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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/pssm__engine_8cpp_source.html below:

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

53 #include "../core/blast_psi_priv.h" 71 if

( !pssm_input_msa ) {

73 "IPssmInputData is NULL"

);

78 "IPssmInputData returns NULL PSIBlastOptions"

);

81 if

( !pssm_input_msa->

() ) {

83 "IPssmInputData returns NULL query sequence"

);

88 "Query length provided by IPssmInputData is 0"

);

99 if

( !pssm_input_freqratios ) {

101 "IPssmInputFreqRatios is NULL"

);

104 if

( !pssm_input_freqratios->

() ) {

106 "IPssmInputFreqRatiosFreqRatios returns NULL query sequence"

);

109 const unsigned int

kQueryLength = pssm_input_freqratios->

();

110 if

(kQueryLength == 0) {

112 "Query length provided by IPssmInputFreqRatiosFreqRatios is 0"

);

115 if

(pssm_input_freqratios->

().

() != kQueryLength) {

117 "Number of columns returned by IPssmInputFreqRatiosFreqRatios does " 118 "not match query length"

);

122 "Number of rows returned by IPssmInputFreqRatiosFreqRatios differs " 135 if

( !pssm_input_msa->

() ) {

137 "IPssmInputData returns NULL multiple sequence alignment"

);

142 string msg

(

"IPssmInputData returns invalid PSIBlastOptions: "

);

157 if

( !pssm_input->

() ) {

159 "IPssmInputData returns NULL multiple sequence alignment"

);

164 string msg

(

"IPssmInputData returns invalid PSIBlastOptions: "

);

183 "PSSM frequency ratios cannot have negative values"

);

189

: m_PssmInput(

), m_PssmInputFreqRatios(

)

197

: m_PssmInput(

), m_PssmInputFreqRatios(

)

205

m_PssmInputFreqRatios(

),

206

m_PssmInputCdd(

)

209 input

->GetMatrixName(),

->GetGapExistence(),

210 input

->GetGapExtension());

222 switch

(error_code) {

224

retval =

"No error detected"

;

228

retval =

"Bad argument to function detected"

;

232

retval =

"Out of memory"

;

236

retval =

"Error computing sequence weights"

;

240

retval =

"No matrix frequency ratios were found for requested matrix"

;

244

retval =

"PSSM has positive average score"

;

248

retval =

"No sequences left after purging biased sequences in "

;

249

retval +=

"multiple sequence alignment"

;

253

retval =

"Gap found in query sequence"

;

257

retval =

"Found column with no sequences aligned in it"

;

261

retval =

"Found column with only GAP residues"

;

265

retval =

"Found flanking gap at start of alignment"

;

269

retval =

"Found flanking gap at end of alignment"

;

273

retval =

"Errors in conserved domain profile"

;

277

retval =

"Unknown error code returned from PSSM engine: "

+

300 "processing input data strategies are null"

);

313 for

(

size_t

c = 0; c < m.

(); c++) {

315 for

(

size_t r

= 0;

r

< m.

();

r

++) {

323 for

(

size_t

c = 0; c <

; c++) {

368 if

(

.NotEmpty()) {

403 if

(

.NotEmpty()) {

441 if

(

.NotEmpty()) {

450 unsigned int

query_length)

454 unsigned char

* retval =

;

455

retval = (

unsigned char

*)

(

sizeof

(

unsigned char

)*(query_length + 2));

461

memcpy((

void

*) &retval[1], (

void

*)

, query_length);

468 const int

kNumQueries = 1;

513 unsigned int

query_length,

514 const char

* matrix_name,

574 "Unknown error when setting up BlastScoreBlk"

);

626 const char

* matrix_name,

635 string mtx

(matrix_name);

637

retval->

().SetRpsdbparams().SetMatrixName(

);

652

asn1_pssm.

(pssm->

h

);

656 if

(asn1_pssm.

() ==

false

) {

657 for

(

unsigned int i

= 0;

i

< pssm->

;

i

++) {

658 for

(

unsigned int

j = 0; j < pssm->

; j++) {

660

push_back(pssm->

[

i

][j]);

664 for

(

unsigned int i

= 0;

i

< pssm->

;

i

++) {

665 for

(

unsigned int

j = 0; j < pssm->

; j++) {

667

push_back(pssm->

[j][

i

]);

677 if

( !diagnostics ) {

695 if

(asn1_pssm.

