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NCBI C++ ToolKit: src/app/cn3d/cn3d_blast.cpp Source File

84

ts->originalFullSequence = pair->

GetMaster

();

99

ts->fromIndex = uaBlocks.front()->GetRangeOfRow(0)->from - extension;

100 if

(ts->fromIndex < 0)

102

ts->toIndex = uaBlocks.back()->GetRangeOfRow(0)->to + extension;

103 if

(ts->toIndex >= (

int

)ts->originalFullSequence->Length())

104

ts->toIndex = ts->originalFullSequence->Length() - 1;

110

ts->toIndex = ts->originalFullSequence->Length() - 1;

131

ts->toIndex = ts->originalFullSequence->Length() - 1;

137 CBioseq

& bioseq = ts->truncatedSequence->SetSeq();

139 id

->SetLocal().SetId(alnNum);

140

bioseq.

SetId

().push_back(

id

);

143

bioseq.

SetInst

().SetLength(ts->toIndex - ts->fromIndex + 1);

144 TRACEMSG

(

"truncated "

<< ts->originalFullSequence->identifier->ToString()

145

" from "

<< (ts->fromIndex+1) <<

" to "

<< (ts->toIndex+1) <<

"; length "

<< bioseq.

GetInst

().

GetLength

());

146

bioseq.

SetInst

().SetSeq_data().SetNcbistdaa().Set().resize(ts->toIndex - ts->fromIndex + 1);

147 for

(

int

j=ts->fromIndex; j<=ts->toIndex; ++j)

148

bioseq.

SetInst

().SetSeq_data().SetNcbistdaa().Set()[j - ts->fromIndex] =

193

vector < int > masterLoc(length);

195 for

(

=0;

<length; ++

)

196

masterLoc[

] = multiple->

GetPSSM

().MapConsensusToMaster(consensusStart +

);

199 for

(

=0;

<length; ++

) {

202 if

(!subBlock && masterLoc[

] >= 0) {

205

subBlock->

SetRangeOfRow

(1, dependentStart +

, dependentStart +

);

206

subBlock->

width

= 1;

213 if

(

== length - 1 ||

214

masterLoc[

+ 1] < 0 ||

215

masterLoc[

+ 1] != masterLoc[

] + 1)

227

++(subBlock->

width

);

233 ERRORMSG

(

"MapBlockFromConsensusToMaster() - unterminated sub-block"

);

239 om

->GetRegisteredNames(loader_names);

241 om

->RevokeDataLoader(*itr);

266

newAlignments->clear();

268 ERRORMSG

(

"usePSSM true, but NULL or zero-aligned block multiple alignment"

);

271 if

(!usePSSM && toRealign.size() > 1) {

272 ERRORMSG

(

"CreateNewPairwiseAlignmentsByBlast() - currently can only do single blast-2-sequences at a time"

);

275 if

(toRealign.size() == 0)

283 WARNINGMSG

(

"Can't get footprint residue extension from registry"

);

291

blast::CBlastQueryVector queryVector, subjectVector;

297

AlignmentList::const_iterator

, ae = toRealign.end();

298 for

(

=toRealign.begin();

!=ae; ++

, ++localID) {

300

master = (*a)->GetMaster();

301 if

((*a)->GetMaster() != master) {

302 ERRORMSG

(

"CreateNewPairwiseAlignmentsByBlast() - all masters must be the same"

);

305 if

((*a)->NRows() != 2) {

306 ERRORMSG

(

"CreateNewPairwiseAlignmentsByBlast() - can only realign pairwise alignments"

);

312

subjectBioseq = &(subjectTSs.back()->truncatedSequence->SetSeq());

317

subjectVector.AddQuery(bsqSubject);

332

pssmOptions.

Reset

(

new

blast::CPSIBlastOptionsHandle);

335

pssmOptions->SetDbLength(1196146007);

336

pssmOptions->SetDbSeqNum(3479934);

337

pssmOptions->SetHitlistSize(subjectTSs.size());

338

pssmOptions->SetMatrixName(

"BLOSUM62"

);

340

pssmOptions->SetSegFiltering(

false

);

342

blastEngine.

Reset

(

new 357

queryBioseq = &(masterTS->truncatedSequence->SetSeq());

361

queryVector.AddQuery(bsqQuery);

363

sequenceQuery.

Reset

(

new

blast::CObjMgr_QueryFactory(queryVector));

365

sequenceOptions.

Reset

(

new

blast::CBlastProteinOptionsHandle);

366

sequenceOptions->SetMatrixName(

"BLOSUM62"

);

367

sequenceOptions->SetHitlistSize(subjectTSs.size());

368

blastEngine.

