/dports/biology/bowtie2/bowtie2-2.4.4/ |
H A D | aligner_bt.cpp | 58 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() [all …]
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H A D | aligner_bt.h | 555 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() [all …]
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/dports/biology/hisat2/hisat2-2.2.1/ |
H A D | aligner_bt.cpp | 58 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() [all …]
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/dports/math/py-cvxpy/cvxpy-1.1.17/cvxpy/reductions/solvers/qp_solvers/ |
H A D | xpress_qpif.py | 18 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() [all …]
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/dports/biology/diamond/diamond-2.0.13/src/lib/alp/ |
H A D | njn_localmaxstatutil.cpp | 69 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() [all …]
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H A D | njn_localmaxstatutil.hpp | 66 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 [all …]
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H A D | njn_localmaxstat.cpp | 93 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()
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H A D | njn_dynprogproblim.hpp | 74 …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()
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/dports/biology/mmseqs2/MMseqs2-13-45111/lib/alp/ |
H A D | njn_localmaxstatutil.cpp | 69 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() [all …]
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H A D | njn_localmaxstatutil.hpp | 66 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 [all …]
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H A D | njn_localmaxstat.cpp | 93 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()
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H A D | njn_dynprogproblim.hpp | 74 …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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/gumbel_params/ |
H A D | njn_localmaxstatutil.cpp | 78 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() [all …]
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H A D | njn_localmaxstatutil.hpp | 73 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 [all …]
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H A D | njn_localmaxstat.cpp | 100 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()
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/dports/math/osi/Osi-0.108.6/Osi/src/OsiXpr/ |
H A D | OsiXprSolverInterface.cpp | 77 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() [all …]
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/dports/math/clp/Clp-1.17.3/Osi/src/OsiXpr/ |
H A D | OsiXprSolverInterface.cpp | 77 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() [all …]
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/dports/math/py-cvxpy/cvxpy-1.1.17/cvxpy/reductions/solvers/conic_solvers/ |
H A D | xpress_conif.py | 49 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_, [all …]
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/dports/chinese/libime/libime-1.0.9/src/libime/core/kenlm/lm/ |
H A D | left.hh | 68 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() [all …]
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/dports/graphics/pcl-pointclouds/pcl-pcl-1.12.0/ml/include/pcl/ml/ |
H A D | svm_wrapper.h | 191 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() [all …]
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/dports/graphics/pcl-pointclouds/pcl-pcl-1.12.0/ml/src/ |
H A D | svm_wrapper.cpp | 88 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() [all …]
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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 D | ROL_CVaR.hpp | 81 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()
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H A D | ROL_MixedCVaR.hpp | 91 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()
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H A D | ROL_QuantileRadius.hpp | 58 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()
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/dports/games/dungeon/dungeon-3.2_1/ |
H A D | DSO4.C | 72 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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