() ==

false

) {

696 for

(

unsigned int i

= 0;

i

< pssm->

;

i

++) {

697 for

(

unsigned int

j = 0; j < pssm->

; j++) {

702 for

(

unsigned int i

= 0;

i

< pssm->

;

i

++) {

703 for

(

unsigned int

j = 0; j < pssm->

; j++) {

713 if

(asn1_pssm.

() ==

false

) {

714 for

(

unsigned int i

= 0;

i

< pssm->

;

i

++) {

715 for

(

unsigned int

j = 0; j < pssm->

; j++) {

721 for

(

unsigned int i

= 0;

i

< pssm->

;

i

++) {

722 for

(

unsigned int

j = 0; j < pssm->

; j++) {

733 if

(asn1_pssm.

() ==

false

) {

734 for

(

unsigned int i

= 0;

i

< pssm->

;

i

++) {

735 for

(

unsigned int

j = 0; j < pssm->

; j++) {

740 for

(

unsigned int i

= 0;

i

< pssm->

;

i

++) {

741 for

(

unsigned int

j = 0; j < pssm->

; j++) {

756 if

(diagnostics->

) {

760

sigma.push_back(diagnostics->

[

i

]);

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.

Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to ...

Blast_Message * Blast_MessageFree(Blast_Message *blast_msg)

Deallocates message memory.

The structures and functions in blast_options.

Int2 PSIBlastOptionsValidate(const PSIBlastOptions *psi_options, Blast_Message **blast_msg)

Validates the PSI BLAST options so that they have sane values.

Int2 BlastScoringOptionsNew(EBlastProgramType program, BlastScoringOptions **options)

Allocate memory for BlastScoringOptions and fill with default values.

Int2 BlastScoringOptionsSetMatrix(BlastScoringOptions *opts, const char *matrix_name)

Resets matrix name option.

const double kPSSM_NoImpalaScaling

Value used to indicate that no IMPALA-style scaling should be performed when scaling a PSSM.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

int PSICreatePssmFromCDD(const PSICdMsa *cd_msa, const PSIBlastOptions *options, BlastScoreBlk *sbp, const PSIDiagnosticsRequest *request, PSIMatrix **pssm, PSIDiagnosticsResponse **diagnostics)

Main entry point to core PSSM engine for computing CDD-based PSSMs.

int PSICreatePssmFromFrequencyRatios(const Uint1 *query, Uint4 query_length, BlastScoreBlk *sbp, double **freq_ratios, double impala_scaling_factor, PSIMatrix **pssm)

Top-level function to create a PSSM given a matrix of frequency ratios and perform scaling on the res...

int PSICreatePssmWithDiagnostics(const PSIMsa *msap, const PSIBlastOptions *options, BlastScoreBlk *sbp, const PSIDiagnosticsRequest *request, PSIMatrix **pssm, PSIDiagnosticsResponse **diagnostics)

Main entry point to core PSSM engine which allows to request diagnostics information.

#define PSIERR_BADPARAM

Bad parameter used in function.

#define PSIERR_ENDINGGAP

Found flanking gap at end of alignment.

#define PSIERR_COLUMNOFGAPS

Found an entire column full of GAP residues.

#define PSIERR_OUTOFMEM

Out of memory.

#define PSIERR_BADPROFILE

Errors in conserved domain profile.

#define PSIERR_POSITIVEAVGSCORE

Positive average score found when scaling matrix.

#define PSIERR_NOALIGNEDSEQS

After purge stage of PSSM creation, no sequences are left.

#define PSIERR_NOFREQRATIOS

No frequency ratios were found for the given scoring matrix.

#define PSIERR_STARTINGGAP

Found flanking gap at start of alignment.

#define PSIERR_BADSEQWEIGHTS

Sequence weights do not add to 1.

#define PSI_SUCCESS

Successful operation.

#define PSIERR_UNALIGNEDCOLUMN

Found an entire column with no participating sequences.

