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Searched refs:prob_ (Results 1 – 25 of 99) sorted by relevance

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/dports/biology/bowtie2/bowtie2-2.4.4/
H A Daligner_bt.cpp58 assert(prob_.usecp_ && prob_.fill_); in triangleFill()
339 prob_, in triangleFill()
404 int qc = prob_.qry_[rowc], qq = prob_.qual_[rowc]; in triangleFill()
428 prob_, in triangleFill()
461 prob_, in triangleFill()
491 prob_, in triangleFill()
608 assert(prob_.usecp_ && prob_.fill_); in squareFill()
660 int qc = prob_.qry_[yi], qq = prob_.qual_[yi]; in squareFill()
885 prob_, in squareFill()
1007 prob_, in squareFill()
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H A Daligner_bt.h555 assert(!bs_[id].isSolution(prob_)); in add()
563 assert(bs_[id].isSolution(prob_)); in addSolution()
694 prob_.initBt(row, col, fill, usecp, escore); in initBt()
717 if(!prob_.fill_) { in initBt()
720 prob_, in initBt()
730 if(bs_[id].isSolution(prob_)) { in initBt()
737 TAlScore targsc = prob_.targ_; in initBt()
757 prob_.targ_, // score of alignment we're looking for in initBt()
771 prob_.targ_, // score of alignment we're looking for in initBt()
809 return prob_.inited(); in inited()
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/dports/biology/hisat2/hisat2-2.2.1/
H A Daligner_bt.cpp58 assert(prob_.usecp_ && prob_.fill_); in triangleFill()
339 prob_, in triangleFill()
404 int qc = prob_.qry_[rowc], qq = prob_.qual_[rowc]; in triangleFill()
428 prob_, in triangleFill()
461 prob_, in triangleFill()
491 prob_, in triangleFill()
608 assert(prob_.usecp_ && prob_.fill_); in squareFill()
660 int qc = prob_.qry_[yi], qq = prob_.qual_[yi]; in squareFill()
885 prob_, in squareFill()
1007 prob_, in squareFill()
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/dports/math/py-cvxpy/cvxpy-1.1.17/cvxpy/reductions/solvers/qp_solvers/
H A Dxpress_qpif.py18 self.prob_ = None
109 self.prob_ = xp.problem()
144 self.prob_.controls.miplog = 2
145 self.prob_.controls.lplog = 1
146 self.prob_.controls.outputlog = 1
148 self.prob_.controls.miplog = 0
149 self.prob_.controls.lplog = 0
150 self.prob_.controls.outputlog = 0
151 self.prob_.controls.xslp_log = -1
227 self.prob_.solve()
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/dports/biology/diamond/diamond-2.0.13/src/lib/alp/
H A Dnjn_localmaxstatutil.cpp69 sum += prob_ [i][j]; in flatten()
173 const double *prob_, // probabilities in n_setParameters() argument
178 n_prob = prob_; in n_setParameters()
221 const double *prob_) // corresponding probabilities in mu() argument
235 n_setParameters (dimension_, score_, prob_); in lambda()
252 n_setParameters (dimension_, score_, prob_); in muPowerAssoc()
275 n_setParameters (dimension_, score_, prob_); in thetaMin()
293 n_setParameters (dimension_, score_, prob_); in rMin()
504 if (prob_ [i] < 0.0 || 1.0 < prob_ [i]) return false; in isProbDist()
505 sum += prob_ [i]; in isProbDist()
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H A Dnjn_localmaxstatutil.hpp66 const double *prob_); // probability of corresponding value
71 const double *prob_); // probability of corresponding value
77 const double *prob_, // corresponding probabilities
83 const double *prob_, // corresponding probabilities
90 const double *prob_, // probability of corresponding value
97 const double *prob_, // probability of corresponding value
105 const double *prob_, // probability of corresponding value
121 const double *prob_, // probability of corresponding value
136 const double *prob_, // probability of corresponding value
155 const double *prob_); // corresponding probabilities
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H A Dnjn_localmaxstat.cpp93 const double *prob_, // probabilities in copy() argument
