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

vector<double>& seq1_residue_probs,

vector<double>& seq2_residue_rpobs);

{

(*m_ScoreMatrix).GetMatrix();}

{

(*m_ScoreMatrix).GetScore(

, j);}

Score matrix that can take any value.

EScoreMatrixName

Names of standard scoring matrices.

Wrapper for Gumbel parameter calculation.

void SetRandParams(const CRef< CGumbelParamsRandDiagnostics > &rand_opts)

Set randomization parameters.

CGumbelParamsCalc & operator=(const CGumbelParamsCalc &)

Forbid assignment oprator.

static const int kMinorVersion

Minor version.

CRef< CGumbelParamsResult > m_Result

const SGumbelParams & GetGumbelParams(void) const

CRef< CGumbelParamsRandDiagnostics > GetRandParams(void)

Get randomization parameters.

static const int kPatchVersion

Patch version.

static const int kMajorVersion

Major version.

CConstRef< CGumbelParamsOptions > m_Options

CRef< CGumbelParamsResult > Run(void)

Perform Gumbel parameter calculation.

CConstRef< CGumbelParamsOptions > GetOptions(void) const

Get claculation options.

CGumbelParamsCalc(const CGumbelParamsCalc &)

Forbid copy constructor.

CRef< CGumbelParamsRandDiagnostics > m_RandParams

CGumbelParamsCalc(const CRef< CGumbelParamsOptions > &opts)

Create calculation object with given options.

CRef< CGumbelParamsResult > GetResult(void)

Get computation result.

NCBI_EXCEPTION_DEFAULT(CGumbelParamsException, CException)

virtual const char * GetErrCodeString(void) const override

Get error code interpreted as text.

Class used for creation of sets of input parameters.

static CRef< CGumbelParamsOptions > CreateStandard20AAOptions(CGeneralScoreMatrix::EScoreMatrixName smat=CGeneralScoreMatrix::eBlosum62)

Creates standard options with score matrix and residue frequenceis for 20 aa alphabet.

static CRef< CGumbelParamsOptions > CreateBasicOptions(void)

Creates standard options with no score matrix or resiudie frequencies.

Input parameters for Gumbel parameters calculation.

void SetSeq2ResidueProbs(const TFrequencies &probs)

Set residue probabilities for sequence 2.

void SetLambdaAccuracy(double lambda_err)

Set relative error threshold for lambda parameter calculation for gapped aligmment.

bool Validate(void)

Validate parameter values.

const TFrequencies & GetSeq2ResidueProbs(void) const

Get sequence 2 residue probabilities.

CGumbelParamsOptions(void)

Create empty options object.

bool m_IsGapped

Gapped/gapless regime, true for gapped, false for gapless.

CGumbelParamsOptions & operator=(const CGumbelParamsOptions &)

Forbid assignment operator.

void SetGapExtension(Int4 g_exten)

Set gap extention penalty.

vector< double > TFrequencies

const TFrequencies & GetSeq1ResidueProbs(void) const

Get sequence 1 residue probabilities.

CConstRef< CGeneralScoreMatrix > m_ScoreMatrix

Scoring matrix.

Int4 x_GetScore(Uint4 i, Uint4 j) const

Get socre matrix value for i-th and j-th residues.

double GetMaxCalcMemory(void) const

Get maximum memory allowed for computation.

void SetGapped(bool gapped)

Set gapped/gapless regime.

bool IsMessage(void) const

Check whether there are any error/warning messages.

double m_KAccuracy

Desired accuracy for parameter K computation only for gapped alignment.

const vector< string > & GetMessages(void) const

Get error/warning messages.

void SetMaxCalcTime(double time)

Set maximum calculation time allowed.

double m_MaxCalcTime

Maximum allowed calculation time.

double GetMaxCalcTime(void) const

Get maximum calculation time allowed.

double m_MaxCalcMemory

Maximum allowed calculation memory.

void SetKAccuracy(double k_err)

Set relative error threshold for K parameter calculation for gapped alignment.

Int4 m_GapOpening

Gap opening penalty.