#define PSIERR_GAPINQUERY

GAP residue found in query sequence.

BlastQueryInfo * BlastQueryInfoNew(EBlastProgramType program, int num_queries)

Allocate memory for query information structure.

Utilities initialize/setup BLAST.

Int2 BlastSetup_ScoreBlkInit(BLAST_SequenceBlk *query_blk, const BlastQueryInfo *query_info, const BlastScoringOptions *scoring_options, EBlastProgramType program_number, BlastScoreBlk **sbpp, double scale_factor, Blast_Message **blast_message, GET_MATRIX_PATH get_path)

Initializes the score block structure.

Internal auxiliary setup classes/functions for C++ BLAST APIs.

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

BlastScoreBlk * BlastScoreBlkFree(BlastScoreBlk *sbp)

Deallocates BlastScoreBlk as well as all associated structures.

Int2 BlastSeqBlkSetSequence(BLAST_SequenceBlk *seq_blk, const Uint1 *sequence, Int4 seqlen)

Stores the sequence in the sequence block structure.

Int2 BlastSeqBlkNew(BLAST_SequenceBlk **retval)

Allocates a new sequence block structure.

Wrapper class for BLAST_SequenceBlk .

Defines BLAST error codes (user errors included)

Wrapper class for BlastQueryInfo .

Wrapper class for BlastScoringOptions .

Defines system exceptions occurred while running BLAST.

size_t GetRows() const

get the number of rows in this matrix

size_t GetCols() const

get the number of columns in this matrix

Wrapper class for PSIDiagnosticsResponse .

Wrapper class for PSIMatrix .

Exception class for the CPssmEngine class.

CSeq_entry & SetQuery()

Retrieve the query sequence.

void SetHUngapped(double val)

void SetLambdaUngapped(double val)

void SetKappa(double val)

void SetKappaUngapped(double val)

void SetLambda(double val)

Interface for strategy to pre-process multiple alignment of conserved domains matches as input data f...

virtual void Process()=0

Algorithm to produce multiple sequence alignment structure should be implemented in this method.

static void s_CheckAgainstNullData(IPssmInputData *pssm_input_msa)

This function makes sure that none of the required data is returned as NULL or "empty".

CRef< objects::CPssmWithParameters > x_CreatePssmFromMsa()

Using IPssmInputData as a delegate to provide input data in the form of a multiple sequence alignment...

CRef< objects::CPssmWithParameters > x_CreatePssmFromFreqRatios()

Using IPssmInputFreqRatios as a delegate to provide the input PSSM's frequency ratios,...

CBlastScoreBlk m_ScoreBlk

Blast score block structure.

CRef< objects::CPssmWithParameters > Run()

Runs the PSSM engine to compute the PSSM.

const Blast_KarlinBlk * GetPsiGappedKarlinBlk() const

Retrieve PSI-BLAST gapped Karlin parameters.

const char * x_GetMatrixName() const

Private interface to retrieve matrix name from its data source interface.

virtual void Process(void)=0

Pre-process CDs used for PSSM computation.

static unsigned char * x_GuardProteinQuery(const unsigned char *query, unsigned int query_length)

Copies query sequence and adds protein sentinel bytes at the beginning and at the end of the sequence...

virtual const char * GetMatrixName()

Obtain the name of the underlying matrix to use when building the PSSM.

CRef< objects::CPssmWithParameters > x_CreatePssmFromCDD()

Using IPssmInputCdd as a delegate to provide data in the form of multiple alignment of CDs,...

static CRef< objects::CPssmWithParameters > x_PSIMatrix2Asn1(const PSIMatrix *pssm, const char *matrix_name, const PSIBlastOptions *opts=NULL, const PSIDiagnosticsResponse *diagnostics=NULL)

Converts the PSIMatrix structure into a ASN.1 CPssmWithParameters object.

#define BLASTAA_SIZE

Size of aminoacid alphabet.