112 memcpy (d_prob_p, prob_, sizeof (double) * getDimension ()); in copy()
132 const double *prob_) // corresponding probabilities in copy() argument
140 if (! LocalMaxStatUtil::isLogarithmic (dimension_, score_, prob_)) in copy()
155 memcpy (d_prob_p, prob_, sizeof (double) * getDimension ()); in copy()
162 … d_sigma += static_cast <double> (score_ [i]) * static_cast <double> (score_ [i]) * prob_ [i]; in copy()
H A Dnjn_dynprogproblim.hpp74 …const double *prob_ = 0) // "probabilities" prob [valueLower_, valueUpper_) corresponding to the l… in DynProgProbLim() argument
79 : DynProgProb (valueFct_, dimInputProb_, inputProb_, valueLower_, valueUpper_, prob_), in DynProgProbLim()
122 …const double *prob_ = 0) // "probabilities" prob_ [valueLower_, valueUpper_) corresponding to the … in clear() argument
126 DynProgProb::clear (valueLower_, valueUpper_, prob_); in clear()
/dports/biology/mmseqs2/MMseqs2-13-45111/lib/alp/
H A Dnjn_localmaxstatutil.cpp69 sum += prob_ [i][j]; in flatten()
173 const double *prob_, // probabilities in n_setParameters() argument
178 n_prob = prob_; in n_setParameters()
221 const double *prob_) // corresponding probabilities in mu() argument
235 n_setParameters (dimension_, score_, prob_); in lambda()
252 n_setParameters (dimension_, score_, prob_); in muPowerAssoc()
275 n_setParameters (dimension_, score_, prob_); in thetaMin()
293 n_setParameters (dimension_, score_, prob_); in rMin()
504 if (prob_ [i] < 0.0 || 1.0 < prob_ [i]) return false; in isProbDist()
505 sum += prob_ [i]; in isProbDist()
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H A Dnjn_localmaxstatutil.hpp66 const double *prob_); // probability of corresponding value
71 const double *prob_); // probability of corresponding value
77 const double *prob_, // corresponding probabilities
83 const double *prob_, // corresponding probabilities
90 const double *prob_, // probability of corresponding value
97 const double *prob_, // probability of corresponding value
105 const double *prob_, // probability of corresponding value
121 const double *prob_, // probability of corresponding value
136 const double *prob_, // probability of corresponding value
155 const double *prob_); // corresponding probabilities
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H A Dnjn_localmaxstat.cpp93 const double *prob_, // probabilities in copy() argument
112 memcpy (d_prob_p, prob_, sizeof (double) * getDimension ()); in copy()
132 const double *prob_) // corresponding probabilities in copy() argument
140 if (! LocalMaxStatUtil::isLogarithmic (dimension_, score_, prob_)) in copy()
155 memcpy (d_prob_p, prob_, sizeof (double) * getDimension ()); in copy()
162 … d_sigma += static_cast <double> (score_ [i]) * static_cast <double> (score_ [i]) * prob_ [i]; in copy()
H A Dnjn_dynprogproblim.hpp74 …const double *prob_ = 0) // "probabilities" prob [valueLower_, valueUpper_) corresponding to the l… in DynProgProbLim() argument
79 : DynProgProb (valueFct_, dimInputProb_, inputProb_, valueLower_, valueUpper_, prob_), in DynProgProbLim()
122 …const double *prob_ = 0) // "probabilities" prob_ [valueLower_, valueUpper_) corresponding to the … in clear() argument
126 DynProgProb::clear (valueLower_, valueUpper_, prob_); in clear()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/gumbel_params/
H A Dnjn_localmaxstatutil.cpp78 sum += prob_ [i][j]; in flatten()
183 const double *prob_, // probabilities in n_setParameters() argument
188 n_prob = prob_; in n_setParameters()
234 const double *prob_) // corresponding probabilities in mu() argument
248 n_setParameters (dimension_, score_, prob_); in lambda()
265 n_setParameters (dimension_, score_, prob_); in muPowerAssoc()
288 n_setParameters (dimension_, score_, prob_); in thetaMin()
306 n_setParameters (dimension_, score_, prob_); in rMin()
