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NCBI C++ ToolKit: src/algo/blast/api/psiblast_aux_priv.cpp Source File

( !score_blk->protein_alphabet ) {

);

score_blk->kbp_psi[0]->Lambda = pssm->GetPssm().GetLambdaUngapped();

}

(score_blk->kbp_std[0]->Lambda > 0.0) {

score_blk->kbp_psi[0]->Lambda = score_blk->kbp_std[0]->Lambda;

score_blk->kbp_psi[0]->K = pssm->GetPssm().GetKappaUngapped();

}

(score_blk->kbp_std[0]->K > 0.0) {

score_blk->kbp_psi[0]->K = score_blk->kbp_std[0]->K;

score_blk->kbp_psi[0]->logK =

(score_blk->kbp_psi[0]->K);

score_blk->kbp_psi[0]->H = pssm->GetPssm().GetHUngapped();

}

(score_blk->kbp_std[0]->K > 0.0) {

score_blk->kbp_psi[0]->H = score_blk->kbp_std[0]->H;

score_blk->kbp_gap_psi[0]->Lambda = pssm->GetPssm().GetLambda();

}

(score_blk->kbp_gap_std[0]->Lambda > 0.0) {

score_blk->kbp_gap_psi[0]->Lambda = score_blk->kbp_gap_std[0]->Lambda;

score_blk->kbp_gap_psi[0]->K = pssm->GetPssm().GetKappa();

}

(score_blk->kbp_gap_std[0]->K > 0.0) {

score_blk->kbp_gap_psi[0]->K = score_blk->kbp_gap_std[0]->K;

score_blk->kbp_gap_psi[0]->logK =

(score_blk->kbp_gap_psi[0]->K);

score_blk->kbp_gap_psi[0]->H = pssm->GetPssm().GetH();

}

(score_blk->kbp_gap_std[0]->H > 0.0) {

score_blk->kbp_gap_psi[0]->H = score_blk->kbp_gap_std[0]->H;

kQueryLength = pssm->GetPssm().GetNumColumns();

missing_scores =

;

unique_ptr< CNcbiMatrix<int> > scores

(score_blk->psi_matrix->pssm->ncols == scores->GetCols());

(score_blk->psi_matrix->pssm->nrows == scores->GetRows());

(

c = 0; c < scores->GetCols(); c++) {

(

= 0;

< scores->GetRows();

++) {

score_blk->psi_matrix->pssm->data[c][

] = (*scores)(

, c);

}

(

std::runtime_error&) {

missing_scores =

;

missing_freq_ratios =

;

freq_ratios_all_zeros =

;

unique_ptr< CNcbiMatrix<double> > freq_ratios

(score_blk->psi_matrix->pssm->ncols ==

freq_ratios->GetCols());

(score_blk->psi_matrix->pssm->nrows ==

freq_ratios->GetRows());

(

c = 0; c < freq_ratios->GetCols(); c++) {

(

= 0;

< freq_ratios->GetRows();

++) {

score_blk->psi_matrix->freq_ratios[c][

] =

(*freq_ratios)(

, c);

freq_ratios_all_zeros =

;

}

(

std::runtime_error&) {

missing_freq_ratios =

;

(missing_scores && missing_freq_ratios) {

);

freq_ratios_all_zeros) {

os <<

;

os << options->GetMatrixName() <<

;

os <<

;

(messages.size() == 1);

messages.front().push_back(sm);

os <<

<<

<<

<<

;

(messages.size() == 1);

messages.front().push_back(sm);

list<T>::const_iterator itr =

.begin();

(by_row ==

) {

(

c = 0; c < num_columns; c++) {

dest(

, c) = *itr++;

(

c = 0; c < num_columns; c++) {

dest(

, c) = *itr++;

( !pssm_asn.GetPssm().CanGetFinalData() ||

!pssm_asn.GetPssm().GetFinalData().CanGetScores() ||

pssm_asn.GetPssm().GetFinalData().GetScores().empty() ) {

runtime_error(

);

& pssm = pssm_asn.GetPssm();

(

)pssm.

()*pssm_asn.GetPssm().GetNumColumns());

unique_ptr< CNcbiMatrix<int> > retval

retval.release();

( !pssm_asn.GetPssm().CanGetIntermediateData() ||

!pssm_asn.GetPssm().GetIntermediateData().CanGetFreqRatios() ||

pssm_asn.GetPssm().GetIntermediateData().GetFreqRatios().empty() ) {

runtime_error(

);

& pssm = pssm_asn.GetPssm();

(

)pssm.