CPssmEngine()

Default constructor available for derived test classes.

size_t m_NumCols

number of columns in the matrix (for deallocation)

virtual unsigned char * GetQuery()=0

Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding.

virtual const PSIDiagnosticsRequest * GetDiagnosticsRequest(void)

Get diagnostics options.

void x_InitializeScoreBlock(const unsigned char *query, unsigned int query_length, const char *matrix_name, int gap_existence, int gap_extension)

Initializes the BlastScoreBlk data member required to run the PSSM engine.

BlastScoreBlk * Get() const

virtual const PSIDiagnosticsRequest * GetDiagnosticsRequest()

Obtain the diagnostics data that is requested from the PSSM engine Its results will be populated in t...

virtual double GetImpalaScaleFactor()

int x_GetGapExtension() const

Private interface to retrieve gap extension cost from data source.

virtual int GetGapExistence()

Obtain the gap existence value for the underlying matrix used to build the PSSM.

virtual unsigned int GetQueryLength()=0

Get the query's length.

int x_GetGapExistence() const

Private interface to retrieve gap existence cost from data source.

IPssmInputFreqRatios * m_PssmInputFreqRatios

Pointer to input data to create PSSM from frequency ratios.

const Blast_KarlinBlk * GetPsiUngappedKarlinBlk() const

Retrieve PSI-BLAST ungapped Karlin parameters.

IPssmInputData * m_PssmInput

Handle to strategy to process raw PSSM input data.

virtual int GetGapExtension()

Obtain the gap extension value for the underlying matrix used to build the PSSM.

virtual const PSIBlastOptions * GetOptions()=0

Obtain the options for the PSSM engine.

virtual const PSIBlastOptions * GetOptions(void)=0

Get CDD-related PSI-BLAST options.

SNcbiMatrix2DoubleMatrix(const CNcbiMatrix< double > &m)

Constructor.

static void s_Validate(IPssmInputData *pssm_input_msa)

Performs validation on data provided before invoking the CORE PSSM engine.

IPssmInputCdd * m_PssmInputCdd

Pointer to strategy to process raw PSSM input data Note: Only one m_PssmInput* should be non-NULL.

char * BlastFindMatrixPath(const char *matrix_name, Boolean is_prot)

Returns the path to a specified matrix.

virtual const CNcbiMatrix< double > & GetData()=0

Obtain a matrix of frequency ratios with this->GetQueryLength() columns and BLASTAA_SIZE rows.

virtual PSICdMsa * GetData(void)=0

Get CD data for PSSM computation.

unsigned int x_GetQueryLength() const

Private interface to retrieve query length from its data source interface.

void Reset(BlastScoreBlk *p=NULL)

~CPssmEngine()

Destructor.

void SetUngappedStatisticalParams(CConstRef< CBlastAncillaryData > ancillary_data)

Sets the Karlin & Altschul parameters in the BlastScoreBlk to be used in PSSM generation.

virtual void Process()=0

Algorithm to produce the PSSM's frequecy ratios should be implemented in this method.

virtual PSIMsa * GetData()=0

Obtain the multiple sequence alignment structure.

static std::string x_ErrorCodeToString(int error_code)

Convert a PSSM return status into a string.

virtual CRef< objects::CBioseq > GetQueryForPssm()

Get a CBioseq object for attachment into the CPssmWithParameters that CPssmEngine produces (only atta...

unsigned char * x_GetQuery() const

Private interface to retrieve query sequence from its data source interface.

double ** m_Data

double** representation of a CNcbiMatrix

~SNcbiMatrix2DoubleMatrix()

Destructor.

Uint1 GetSentinelByte(EBlastEncoding encoding) THROWS((CBlastException))

Convenience function to centralize the knowledge of which sentinel bytes we use for supported encodin...

BlastQueryInfo * x_InitializeQueryInfo(unsigned int query_length)

Initialiazes the core BlastQueryInfo structure for a single protein sequence.

@ eBlastEncodingProtein

NCBIstdaa.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * release(void)

Release will release ownership of pointer to caller.

#define NCBI_THROW(exception_class, err_code, message)

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

bool NotEmpty(void) const THROWS_NONE

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

uint32_t Uint4

4-byte (32-bit) unsigned integer

#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.