Reset

(

new 379 if

(

results

->size() != toRealign.size())

381 ERRORMSG

(

"CreateNewPairwiseAlignmentsByBlast() - did not get one result alignment per input sequence"

);

386 for

(

unsigned int i

=0;

results

->size(); ++

, ++localID) {

394

(*seqs)[1] = subjectTSs[localID]->originalFullSequence;

395 string

dependentTitle = subjectTSs[localID]->originalFullSequence->

identifier

ToString

();

396

unique_ptr < BlockMultipleAlignment > newAlignment(

402 if

(!((*

results

)[

].HasAlignments())) {

403 WARNINGMSG

(

"BLAST did not find a significant alignment for " 404

<< dependentTitle <<

" with "

<< (usePSSM ?

string

(

"PSSM"

) : master->

identifier

ToString

()));

408 const CSeq_align

& sa = (*results)[

].GetSeqAlign()->Get().front().GetObject();

411 ERRORMSG

(

"CreateNewPairwiseAlignmentsByBlast() - returned alignment not in expected format (dim 2, partial)"

);

418 ERRORMSG

(

"CreateNewPairwiseAlignmentsByBlast() - returned alignment format error (denseg dims)"

);

421 ERRORMSG

(

"CreateNewPairwiseAlignmentsByBlast() - returned alignment format error (ids)"

);

425

CDense_seg::TStarts::const_iterator s = ds.

GetStarts

().begin();

426

CDense_seg::TLens::const_iterator

= ds.

GetLens

().end();

428 int

masterStart = *(s++), dependentStart = *(s++);

429 if

(masterStart >= 0 && dependentStart >= 0) {

430

dependentStart += subjectTSs[localID]->fromIndex;

435

masterStart += masterTS->fromIndex;

437

newBlock->

SetRangeOfRow

(0, masterStart, masterStart + (*

) - 1);

438

newBlock->

SetRangeOfRow

(1, dependentStart, dependentStart + (*

) - 1);

440

newAlignment->AddAlignedBlockAtEnd(newBlock);

447 ERRORMSG

(

"CreateNewPairwiseAlignmentsByBlast() - returned alignment in unrecognized format"

);

452 WARNINGMSG

(

"BLAST did not return an alignment score for "

<< dependentTitle);

455

oss <<

"BLAST result scores for "

<< dependentTitle <<

" vs. " 459

CSeq_align::TScore::const_iterator sc, sce = sa.

GetScore

().end();

460 for

(sc=sa.

GetScore

().begin(); sc!=sce; ++sc) {

461 if

((*sc)->IsSetId() && (*sc)->GetId().IsStr()) {

464 if

((*sc)->GetValue().IsReal() && (*sc)->GetId().GetStr() ==

"e_value"

) {

466

newAlignment->SetRowDouble(0, (*sc)->GetValue().GetReal());

467

newAlignment->SetRowDouble(1, (*sc)->GetValue().GetReal());

469

newAlignment->SetRowStatusLine(0, status);

470

newAlignment->SetRowStatusLine(1, status);

471

oss <<

' '

<< status;

475 else if

((*sc)->GetValue().IsInt() && (*sc)->GetId().GetStr() ==

"score"

) {

476

oss <<

" raw: "

<< (*sc)->GetValue().GetInt();

480 else if

((*sc)->GetValue().IsReal() && (*sc)->GetId().GetStr() ==

"bit_score"

) {

481

oss <<

" bit score: "

<< (*sc)->GetValue().GetReal();

488 WARNINGMSG

(

"BLAST did not return an E-value for "

<< dependentTitle);

493 if

(newAlignment->AddUnalignedBlocks() && newAlignment->UpdateBlockMapAndColors(

false

))

494

newAlignments->push_back(newAlignment.release());

496 ERRORMSG

(

"error finalizing alignment"

);

499

}

catch

(exception& e) {

500 ERRORMSG

(

"CreateNewPairwiseAlignmentsByBlast() failed with exception: "

<< e.what());

507 ERRORMSG

(

"NULL multiple alignment"

);

513 WARNINGMSG

(

"Can't get footprint residue extension from registry"

);

517 if

(uaBlocks.size() == 0) {

518 ERRORMSG

(

"Can't calculate self-hits with no aligned blocks"

);

534

range = uaBlocks.back()->GetRangeOfRow(

row

);

538

rowPairs.push_back(newAlignment);

545 ERRORMSG

(

"CalculateSelfHitScores() - CreateNewPairwiseAlignmentsByBlast() didn't return right # alignments"

);

550

AlignmentList::const_iterator

results

.begin();

552 double

score = (*r)->GetRowDouble(1);

558

status =

"No detectable self hit"

;

564 static const double

threshold = 0.01;

565 unsigned int

nSelfHits = 0;

570 INFOMSG

(

"Self hits with E-value <= "

<< setprecision(3) << threshold <<

": " 571

<< (100.0*nSelfHits/multiple->

NRows

()) <<

"% (" 572

<< nSelfHits <<

'/'

<< multiple->

NRows

() <<

')'

<< setprecision(6));

578 static

CharDoubleMap standardProbabilities;

580 if

(standardProbabilities.size() == 0) {

582 ERRORMSG

(

"GetStandardProbability() - confused by BLASTAA_SIZE != 28"

);

586 for

(

unsigned int i

=0;

<28; ++

) {

593

CharDoubleMap::const_iterator

= standardProbabilities.find(

toupper

((

unsigned char

) ch));

594 if

(

!= standardProbabilities.end())

596 WARNINGMSG

(

"GetStandardProbability() - unknown residue character "

<< ch);

User-defined methods of the data storage class.

