID1);

585

idSeq.

Reset

(seqID2);

591

newDD->SetIds().push_back(idMaster);

592

newDD->SetIds().push_back(idSeq);

593

newDD->SetStarts().push_back(st1);

594

newDD->SetStarts().push_back(st2);

596

pDD->push_back(newDD);

610

list< CRef< CSeq_align > >::const_iterator j;

619  if

(++Count == Row)

break

;

622  if

((*j)->GetSegs().IsDendiag()) {

624

pDenDiagSet = &((*j)->GetSegs().GetDendiag());

636

list< CRef< CSeq_align > >::iterator j;

640  if

(Row == 0) j = seqAnnot->

SetData

().SetAlign().begin();

643  for

(j= seqAnnot->

SetData

().SetAlign().begin();

644

j!= seqAnnot->

SetData

().SetAlign().end(); j++) {

645  if

(++Count == Row)

break

;

648  if

((*j)->SetSegs().IsDendiag()) {

650

pDenDiagSet = &((*j)->SetSegs().SetDendiag());

662

list< CRef< CSeq_align > >::iterator j, jend;

665  if

(RowIndex == 0)

return

(

false

);

669

jend = seqAnnot->

SetData

().SetAlign().end();

670  for

(j= seqAnnot->

SetData

().SetAlign().begin(); j != jend; j++) {

671  if

(RowCount == RowIndex) {

672

seqAnnot->

SetData

().SetAlign().erase(j);

676  if

(RowCount > RowIndex)

break

;

685  if

(seqAlign.

Empty

())

691  const

list< CRef< CSeq_align > >& saList = seqAlign->

GetSegs

().

GetDisc

().

Get

();

692  if

(saList.begin() != saList.end())

706

newSa->

Assign

(*denseSegSeqAlign);

711

newSa->

SetSegs

().SetDendiag() = ddList;

730  int

total = numrows * numsegs;

735  bool

strands_exist = ((

int

) strands.size() == total);

736  bool

scores_exist = ((

int

) scores.size() == total);

741

dd->SetLen(lens[seg]);

746

dd->SetIds().push_back(ids[

row

]);

747

dd->SetStarts().push_back(start);

749

dd->SetStrands().push_back(strands[pos]);

752

dd->SetScores().push_back(scores[pos]);

757  if

(rows_per_seg >= 2) {

758

dd->SetDim(rows_per_seg);

767

list <CRef <CUpdate_align> > ::iterator pPen;

771  CSeq_align

* pAl = *((*pPen)->SetSeqannot().SetData().SetAlign().begin());

773

vector < CRef< CSeq_id > >::const_iterator pid=pDDPen->

GetIds

().begin();

789  if

(seqAlign.

Empty

()) {

790

err =

"GetPssmIdFromSeqAlign: Empty Seq_align.\n"

;

792

err =

"GetPssmIdFromSeqAlign: Only Seq_aligns with dim = 2 supported.\n"

;

797

err =

"GetPssmIdFromSeqAlign: Dense_diags not currently supported.\n"

;

799

err.append(

"GetPssmIdFromSeqAlign: Seq_align is an unsupported type (%d).\n"

, seqAlign->

GetType

());

811  if

(seqAlign.

Empty

()) {

812

err =

"GetMasterGIFromSeqAlign: Empty Seq_align.\n"

;

816

gi = seqId->

GetGi

();

818

err =

"GetMasterGIFromSeqAlign: Dense_seg's master sequence is empty or not of type 'GI'.\n"

;

823

gi = seqId->

GetGi

();

825

err =

"GetMasterGIFromSeqAlign: Dense_diag's master sequence is empty or not of type 'GI'.\n"

;

828

err.append(

"GetMasterGIFromSeqAlign: Seq_align is an unsupported type (%d).\n"

, seqAlign->

GetType

());

User-defined methods of the data storage class.

User-defined methods of the data storage class.

int MapPositionToMaster(int childPos, const CSeq_align &align)

void MakeDDFromSeqLoc(CSeq_loc *pAl, TDendiag *pDD)

void MakeSeqLocFromDD(const TDendiag *pDD, CSeq_loc *pAl)

TGi GetMasterGIFromSeqAlign(const CRef< CSeq_align > &seqAlign, string &err)

int GetLowerBound(const CRef< CSeq_align > &seqAlign, bool onMaster)

CRef< CSeq_align > ExtractFirstSeqAlign(CRef< CSeq_align > seqAlign)

bool GetDenDiagSet(const CRef< CSeq_annot > &seqAnnot, int Row, const TDendiag *&pDenDiagSet)

bool CheckSeqIdInDD(const CRef< CSeq_align > &seqAlign)

bool ChangeSeqIdInSeqAlign(CRef< CSeq_align > &sa, const CRef< CSeq_id > &newSeqId, bool onMaster)

int GetAlignedPositions(const CRef< CSeq_align > &align1, const CRef< CSeq_align > &align2, vector< int > &alignedPositions, bool onMaster)

int GetBlockStartsForMaster(const CRef< CSeq_align > &seqAlign, vector< int > &starts)