526 if (prob_ [i] < 0.0 || 1.0 < prob_ [i]) return false; in isProbDist()
527 sum += prob_ [i]; in isProbDist()
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H A Dnjn_localmaxstatutil.hpp73 const double *prob_); // probability of corresponding value
78 const double *prob_); // probability of corresponding value
84 const double *prob_, // corresponding probabilities
90 const double *prob_, // corresponding probabilities
97 const double *prob_, // probability of corresponding value
104 const double *prob_, // probability of corresponding value
112 const double *prob_, // probability of corresponding value
128 const double *prob_, // probability of corresponding value
143 const double *prob_, // probability of corresponding value
162 const double *prob_); // corresponding probabilities
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H A Dnjn_localmaxstat.cpp100 const double *prob_, // probabilities in copy() argument
119 memcpy (d_prob_p, prob_, sizeof (double) * getDimension ()); in copy()
139 const double *prob_) // corresponding probabilities in copy() argument
147 if (! LocalMaxStatUtil::isLogarithmic (dimension_, score_, prob_)) in copy()
159 memcpy (d_prob_p, prob_, sizeof (double) * getDimension ()); in copy()
166 … d_sigma += static_cast <double> (score_ [i]) * static_cast <double> (score_ [i]) * prob_ [i]; in copy()
/dports/math/osi/Osi-0.108.6/Osi/src/OsiXpr/
H A DOsiXprSolverInterface.cpp77 XPRS_CHECKED(XPRSminim, (prob_, "l")); in initialSolve()
79 XPRS_CHECKED(XPRSmaxim, (prob_, "l")); in initialSolve()
98 XPRS_CHECKED(XPRSminim, (prob_, "dl")); in resolve()
100 XPRS_CHECKED(XPRSmaxim, (prob_, "dl")); in resolve()
1760 int iret = XPRSloadlp(prob_, in loadProblem()
2098 XPRSgetprobname(prob_,pname); in readMps()
2258 , prob_(NULL) in OsiXprSolverInterface()
2311 , prob_(NULL) in OsiXprSolverInterface()
2348 XPRSdestroyprob(prob_); in ~OsiXprSolverInterface()
2470 XPRS_CHECKED(XPRScopyprob, (prob_, source.prob_, xprProbname_.c_str())); in gutsOfCopy()
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/dports/math/clp/Clp-1.17.3/Osi/src/OsiXpr/
H A DOsiXprSolverInterface.cpp77 XPRS_CHECKED(XPRSminim, (prob_, "l")); in initialSolve()
79 XPRS_CHECKED(XPRSmaxim, (prob_, "l")); in initialSolve()
98 XPRS_CHECKED(XPRSminim, (prob_, "dl")); in resolve()
100 XPRS_CHECKED(XPRSmaxim, (prob_, "dl")); in resolve()
1760 int iret = XPRSloadlp(prob_, in loadProblem()
2098 XPRSgetprobname(prob_,pname); in readMps()
2258 , prob_(NULL) in OsiXprSolverInterface()
2311 , prob_(NULL) in OsiXprSolverInterface()
2348 XPRSdestroyprob(prob_); in ~OsiXprSolverInterface()
2470 XPRS_CHECKED(XPRScopyprob, (prob_, source.prob_, xprProbname_.c_str())); in gutsOfCopy()
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/dports/math/py-cvxpy/cvxpy-1.1.17/cvxpy/reductions/solvers/conic_solvers/
H A Dxpress_conif.py49 self.prob_ = None
152 self.prob_ = xp.problem()
167 self.prob_.controls.miplog = 2
168 self.prob_.controls.lplog = 1
171 self.prob_.controls.miplog = 0
172 self.prob_.controls.lplog = 0
222 self.prob_.addVariable(conevar)
245 self.prob_.addConstraint(
285 self.prob_.solve()
289 'problem': self.prob_,
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/dports/chinese/libime/libime-1.0.9/src/libime/core/kenlm/lm/
H A Dleft.hh68 if (left_done_) { prob_ += ret.prob; return; } in Terminal()
70 prob_ += ret.prob; in Terminal()
75 prob_ += ret.rest; in Terminal()
82 prob_ = prob; in BeginNonTerminal()
88 prob_ += prob; in NonTerminal()
155 return prob_; in Finish()
159 prob_ = 0.0; in Reset()
192 prob_ += ret.prob; in ProcessRet()
196 prob_ += ret.prob; in ProcessRet()
201 prob_ += ret.rest; in ProcessRet()
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/dports/graphics/pcl-pointclouds/pcl-pcl-1.12.0/ml/include/pcl/ml/
