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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/pssm__engine_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/blast/api/pssm_engine.hpp Source File

1 #ifndef ALGO_BLAST_API__PSSM_ENGINE__HPP 2 #define ALGO_BLAST_API__PSSM_ENGINE__HPP 73  switch

(GetErrCode()) {

74  case

eNullInputData:

return "eNullInputData"

;

75  case

eInvalidInputData:

return "eInvalidInputData"

;

79 #ifndef SKIP_DOXYGEN_PROCESSING 153  static unsigned char

*

154

x_GuardProteinQuery(

const unsigned char

*

query

,

155  unsigned int

query_length);

162

x_InitializeQueryInfo(

unsigned int

query_length);

177

x_InitializeScoreBlock(

const unsigned char

*

query

,

178  unsigned int

query_length,

179  const char

* matrix_name,

185  unsigned char

* x_GetQuery()

const

;

189  unsigned int

x_GetQueryLength()

const

;

193  const char

* x_GetMatrixName()

const

;

196  int

x_GetGapExistence()

const

;

199  int

x_GetGapExtension()

const

;

205

x_CreatePssmFromMsa();

210

x_CreatePssmFromFreqRatios();

216

x_CreatePssmFromCDD();

227

x_PSIMatrix2Asn1(

const PSIMatrix

* pssm,

228  const char

* matrix_name,

237

x_ErrorCodeToString(

int

error_code);

247  friend

class ::CPssmCreateTestFixture;

259

GetScores(

const

objects::CPssmWithParameters& pssm);

266

GetFreqRatios(

const

objects::CPssmWithParameters& pssm);

273

GetInformationContent(

const

objects::CPssmWithParameters& pssm,

274

vector<double>& retval);

282

GetGaplessColumnWeights(

const

objects::CPssmWithParameters& pssm,

283

vector<double>& retval);

291

GetResidueFrequencies(

const

objects::CPssmWithParameters& pssm);

299

GetWeightedResidueFrequencies(

const

objects::CPssmWithParameters& pssm);

306

GetSigma(

const

objects::CPssmWithParameters& pssm, vector<double>& retval);

313

GetIntervalSizes(

const

objects::CPssmWithParameters& pssm,

314

vector<int>& retval);

321

GetNumMatchingSeqs(

const

objects::CPssmWithParameters& pssm,

322

vector<int>& retval);

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

Declares the BLAST exception class.

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

Definition of classes which constitute the results of running a BLAST search.

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

Defines BLAST error codes (user errors included)

Wrapper class for BlastScoreBlk .

This class exists merely to call private methods in CPsiBlastInputData and CPssmEngine.

Exception class for the CPssmEngine class.

Computes a PSSM as specified in PSI-BLAST.

Auxiliary class to convert data encoded in the PSSM to CNcbiMatrix.

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

CBlastScoreBlk m_ScoreBlk

Blast score block structure.

EErrCode

Error types that BLAST can generate.

CPssmEngine()

Default constructor available for derived test classes.

CPssmEngine(const CPssmEngine &rhs)

Prohibit copy constructor.

IPssmInputFreqRatios * m_PssmInputFreqRatios

Pointer to input data to create PSSM from frequency ratios.

CPssmEngine & operator=(const CPssmEngine &rhs)

Prohibit assignment operator.

IPssmInputData * m_PssmInput

Handle to strategy to process raw PSSM input data.

virtual const char * GetErrCodeString(void) const override

Translate from the error code value to its string representation.

IPssmInputCdd * m_PssmInputCdd

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

NCBI_EXCEPTION_DEFAULT(CPssmEngineException, CBlastException)

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

#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.

void Run(void)

Enter the main loop.

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

Defines interface for a sequence alignment processor that can populate a multiple alignment data stru...

The query related information.

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...

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

This is the main return value from the PSSM engine.

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