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

Convert int to string.

static string & ToUpper(string &str)

Convert string to upper case â string& version.

void SetParams(TParams &value)

Assign a value to Params data member.

list< int > TNumMatchingSeqs

void SetIsProtein(TIsProtein value)

Assign a value to IsProtein data member.

list< int > TResFreqsPerPos

void SetByRow(TByRow value)

Assign a value to ByRow data member.

void SetPssm(TPssm &value)

Assign a value to Pssm data member.

void SetIntermediateData(TIntermediateData &value)

Assign a value to IntermediateData data member.

list< double > TWeightedResFreqsPerPos

void SetFinalData(TFinalData &value)

Assign a value to FinalData data member.

list< double > TNumIndeptObsr

TByRow GetByRow(void) const

Get the ByRow member data.

list< double > TFreqRatios

list< int > TIntervalSizes

void SetNumColumns(TNumColumns value)

Assign a value to NumColumns data member.

list< double > TInformationContent

void SetNumRows(TNumRows value)

Assign a value to NumRows data member.

list< double > TGaplessColumnWeights

TSeq & SetSeq(void)

Select the variant.

static const int kScaleFactor

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

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)

Int4 query_length

Length of this query, strand or frame.

Int4 query_offset

Offset of this query, strand or frame in the concatenated super-query.

The query related information.

BlastContextInfo * contexts

Information per context.

Uint4 max_length

Length of the longest among the concatenated queries.

Structure used for scoring calculations.

Blast_KarlinBlk ** kbp

Karlin-Altschul parameters.

Blast_KarlinBlk ** kbp_psi

K-A parameters for position-based alignments.

Blast_KarlinBlk ** kbp_gap

K-A parameters for gapped alignments.

Blast_KarlinBlk * kbp_ideal

Ideal values (for query with average database composition).

Blast_KarlinBlk ** kbp_gap_psi

K-A parameters for psi alignments.

Int4 gap_open

Extra penalty for starting a gap.

Int4 gap_extend

Penalty for each gap residue.

double K

K value used in statistics.

double Lambda

Lambda value used in statistics.

double H

H value used in statistics.

double logK

natural log of K value used in statistics

Structure to hold the a message from the core of the BLAST engine.

char * message

User message to be saved.

Abstract base class to encapsulate the source(s) and pre-processing of PSSM input data as well as opt...

Interface used to retrieve the PSSM frequency ratios to allow for "restart" processing in PSI-BLAST: ...

Options used in protein BLAST only (PSI, PHI, RPS and translated BLAST) Some of these possibly should...

double impala_scaling_factor

Scaling factor as used in IMPALA to do the matrix rescaling.

Int4 pseudo_count

Pseudocount constant.

This structure contains the diagnostics information requested using the PSIDiagnosticsRequest structu...

double * information_content

position information content (query_length elements)

Uint4 ** residue_freqs

observed residue frequencies per position of the PSSM (Dimensions are query_length by alphabet_size)

double ** weighted_residue_freqs

Weighted observed residue frequencies per position of the PSSM.

Uint4 * interval_sizes

interval sizes of aligned regions (query_length elements)

Uint4 alphabet_size

Specifies length of alphabet.

Uint4 query_length

Specifies the number of positions in the PSSM.

double * gapless_column_weights

Weights for columns without gaps (query_length elements)

double * independent_observations

Effective number of observations per column.

Uint4 * num_matching_seqs

number of matching sequences per query position (query_length elements)

double * sigma

sigma (query_length elements)

double ** frequency_ratios

PSSM's frequency ratios (Dimensions are query_length by alphabet_size)

This is the main return value from the PSSM engine.

double ung_lambda

Ungapped Lambda Karlin-Altschul parameter.

double kappa

Kappa Karlin-Altschul parameter.

int ** pssm

Position-specific score matrix.

double ung_kappa

Ungapped Kappa Karlin-Altschul parameter.

Uint4 ncols

Number of columns in PSSM (query_length)

double ung_h

Ungapped H Karlin-Altschul parameter.

double lambda

Lambda Karlin-Altschul parameter.

Uint4 nrows

Number of rows in PSSM (alphabet_size)

double h

H Karlin-Altschul parameter.

Auxiliary class to convert from a CNcbiMatrix into a double** as required by the C API.

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