H A Dsvm_wrapper.h191 if (prob_.l > 0) { in ~SVM()
192 free(prob_.x); in ~SVM()
193 free(prob_.y); in ~SVM()
241 using SVM::prob_;
336 return SVM::loadProblem(filename, prob_); in loadProblem()
384 using SVM::prob_;
424 SVM::adaptInputToLibSVM(training_set_, prob_); in setInputTrainingSet()
494 bool out = SVM::loadProblem(filename, prob_); in loadClassProblem()
495 SVM::adaptLibSVMToInput(training_set_, prob_); in loadClassProblem()
496 scaleProblem(prob_, scaling_); in loadClassProblem()
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/dports/graphics/pcl-pointclouds/pcl-pcl-1.12.0/ml/src/
H A Dsvm_wrapper.cpp88 double y = prob_.y[i]; in doCrossValidation()
104 ((prob_.l * sumvy - sumv * sumy) * (prob_.l * sumvy - sumv * sumy)) / in doCrossValidation()
105 ((prob_.l * sumvv - sumv * sumv) * (prob_.l * sumyy - sumy * sumy))); in doCrossValidation()
461 if (prob_.l == 0) { in saveProblemNorm()
486 myfile << prob_.x[j][i].index << ":" << prob_.x[j][i].value << " "; in saveProblemNorm()
542 if (prob_.l == 0) { in classificationTest()
595 prediction_.resize(prob_.l); in classificationTest()
597 while (ii < prob_.l) { in classificationTest()
664 if (prob_.l == 0) { in classification()
708 prediction_.resize(prob_.l); in classification()
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/dports/science/dakota/dakota-6.13.0-release-public.src-UI/packages/external/trilinos/packages/rol/src/sol/function/randvarfunctional/risk/
H A DROL_CVaR.hpp81 Real prob_; member in ROL::CVaR
100 ROL_TEST_FOR_EXCEPTION((prob_ <= zero) || (prob_ >= one), std::invalid_argument, in checkInputs()
120 : RandVarFunctional<Real>(), plusFunction_(pf), prob_(prob), coeff_(coeff) { in CVaR()
139 prob_ = list.get<Real>("Confidence Level"); in CVaR()
154 val_ += weight_*((one-coeff_)*val + coeff_/(one-prob_)*pf); in updateValue()
165 Real c = (one-coeff_) + coeff_/(one-prob_)*pf; in updateGradient()
186 c = pf2*coeff_/(one-prob_)*(gv-vstat[0]); in updateHessVec()
189 c = (one-coeff_) + coeff_/(one-prob_)*pf1; in updateHessVec()
212 var *= -coeff_/(one-prob_); in getGradient()
227 var *= coeff_/(one-prob_); in getHessVec()
H A DROL_MixedCVaR.hpp91 std::vector<Real> prob_; member in ROL::MixedCVaR
111 size_ = prob_.size(); in initializeMCVAR()
116 int pSize = prob_.size(), cSize = coeff_.size(); in checkInputs()
121 ROL_TEST_FOR_EXCEPTION((prob_[i]>one || prob_[i]<zero), std::invalid_argument, in checkInputs()
141 prob_ = ROL::getArrayFromStringParameter<Real>(list,"Probability Array"); in MixedCVaR()
151 : RandVarFunctional<Real>(), plusFunction_(pf), prob_(prob), coeff_(coeff) { in MixedCVaR()
178 val_ += weight_*coeff_[i]/(one-prob_[i])*pf; in updateValue()
201 c = weight_*coeff_[i]/(one-prob_[i])*pf; in updateGradient()
235 c = weight_*coeff_[i]/(one-prob_[i])*pf2*(gv-vstat[i]); in updateHessVec()
240 c = weight_*coeff_[i]/(one-prob_[i])*pf1; in updateHessVec()
H A DROL_QuantileRadius.hpp58 Real prob_; member in ROL::QuantileRadius
85 ROL_TEST_FOR_EXCEPTION((prob_>one || prob_<zero), std::invalid_argument, in checkInputs()
99 prob_ = list.get<Real>("Confidence Level"); in QuantileRadius()
108 : RandVarFunctional<Real>(), plusFunction_(pf), prob_(prob), coeff_(coeff) { in QuantileRadius()
133 RandVarFunctional<Real>::val_ += weight_*(val + half*coeff_/(one-prob_)*(pf1 + pf2)); in updateValue()
154 Real c = half*weight_*coeff_/(one-prob_); in updateGradient()
185 Real c = half*weight_*coeff_/(one-prob_); in updateHessVec()
/dports/games/dungeon/dungeon-3.2_1/
H A DDSO4.C72 VISIBT) == 0 || ! prob_(pr, pr)) {
113 ret_val = prob_(90, 100);
118 ret_val = prob_(75, 85);
123 ret_val = prob_(50, 30);
128 ret_val = prob_(25, 25);
133 ret_val = prob_(10, 0);

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