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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/pvalues_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/gumbel_params/pvalues.cpp Source File

59

: m_MinScore(min_score), m_MaxScore(max_score), m_Seq1Len(seq1_len),

60

m_Seq2Len(seq2_len), m_GumbelParams(gumbel_result)

64 "The Gumbel parameters object is empty"

);

73 "Bad score range: minimum score is greater than maximum score"

);

78 "Sequence length negative or zero"

);

83 "Gumbel parameters results not set"

);

99 "Sbs arrays are of different lengths"

);

114 static

Sls::pvalues pvalues_obj;

121

Sls::set_of_parameters parameters_set;

123

vector<double> p_values;

124

vector<double> p_values_errors;

133

parameters_set.C = g_params.

;

134

parameters_set.C_error = g_params.

C_error

;

136

parameters_set.K = g_params.

;

137

parameters_set.K_error = g_params.

K_error

;

139

parameters_set.a_I = g_params.

;

140

parameters_set.a_I_error = g_params.

ai_error

;

142

parameters_set.a_J = g_params.

;

143

parameters_set.a_J_error = g_params.

aj_error

;

145

parameters_set.sigma = g_params.

sigma

;

146

parameters_set.sigma_error = g_params.

sigma_error

;

148

parameters_set.alpha_I = g_params.

alpha_i

;

151

parameters_set.alpha_J = g_params.

alpha_j

;

155

= (parameters_set.a_I + parameters_set.a_J) * 0.5;

157

parameters_set.a_error = (parameters_set.a_I_error

158

+ parameters_set.a_J_error)*0.5;

160

parameters_set.alpha = (parameters_set.alpha_I

161

+ parameters_set.alpha_J) * 0.5;

163

parameters_set.alpha_error = (parameters_set.alpha_I_error

164

+ parameters_set.alpha_J_error) * 0.5;

167

parameters_set.gapless_a = g_params.

gapless_a

;

173

parameters_set.G=g_params.

;

179 size_t

size_tmp = sbs_arrays.

lambda_sbs

.size();

182

parameters_set.m_LambdaSbs.resize(size_tmp);

183

parameters_set.m_KSbs.resize(size_tmp);

184

parameters_set.m_CSbs.resize(size_tmp);

185

parameters_set.m_SigmaSbs.resize(size_tmp);

186

parameters_set.m_AlphaISbs.resize(size_tmp);

187

parameters_set.m_AlphaJSbs.resize(size_tmp);

188

parameters_set.m_AISbs.resize(size_tmp);

189

parameters_set.m_AJSbs.resize(size_tmp);

191 for

(

=0;

<size_tmp;

++) {

192

parameters_set.m_LambdaSbs[

] = sbs_arrays.

lambda_sbs

[

];

193

parameters_set.m_KSbs[

] = sbs_arrays.

K_sbs

[

];

194

parameters_set.m_CSbs[

] = sbs_arrays.

C_sbs

[

];

195

parameters_set.m_SigmaSbs[

] = sbs_arrays.

sigma_sbs

[

];

196

parameters_set.m_AlphaISbs[

] = sbs_arrays.

alpha_i_sbs

[

];

197

parameters_set.m_AlphaJSbs[

]= sbs_arrays.

alpha_j_sbs

[

];

198

parameters_set.m_AISbs[

] = sbs_arrays.

ai_sbs

[

];

199

parameters_set.m_AJSbs[

] = sbs_arrays.

aj_sbs

[

];

203

pvalues_obj.calculate_P_values(Score1, Score2, Seq1Len, Seq2Len,

204

parameters_set, p_values,

207

size_tmp=p_values.size();

209 _ASSERT

(p_values_errors.size() == size_tmp);

211

vector<CScorePValues::TPValue>& pv =

result

->SetPValues();

212

vector<CScorePValues::TPValue>& err =

result

->SetErrors();

214

err.resize(size_tmp);

216 for

(

=0;

<size_tmp;

++) {

217

pv[

] = p_values[

];

218

err[

] = p_values_errors[

];

225 catch

(Sls::error er) {

226 switch

(er.error_code) {

228

(

string

)

"Ivalid options: "

+ er.st);

231

(

string

)

"Memory allocation error: "

+ er.st);

235

(

string

)

"Unexpected error: "

+ er.st);

241 "Unexpected error"

);

251 "The result object was not set"

);

const SGumbelParams & GetGumbelParams(void) const

Get Gubmel parameters.

const SSbsArrays & GetSbsArrays(void) const

Get Sbs arrays.

CConstRef< CScorePValuesOptions > m_Options

CRef< CScorePValues > Run(void)

Calculate P-values.

CRef< CScorePValues > m_Result

CRef< CScorePValues > GetResult(void)

Get results of P-values calculation.

const CGumbelParamsResult & GetGumbelParams(void) const

Get Gumbel parameters calculation results.

Int4 GetSeq2Len(void) const

Get length of sequence 2.

CScorePValuesOptions(Int4 min_score, Int4 max_score, Int4 seq1_len, Int4 seq2_len, const CConstRef< CGumbelParamsResult > &gumbel_results)

Create options.

Int4 GetMaxScore(void) const

Get max score for which p-values will be computed.

bool Validate(void) const

Validates parameter values.

Int4 GetMinScore(void) const

Get min score for which p-values will be computed.

Int4 GetSeq1Len(void) const

Get length of sequence 1.

Int4 m_MinScore

P-values will be computed for the range [m_MinScore1,m_MaxScore].

Int4 m_MaxScore

P-values will be computed for the range [m_MinScore1,m_MaxScore].

CConstRef< CGumbelParamsResult > m_GumbelParams

Results of score P-values calculation.

#define NCBI_THROW(exception_class, err_code, message)

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

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty â not pointing to any object which means having a null value.

void Reset(void)

Reset reference object.

bool Empty(void) const THROWS_NONE

Check if CRef is empty â not pointing to any object, which means having a null value.

int32_t Int4

4-byte (32-bit) signed integer

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

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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