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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cn3d__pssm_8cpp_source.html below:

NCBI C++ ToolKit: src/app/cn3d/cn3d_pssm.cpp Source File

61 #define PTHROW(stream) NCBI_THROW(CException, eUnknown, stream) 81

c.SetSequences().SetSet().SetSeq_set().push_back(seq);

89 for

(

unsigned int i

=((bma->

NRows

() > 1) ? 1 : 0); i<bma->NRows(); ++

) {

92

c.SetSequences().SetSet().SetSeq_set().push_back(seq);

94

c.SetSeqannot().front()->SetData().SetAlign().push_back(seqAlign);

98

cd_utils::PssmMaker pm(&c,

true

);

99

cd_utils::PssmMakerOptions options;

100

options.requestFrequencyRatios =

true

;

102

pm.setOptions(options);

106 if

pssm

->GetPssm().IsSetQuery() || !

pssm

->GetPssm().GetQuery().IsSeq())

107 PTHROW

(

"PssmWithParameters from cd_utils::PssmMaker() doesn't contain the master/query sequence"

);

109 id

->SetLocal().SetStr(

"consensus"

);

110 pssm

->SetPssm().SetQuery().SetSeq().SetId().push_front(

id

);

205

}

catch

(exception& e) {

206 ERRORMSG

(

"PSSMWrapper::PSSMWrapper() failed with exception: "

<< e.what());

208 ERRORMSG

(

"PSSMWrapper::PSSMWrapper() failed with unknown exception"

);

214 if

pssm

->GetPssm().IsSetFinalData())

215 PTHROW

(

"UnpackMatrix() - pssm must have finalData"

);

216 unsigned int

nScores =

pssm

->GetPssm().GetNumRows() *

pssm

->GetPssm().GetNumColumns();

217 if

(

pssm

->GetPssm().GetNumRows() != 28 ||

pssm

->GetPssm().GetFinalData().GetScores().size() != nScores)

218 PTHROW

(

"UnpackMatrix() - bad matrix size"

);

225 for

(

=0; (

int

)i<pssm->GetPssm().GetNumColumns(); ++

)

229 unsigned int r

= 0, c = 0;

230

CPssmFinalData::TScores::const_iterator s =

pssm

->GetPssm().GetFinalData().GetScores().begin();

231 for

(

=0;

<nScores; ++

, ++s) {

236 if

(

pssm

->GetPssm().GetByRow()) {

238 if

((

int

)c ==

pssm

->GetPssm().GetNumColumns()) {

244 if

((

int

)

pssm

->GetPssm().GetNumRows()) {

252 if

((

int

)pm.getConsensus().size() !=

pssm

->GetPssm().GetNumColumns())

253 PTHROW

(

"Consensus sequence does not match PSSM size"

);

255

cd_utils::BlockModelPair

bmp

(pm.getGuideAlignment());

257 for

(

=0;

<pm.getConsensus().

size

(); ++

)

270 if

copy

.GetPssm().IsSetQuery() || !

copy

.GetPssm().GetQuery().IsSeq()) {

271 ERRORMSG

(

"PssmWithParameters from cd_utils::PssmMaker() doesn't contain the master/query sequence"

);

276

CBioseq::TId::iterator

, ie =

copy

.SetPssm().SetQuery().SetSeq().SetId().end();

277 for

(

copy

.SetPssm().SetQuery().SetSeq().SetId().begin();

!=ie; ++

) {

278 if

((*i)->IsLocal() && (*i)->GetLocal().IsStr())

279

(*i)->SetLocal().SetStr(title);

280 if

(!(*i)->IsGeneral() || (*i)->GetGeneral().GetDb() !=

"Cdd"

)

281

keep.push_back(*

);

283 copy

.SetPssm().SetQuery().SetSeq().SetId() = keep;

285

CSeq_descr::Tdata::iterator d, de =

copy

.SetPssm().SetQuery().SetSeq().SetDescr().Set().end();

286 for

(d=

copy

.SetPssm().SetQuery().SetSeq().SetDescr().Set().begin(); d!=de; ++d) {

287 if

((*d)->IsTitle()) {

288

(*d)->SetTitle(title);

295 copy

.SetPssm().SetQuery().SetSeq().SetDescr().Set().push_front(descr);

299 copy

.SetPssm().ResetFinalData();

300 if

copy

.GetPssm().IsSetIntermediateData() || !

copy

.GetPssm().GetIntermediateData().IsSetFreqRatios())

301 ERRORMSG

(

"PSSM is missing frequency ratios"

);

307 static inline int Round

(

double

Num)

310 return

((

int

)(Num + 0.5));

312 return

((

int

)(Num - 0.5));

318 ERRORMSG

(

"PSSMWrapper::GetPSSMScore() - invalid parameters"

);

324 if

(consensusIndex >= 0) {

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

std::vector< Column > scaledMatrix

std::vector< int > master2consensus

ncbi::CRef< ncbi::objects::CPssmWithParameters > pssm

PSSMWrapper(const BlockMultipleAlignment *bma)

void UnpackMatrix(ncbi::cd_utils::PssmMaker &pm)

std::vector< int > consensus2master

int GetPSSMScore(unsigned char ncbistdaa, unsigned int realMasterIndex) const

const BlockMultipleAlignment * multiple

void OutputPSSM(ncbi::CNcbiOstream &os, const std::string &title) const

unsigned int Length(void) const

CConstRef< objects::CBioseq > bioseqASN

static int Round(double Num)

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

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

main entry point for tests

thread_local unique_ptr< FtaMsgPost > bmp

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

Set object to copy of another one.

void Reset(void)

Reset reference object.

TObjectType & GetObject(void) const

Get object.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

TSeq & SetSeq(void)

Select the variant.

TTitle & SetTitle(void)

Select the variant.

list< CRef< CSeq_id > > TId

unsigned int

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

const struct ncbi::grid::netcache::search::fields::SIZE size

void resize(vector< SMethodDef > &container)

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

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

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

static DP_BlockInfo * blocks

static int GetBLOSUM62Score(char a, char b)

ncbi::objects::CSeq_align * CreatePairwiseSeqAlignFromMultipleRow(const BlockMultipleAlignment *multiple, const BlockMultipleAlignment::UngappedAlignedBlockList &blocks, unsigned int slaveRow)

char LookupCharacterFromNCBIStdaaNumber(unsigned char n)

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