()*pssm_asn.GetPssm().GetNumColumns());

unique_ptr< CNcbiMatrix<double> > retval

retval.release();

(

objects::CPssmWithParameters& pssm_asn)

( !pssm_asn.GetPssm().CanGetIntermediateData() ||

!pssm_asn.GetPssm().GetIntermediateData().CanGetResFreqsPerPos() ||

pssm_asn.GetPssm().GetIntermediateData().GetResFreqsPerPos().empty() )

& pssm = pssm_asn.GetPssm();

(

)pssm.

()*pssm_asn.GetPssm().GetNumColumns());

unique_ptr< CNcbiMatrix<int> > retval

retval.release();

(

objects::CPssmWithParameters& pssm_asn)

( !pssm_asn.GetPssm().CanGetIntermediateData() ||

!pssm_asn.GetPssm().GetIntermediateData().

CanGetWeightedResFreqsPerPos() ||

pssm_asn.GetPssm().GetIntermediateData().

GetWeightedResFreqsPerPos().

() ) {

& pssm = pssm_asn.GetPssm();

GetWeightedResFreqsPerPos().

() ==

(

)pssm.

()*pssm_asn.GetPssm().GetNumColumns());

unique_ptr< CNcbiMatrix<double> > retval

retval.release();

(

objects::CPssmWithParameters& pssm_asn,

vector<double>& retval)

( !pssm_asn.GetPssm().CanGetIntermediateData() ||

!pssm_asn.GetPssm().GetIntermediateData().CanGetInformationContent() ||

& pssm = pssm_asn.GetPssm();

back_inserter(retval));

(

objects::CPssmWithParameters& pssm_asn,

vector<double>& retval)

( !pssm_asn.GetPssm().CanGetIntermediateData() ||

GetIntermediateData().CanGetGaplessColumnWeights() ||

& pssm = pssm_asn.GetPssm();

back_inserter(retval));

vector<double>& retval)

( !pssm_asn.GetPssm().CanGetIntermediateData() ||

!pssm_asn.GetPssm().GetIntermediateData().CanGetSigma() ||

pssm_asn.GetPssm().GetIntermediateData().GetSigma().empty() ) {

& pssm = pssm_asn.GetPssm();

back_inserter(retval));

(

objects::CPssmWithParameters& pssm_asn, vector<int>& retval)

( !pssm_asn.GetPssm().CanGetIntermediateData() ||

GetIntermediateData().CanGetIntervalSizes() ||

& pssm = pssm_asn.GetPssm();

back_inserter(retval));

(

objects::CPssmWithParameters& pssm_asn, vector<int>& retval)

( !pssm_asn.GetPssm().CanGetIntermediateData() ||

GetIntermediateData().CanGetNumMatchingSeqs() ||

& pssm = pssm_asn.GetPssm();

back_inserter(retval));

(pssm.GetParams().GetRpsdbparams().IsSetMatrixName());

pssm.SetParams().SetRpsdbparams().SetGapOpen(gap_open);

pssm.SetParams().SetRpsdbparams().SetGapExtend(gap_extend);

(pssm.GetPssm().CanGetFinalData()) {

(pssm.GetPssm().GetFinalData().GetScores().size() ==

(

)

*pssm.GetPssm().GetNumColumns());

diff = (size_t)

- pssm.GetPssm().GetNumRows();

pssm.SetPssm().SetIntermediateData().SetFreqRatios();

(pssm.GetPssm().GetByRow() ==

) {

freq_ratios.resize(pssm.GetPssm().GetNumColumns() *

, 0.0);

CPssmIntermediateData::TFreqRatios::iterator itr = freq_ratios.begin();

(

c = 0; c < pssm.GetPssm().GetNumColumns(); c++) {

advance(itr, pssm.GetPssm().GetNumRows());

freq_ratios.insert(itr, diff, 0.0);

(

)pssm->GetPssm().GetNumColumns());

unique_ptr< CNcbiMatrix<double> > freq_ratios

(pssm->GetPssm().GetNumRows() !=

pssm->SetPssm().SetFinalData().SetScores() =

pssm->SetPssm().SetFinalData().SetLambda() =

pssm->SetPssm().SetFinalData().SetKappa() =

pssm->SetPssm().SetFinalData().SetH() =

(score_type ==

|| score_type ==

)) {

(score.

().