CRef< CSeq_align > Denseg2DenseDiagList(const CRef< CSeq_align > &denseSegSeqAlign)

int GetBlockNumberForResidue(int residue, const CRef< CSeq_align > &seqAlign, bool onMaster, vector< int > *starts, vector< int > *lengths)

int GetBlockCount(const CRef< CSeq_align > &seqAlign)

bool GetSeqID(const CRef< CSeq_align > &seqAlign, CRef< CSeq_id > &SeqID, bool getSlave)

bool SetDenDiagSet(CRef< CSeq_annot > &seqAnnot, int Row, TDendiag *&pDenDiagSet)

int MapPosition(const CSeq_align &seqAlign, int Position, CoordMapDir mapDir)

void SetAlignedResiduesOnSequence(const CRef< CSeq_align > &align, const string &sequenceString, char *&pAlignedRes, bool isMaster)

bool IsPositionAligned(const CSeq_align &seqAlign, int Position, bool onMaster)

void AddIntervalToDD(TDendiag *pDD, CRef< CSeq_id > seqID1, CRef< CSeq_id > seqID2, TSeqPos st1, TSeqPos st2, TSeqPos lll)

int GetNumAlignedResidues(const CRef< CSeq_align > &seqAlign)

int GetBlockLengths(const CRef< CSeq_align > &seqAlign, vector< int > &lengths)

bool GetFirstOrLastDenDiag(const CRef< CSeq_align > &seqAlign, bool First, CRef< CDense_diag > &DenDiag)

bool GetPendingSeqId(CCdCore *pCD, int irow, CRef< CSeq_id > &seqID)

int MapPositionToChild(int masterPos, const CSeq_align &align)

int GetBlockStarts(const CRef< CSeq_align > &seqAlign, vector< int > &starts, bool onMaster)

int GetUpperBound(const CRef< CSeq_align > &seqAlign, bool onMaster)

int GetPssmIdFromSeqAlign(const CRef< CSeq_align > &seqAlign, string &err)

bool GetDDSetFromSeqAlign(const CSeq_align &align, const TDendiag *&dd)

bool EraseRow(CRef< CSeq_annot > &seqAnnot, int RowIndex)

TDendiag::const_iterator TDendiag_cit

CSeq_align::C_Segs::TDendiag TDendiag

TDendiag::iterator TDendiag_it

const int INVALID_POSITION

bool SeqIdsMatch(const CRef< CSeq_id > &id1, const CRef< CSeq_id > &id2)

int GetCDDPssmIdFromSeqId(const CRef< CSeq_id > &id)

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

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

Set object to copy of another one.

void SetPacked_int(TPacked_int &v)

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

TPending & SetPending(void)

Assign a value to Pending data member.

const TDenseg & GetDenseg(void) const

Get the variant data.

bool CanGet(void) const

Check if it is safe to call Get method.

const TStarts & GetStarts(void) const

Get the Starts member data.

TDim GetDim(void) const

Get the Dim member data.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

vector< ENa_strand > TStrands

const TLens & GetLens(void) const

Get the Lens member data.

vector< TSignedSeqPos > TStarts

vector< CRef< CSeq_id > > TIds

vector< CRef< CSeq_id > > TIds

const TIds & GetIds(void) const

Get the Ids member data.

bool IsDendiag(void) const

Check if variant Dendiag is selected.

TDim GetDim(void) const

Get the Dim member data.

const TDendiag & GetDendiag(void) const

Get the variant data.

bool IsDisc(void) const

Check if variant Disc is selected.

TType GetType(void) const

Get the Type member data.

bool IsSetDim(void) const

dimensionality Check if a value has been assigned to Dim data member.

const TIds & GetIds(void) const

Get the Ids member data.

vector< CRef< CScore > > TScores

TNumseg GetNumseg(void) const

Get the Numseg member data.

const TScores & GetScores(void) const

Get the Scores member data.

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.

bool IsDenseg(void) const

Check if variant Denseg is selected.

void SetTo(TTo value)

Assign a value to To data member.

void SetId(TId &value)

Assign a value to Id data member.

void SetFrom(TFrom value)

Assign a value to From data member.

TGi GetGi(void) const

Get the variant data.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

bool IsGi(void) const

Check if variant Gi is selected.

bool IsInt(void) const

Check if variant Int is selected.

bool IsAlign(void) const

Check if variant Align is selected.

void SetData(TData &value)

Assign a value to Data data member.

const TAlign & GetAlign(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

unsigned int

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

#define row(bind, expected)

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