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

double * BLAST_GetStandardAaProbabilities(void)

Get the standard amino acid probabilities.

std::list< BlockMultipleAlignment * > AlignmentList

void CalculateSelfHitScores(const BlockMultipleAlignment *multiple)

void CreateNewPairwiseAlignmentsByBlast(const BlockMultipleAlignment *multiple, const AlignmentList &toRealign, AlignmentList *newAlignments, bool usePSSM)

std::vector< const Sequence * > SequenceList

void SetRowDouble(unsigned int row, double value) const

const BLAST_Matrix * GetPSSM(void) const

void SetRowStatusLine(unsigned int row, const std::string &value) const

const Sequence * GetMaster(void) const

std::vector< const UngappedAlignedBlock * > UngappedAlignedBlockList

const Sequence * GetSequenceOfRow(unsigned int row) const

void GetUngappedAlignedBlocks(UngappedAlignedBlockList *blocks) const

unsigned int NRows(void) const

bool HasNoAlignedBlocks(void) const

double GetRowDouble(unsigned int row) const

bool AddAlignedBlockAtEnd(UngappedAlignedBlock *newBlock)

void SetRangeOfRow(unsigned int row, int from, int to)

const Range * GetRangeOfRow(int row) const

const CSeq_id * GetFirstId() const

TSeqPos GetLength(void) const

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

std::string ToString(void) const

const MoleculeIdentifier * identifier

unsigned int Length(void) const

AlignmentManager * alignmentManager

const Sequence * originalFullSequence

CRef< CSeq_entry > truncatedSequence

double GetStandardProbability(char ch)

static void RemoveAllDataLoaders()

static CRef< TruncatedSequence > CreateTruncatedSequence(const BlockMultipleAlignment *multiple, const BlockMultipleAlignment *pair, int alnNum, bool isMaster, int extension)

static bool SeqIdMatchesMaster(const CSeq_id &sid, bool usePSSM)

static void MapBlockFromConsensusToMaster(int consensusStart, int dependentStart, int length, BlockMultipleAlignment *newAlignment, const BlockMultipleAlignment *multiple)

static bool SimpleSeqLocFromBioseq(const CRef< CBioseq > &bs, CSeq_loc &seqLoc)

vector< CRef< TruncatedSequence > > TruncatedSequences

static bool IsLocalID(const CSeq_id &sid, int localID)

@ eCompositionBasedStats

Composition-based statistics as in NAR 29:2994-3005, 2001.

Include a standard set of the NCBI C++ Toolkit most basic headers.

The NCBI C++ standard methods for dealing with std::string.

#define BLASTAA_SIZE

Size of aminoacid alphabet.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

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

Set object to copy of another one.

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

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

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

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

vector< string > TRegisteredNames

void ResetDataAndHistory(void)

Clear all information in the scope except added data loaders.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

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

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

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

Convert int to string.

bool IsStr(void) const

Check if variant Str is selected.

bool IsId(void) const

Check if variant Id is selected.

const TStr & GetStr(void) const

Get the variant data.

TId GetId(void) const

Get the variant data.

const TDenseg & GetDenseg(void) const

Get the variant data.

bool IsSetDim(void) const

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

const TStarts & GetStarts(void) const

Get the Starts member data.

TDim GetDim(void) const

Get the Dim member data.

const TLens & GetLens(void) const

Get the Lens member data.

TDim GetDim(void) const

Get the Dim member data.

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.

bool IsSetScore(void) const

for whole alignment Check if a value has been assigned to Score data member.

TNumseg GetNumseg(void) const

Get the Numseg member data.

const TScore & GetScore(void) const

Get the Score member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

@ eType_partial

mapping pieces together

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.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsLocal(void) const

Check if variant Local is selected.

TId & SetId(void)

Assign a value to Id data member.

const TInst & GetInst(void) const

Get the Inst member data.

TLength GetLength(void) const

Get the Length member data.

void SetInst(TInst &value)

Assign a value to Inst data member.

@ eRepr_raw

continuous sequence

bool le(T x_, T y_, T round_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

Declares CPsiBl2Seq, the C++ API for the PSI-BLAST 2 Sequences engine.

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

CRef< objects::CObjectManager > om

#define row(bind, expected)

#define DELETE_ALL_AND_CLEAR(container, ContainerType)

unsigned char LookupNCBIStdaaNumberFromCharacter(char r)

char LookupCharacterFromNCBIStdaaNumber(unsigned char n)

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