Int4 GetGapOpening(void) const

Get gap opening penalty.

double GetKAccuracy(void) const

Get relative error threshold for K parameter calculation for gapped alignment.

Int4 GetNumResidues(void) const

Get number of residues in utilized alphabet.

bool GetGapped(void) const

Get gapped/gapless regime.

const Int4 ** GetScoreMatrix(void) const

Get score matrix.

void SetGapOpening(Int4 g_open)

Set the value of gap opening penalty.

Int4 m_NumResidues

Number of residues in alphabet.

double GetLambdaAccuracy(void) const

Get relative error threshold for lambda parameter calculation for gapped aligmment.

void SetMaxCalcMemory(double mem)

Set maximum memory allowed for computation.

void SetScoreMatrix(const CGeneralScoreMatrix &smatrix)

Set score matrix.

TFrequencies m_Seq2ResidueProbs

Residue frequencies for sequence 2.

void SetSeq1ResidueProbs(const TFrequencies &probs)

Set residue probabilities for sequence 1.

Int4 GetGapExtension(void) const

Get gap extention penalty.

double m_LambdaAccuracy

Desired accuracy for lambda computation only for gapped aligmment.

vector< string > m_Messages

Warning messages.

Int4 m_GapExtension

Gap extension penalty.

TFrequencies m_Seq1ResidueProbs

Residue frequencies for sequence 1.

Options that control random values used in internal parts of Gumbel parameter calculation for gapped ...

Int4 GetTotalReNumber(void) const

Get total realizations number.

vector< Int4 > & SetPrelimReNumbers(void)

Set preliminary realizations numbers.

const vector< Int4 > & GetPrelimReNumbersKilling(void) const

Get perliminary realizations numbers killing array.

const vector< Int4 > & GetFirstStagePrelimReNumbers(void) const

Get first stage preliminary realizations numbers.

vector< Int4 > & SetFirstStagePrelimReNumbers(void)

Set first stage preliminary realizations numbers.

Int4 GetTotalReNumberKilling(void) const

Get total realizations number killing.

Int4 m_TotalReNumber

Total realizations number ALP.

Uint4 m_RandomSeed

Random seed.

vector< Int4 > m_FirstStagePrelimReNumbers

Frist stage preliminary realizations numbers ALP.

vector< Int4 > m_PrelimReNumbersKilling

Preliminary realizations numbers killing.

void SetTotalReNumber(Int4 num)

Set total realizations number.

vector< Int4 > m_PrelimReNumbers

void SetRandomSeed(Uint4 val)

Set random seed.

Uint4 GetRandomSeed(void) const

Get random seed.

void SetTotalReNumberKilling(Int4 num)

Set total realizations number killing.

CGumbelParamsRandDiagnostics(void)

Constructor.

const vector< Int4 > & GetPrelimReNumbers(void) const

Get preliminary realizations numbers.

Int4 m_TotalReNumberKilling

vector< Int4 > & SetPrelimReNumbersKilling(void)

Set perliminary realizations numbers killing array.

Result of Gumbel parameters calculation along with diagnostic info.

CGumbelParamsResult & operator=(const CGumbelParamsResult &)

Forbid assignment operator.

SGumbelParams & SetGumbelParams(void)

Set Gumbel parameters values.

void SetCalcTime(double time)

Set calculation time.

SSbsArrays & SetSbsArrays(void)

Set Sbs arrays.

const SGumbelParams & GetGumbelParams(void) const

Get Gubmel parameters.

SGumbelParams m_GumbelParams

const SSbsArrays & GetSbsArrays(void) const

Get Sbs arrays.

CGumbelParamsResult(void)

Create empty results.

double GetCalcTime(void) const

Get calculation time.

CGumbelParamsResult(const CGumbelParamsResult &result)

Forbid Copy constructor.

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

#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.

struct SGumbelParams SGumbelParams

Gumbel parameters and estimation errors.

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

vector< double > lambda_sbs

vector< double > alpha_i_sbs

vector< double > sigma_sbs

vector< double > alpha_j_sbs

Gumbel parameters and estimation errors.

double gapless_alpha_error

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