() && score_type ==

) {

CPsiBlastAlignmentProcessor::operator()

(

objects::CSeq_align_set& alignments,

evalue_inclusion_threshold,

(e < evalue_inclusion_threshold) {

( !pssm.CanGetPssm() ) {

);

missing_scores(

);

( !pssm.GetPssm().CanGetFinalData() ||

!pssm.GetPssm().GetFinalData().CanGetScores() ||

pssm.GetPssm().GetFinalData().GetScores().empty() ) {

missing_scores =

;

missing_freq_ratios(

);

( !pssm.GetPssm().CanGetIntermediateData() ||

!pssm.GetPssm().GetIntermediateData().CanGetFreqRatios() ||

pssm.GetPssm().GetIntermediateData().GetFreqRatios().empty() ) {

missing_freq_ratios =

;

(missing_freq_ratios && missing_scores) {

);

(missing_scores && require_scores) {

);

(!missing_scores &&

pssm.GetPssm().GetFinalData().CanGetScalingFactor() &&

pssm.GetPssm().GetFinalData().GetScalingFactor() != 1) {

(

);

.GetScalingFactor());

+=

;

( !pssm.HasQuery() ) {

);

( !pssm.GetQuery().IsSeq() ) {

);

( !pssm.GetPssm().GetIsProtein() ) {

);

excpt_msg(

);

excpt_msg +=

;

excpt_msg +=

;

(e.

().find(

) !=

) {

(sblk->

));

excpt_msg.assign(

);

excpt_msg += (qf_type ==

?

:

);

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.

Auxiliary functions for BLAST.

Declarations of static arrays used to define some NCBI encodings to be used in a toolkit independent ...

Declares the BLAST exception class.

The structures and functions in blast_options.

#define BLAST_EXPECT_VALUE

Default parameters for saving hits.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

const double kEpsilon

Small constant to test against 0.

Definitions and prototypes used by blast_stat.c to calculate BLAST statistics.

#define BLAST_SCORE_MIN

minimum allowed score (for one letter comparison).

SPsiBlastScoreMatrix * SPsiBlastScoreMatrixNew(size_t ncols)

Allocates a new SPsiBlastScoreMatrix structure of dimensions ncols by BLASTAA_SIZE.

@ eDeltaBlast

Delta Blast.

Defines BLAST error codes (user errors included)

Handle to the options to the BLAST algorithm.

Encapsulates ALL the BLAST algorithm's options.

static ESequenceType SequenceType(const char *str, unsigned length=0, ESTStrictness strictness=eST_Default)

Guess sequence type.

NCBI C++ Object Manager free implementation of IQueryFactory.

Implements the interface to retrieve data for the last 2 stages of the PSSM creation.

Computes a PSSM as specified in PSI-BLAST.

static const double kInvalidStat

Error or Warning Message from search.

typedef for the messages for an entire BLAST search, which could be comprised of multiple query seque...

@ eCompositionBasedStats

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

@ eNoCompositionBasedStats

Don't use composition based statistics.

static SQLCHAR output[256]

static void QueryFactory(CRef< IQueryFactory > query_factory, const CBlastOptionsHandle &opts_handle, EQueryFactoryType query_factory_type=eQFT_Query)

Function to perform sanity checks on the query factory.

static CNcbiMatrix< int > * GetResidueFrequencies(const objects::CPssmWithParameters &pssm)

Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastS...

CRef< objects::CPssmWithParameters > Run()

Runs the PSSM engine to compute the PSSM.

void PsiBlastSetupScoreBlock(BlastScoreBlk *score_blk, CConstRef< objects::CPssmWithParameters > pssm, TSearchMessages &messages, CConstRef< CBlastOptions > options)

Setup CORE BLAST score block structure with data from the scoremat PSSM.

void Convert2Matrix(const list< T > &source, CNcbiMatrix< T > &dest, bool by_row, SIZE_TYPE num_rows, SIZE_TYPE num_columns)

Convert a list of values into a CNcbiMatrix.

static CNcbiMatrix< int > * GetScores(const objects::CPssmWithParameters &pssm)

Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastS...

#define BLASTAA_SIZE

Size of aminoacid alphabet.

static void GetSigma(const objects::CPssmWithParameters &pssm, vector< double > &retval)

Data used in sequence weights computation.

static CNcbiMatrix< double > * GetWeightedResidueFrequencies(const objects::CPssmWithParameters &pssm)

Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastS...

virtual BLAST_SequenceBlk * GetSequenceBlk()=0

Accessor for the BLAST_SequenceBlk structure.

CRef< ILocalQueryData > MakeLocalQueryData(const CBlastOptions *opts)

Creates and caches an ILocalQueryData.

EQueryFactoryType

Enumeration to specify the different uses of the query factory.

int GetGapExtensionCost() const

static double s_GetBitScore(const CScore &score)

Returns the bit_score from this score object.

static void s_AdjustFrequencyRatiosMatrixToMatchScoreMatrix(objects::CPssmWithParameters &pssm)

After creating the PSSM from frequency ratios, adjust the frequency ratios matrix to match the dimens...

static double s_GetEvalue(const CScore &score)

Returns the evalue from this score object.

static CNcbiMatrix< double > * GetFreqRatios(const objects::CPssmWithParameters &pssm)

Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastS...

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

static void GetNumMatchingSeqs(const objects::CPssmWithParameters &pssm, vector< int > &retval)

Gets the number of matching sequences per position of the PSSM.

void PsiBlastComputePssmScores(CRef< objects::CPssmWithParameters > pssm, const CBlastOptions &opts)

Given a PSSM with frequency ratios and options, invoke the PSSM engine to compute the scores.

virtual size_t GetNumQueries()=0

Get the number of queries.

double GetLowestEvalue(const objects::CDense_seg::TScores &scores, double *bit_score)

Returns the lowest score from the list of scores in CDense_seg::TScores.

void PsiBlastAddAncillaryPssmData(objects::CPssmWithParameters &pssm, int gap_open, int gap_extend)

Even though the query sequence and the matrix gap costs are not a product of the PSSM engine,...

static void Pssm(const objects::CPssmWithParameters &pssm, bool require_scores=false)

Perform validation on the PSSM.

static void GetGaplessColumnWeights(const objects::CPssmWithParameters &pssm, vector< double > &retval)

Returns the relative gapless PSSM column weights to pseudocounts for the provided PSSM.

virtual size_t GetSeqLength(size_t index)=0

Get the length of the sequence indicated by index.

int GetGapOpeningCost() const

static void GetInformationContent(const objects::CPssmWithParameters &pssm, vector< double > &retval)

Returns the information content per position of the PSSM.

const char * GetMatrixName() const

static void GetIntervalSizes(const objects::CPssmWithParameters &pssm, vector< int > &retval)

Length of the aligned regions per position of the query sequence.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

NCBI_NS_STD::string::size_type SIZE_TYPE

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

Convert int to string.

const TStr & GetStr(void) const

Get the variant data.

const TFreqRatios & GetFreqRatios(void) const

Get the FreqRatios member data.

const TNumMatchingSeqs & GetNumMatchingSeqs(void) const

Get the NumMatchingSeqs member data.

TNumRows GetNumRows(void) const

Get the NumRows member data.

const TGaplessColumnWeights & GetGaplessColumnWeights(void) const

Get the GaplessColumnWeights member data.

TH GetH(void) const

Get the H member data.

TKappa GetKappa(void) const

Get the Kappa member data.

const TScores & GetScores(void) const

Get the Scores member data.

const TWeightedResFreqsPerPos & GetWeightedResFreqsPerPos(void) const

Get the WeightedResFreqsPerPos member data.

const TIntervalSizes & GetIntervalSizes(void) const

Get the IntervalSizes member data.

const TSigma & GetSigma(void) const

Get the Sigma member data.

const TInformationContent & GetInformationContent(void) const

Get the InformationContent member data.

const TFinalData & GetFinalData(void) const

Get the FinalData member data.

TNumColumns GetNumColumns(void) const

Get the NumColumns member data.

const TIntermediateData & GetIntermediateData(void) const

Get the IntermediateData member data.

TByRow GetByRow(void) const

Get the ByRow member data.

list< double > TFreqRatios

const TResFreqsPerPos & GetResFreqsPerPos(void) const

Get the ResFreqsPerPos member data.

const TPssm & GetPssm(void) const

Get the Pssm member data.

TLambda GetLambda(void) const

Get the Lambda member data.

bool IsReal(void) const

Check if variant Real is selected.

const TValue & GetValue(void) const

Get the Value member data.

vector< CRef< CScore > > TScores

list< CRef< CSeq_align > > Tdata

TReal GetReal(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

constexpr bool empty(list< Ts... >) noexcept

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

const CharType(& source)[N]

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

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

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

Defines a concrete strategy to obtain PSSM input data for PSI-BLAST.

Declarations of auxiliary functions/classes for PSI-BLAST.

C++ API for the PSI-BLAST PSSM engine.

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

Structure to hold a sequence.

Uint1 * sequence_start

Start of sequence, usually one byte before sequence as that byte is a NULL sentinel byte.

Int4 length

Length of sequence.

Uint1 * sequence

Sequence used for search (could be translation).

Structure used for scoring calculations.

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