/dports/biology/iqtree/IQ-TREE-2.0.6/tree/ |
H A D | phylokernelsitemodel.h | 34 size_t nptn = aln->size(), tip_block_size = get_safe_upper_limit(nptn)*nstates; in computeSitemodelPartialLikelihoodEigenSIMD() local 40 ASSERT(models->size() == nptn); in computeSitemodelPartialLikelihoodEigenSIMD() 108 for (ptn = 0; ptn < nptn; ptn++) { in computeSitemodelPartialLikelihoodEigenSIMD() 178 for (ptn = 0; ptn < nptn; ptn++) { in computeSitemodelPartialLikelihoodEigenSIMD() 276 for (ptn = 0; ptn < nptn; ptn++) { in computeSitemodelPartialLikelihoodEigenSIMD() 399 size_t nptn = aln->size(); in computeSitemodelLikelihoodDervEigenSIMD() local 446 if (nptn < maxptn) { in computeSitemodelLikelihoodDervEigenSIMD() 477 if (ptn+j < nptn) { in computeSitemodelLikelihoodDervEigenSIMD() 561 size_t nptn = aln->size(); in computeSitemodelLikelihoodBranchEigenSIMD() local 738 size_t nptn = aln->size(); in computeSitemodelLikelihoodFromBufferEigenSIMD() local [all …]
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H A D | phylotreesse.cpp | 383 if (ptn+v < nptn) in computeTipPartialLikelihood() 621 size_t nptn = aln->getNPattern(); in computePtnFreq() local 624 for (ptn = 0; ptn < nptn; ptn++) in computePtnFreq() 626 for (ptn = nptn; ptn < maxptn; ptn++) in computePtnFreq() 631 size_t nptn = aln->getNPattern(), ptn; in computePtnInvar() local 655 for (ptn = 0; ptn < nptn; ptn++) { in computePtnInvar() 689 for (ptn = nptn; ptn < maxptn; ptn++) in computePtnInvar() 1532 size_t nptn = getAlnNPattern(); in initMarginalAncestralState() local 1541 size_t nptn = getAlnNPattern(); in computeMarginalAncestralState() local 1818 size_t nptn = aln->getNPattern(); in computeAncestralLikelihood() local [all …]
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H A D | phylokernelmixrate.h | 210 for (ptn = 0; ptn < nptn; ptn++) { in computeMixratePartialLikelihoodEigenSIMD() 299 for (ptn = 0; ptn < nptn; ptn++) { in computeMixratePartialLikelihoodEigenSIMD() 376 for (ptn = 0; ptn < nptn; ptn++) { in computeMixratePartialLikelihoodEigenSIMD() 540 if (nptn < maxptn) { in computeMixrateLikelihoodDervEigenSIMD() 621 if (orig_nptn < nptn) { in computeMixrateLikelihoodDervEigenSIMD() 831 if (orig_nptn < nptn) { in computeMixrateLikelihoodBranchEigenSIMD() 854 switch ((nptn-orig_nptn)%VCSIZE) { in computeMixrateLikelihoodBranchEigenSIMD() 922 if (orig_nptn < nptn) { in computeMixrateLikelihoodBranchEigenSIMD() 953 switch ((nptn-orig_nptn)%VCSIZE) { in computeMixrateLikelihoodBranchEigenSIMD() 963 if (orig_nptn < nptn) { in computeMixrateLikelihoodBranchEigenSIMD() [all …]
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H A D | phylokernelsitemodel.cpp | 25 size_t nptn = aln->size(), tip_block_size = get_safe_upper_limit(nptn)*nstates; in computeSitemodelPartialLikelihoodEigen() local 31 ASSERT(models->size() == nptn); in computeSitemodelPartialLikelihoodEigen() 92 for (ptn = 0; ptn < nptn; ptn++) { in computeSitemodelPartialLikelihoodEigen() 218 for (ptn = 0; ptn < nptn; ptn++) { in computeSitemodelPartialLikelihoodEigen() 276 for (ptn = 0; ptn < nptn; ptn++) { in computeSitemodelPartialLikelihoodEigen() 359 for (ptn = 0; ptn < nptn; ptn++) { in computeSitemodelPartialLikelihoodEigen() 467 size_t nptn = aln->size(); in computeSitemodelLikelihoodDervEigen() local 520 for (ptn = 0; ptn < nptn; ptn++) { in computeSitemodelLikelihoodDervEigen() 590 size_t nptn = aln->size(); in computeSitemodelLikelihoodBranchEigen() local 698 size_t nptn = aln->size(); in computeSitemodelLikelihoodFromBufferEigen() local [all …]
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H A D | phylokernelmixture.h | 221 for (ptn = 0; ptn < nptn; ptn++) { in computeMixturePartialLikelihoodEigenSIMD() 313 for (ptn = 0; ptn < nptn; ptn++) { in computeMixturePartialLikelihoodEigenSIMD() 389 for (ptn = 0; ptn < nptn; ptn++) { in computeMixturePartialLikelihoodEigenSIMD() 571 if (nptn < maxptn) { in computeMixtureLikelihoodDervEigenSIMD() 651 if (orig_nptn < nptn) { in computeMixtureLikelihoodDervEigenSIMD() 894 if (orig_nptn < nptn) { in computeMixtureLikelihoodBranchEigenSIMD() 937 switch ((nptn-orig_nptn)%VCSIZE) { in computeMixtureLikelihoodBranchEigenSIMD() 1004 if (orig_nptn < nptn) { in computeMixtureLikelihoodBranchEigenSIMD() 1035 switch ((nptn-orig_nptn)%VCSIZE) { in computeMixtureLikelihoodBranchEigenSIMD() 1045 if (orig_nptn < nptn) { in computeMixtureLikelihoodBranchEigenSIMD() [all …]
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H A D | phylokernelsafe.h | 114 size_t scale_size = nptn * ncat_mix; in computePartialLikelihoodEigenSIMD() 353 for (ptn = 0; ptn < nptn; ptn++) { in computePartialLikelihoodEigenSIMD() 420 for (ptn = 0; ptn < nptn; ptn++) { in computePartialLikelihoodEigenSIMD() 493 for (ptn = 0; ptn < nptn; ptn++) { in computePartialLikelihoodEigenSIMD() 635 for (ptn = 0; ptn < nptn; ptn++) { in computeLikelihoodDervEigenSIMD() 702 if (nptn < maxptn) { in computeLikelihoodDervEigenSIMD() 780 if (orig_nptn < nptn) { in computeLikelihoodDervEigenSIMD() 1013 if (orig_nptn < nptn) { in computeLikelihoodBranchEigenSIMD() 1141 if (orig_nptn < nptn) { in computeLikelihoodBranchEigenSIMD() 1216 if (orig_nptn < nptn) { in computeLikelihoodBranchEigenSIMD() [all …]
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H A D | phylokernelnonrev.h | 139 else if (ptn+x < nptn) 275 else if (ptn+x < nptn) 302 } else if (ptn+x < nptn) { 384 else if (ptn+x < nptn) 761 else if (ptn+i < nptn) 808 lh_ptn.cutoff(nptn-ptn); 809 df_ptn.cutoff(nptn-ptn); 966 lh_ptn.cutoff(nptn-ptn); 967 df_ptn.cutoff(nptn-ptn); 1166 else if (ptn+i < nptn) [all …]
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H A D | phylotreemixlen.cpp | 432 size_t nptn = aln->getNPattern(); in optimizeOneBranch() local 451 for (ptn = 0; ptn < nptn; ptn++) { in optimizeOneBranch() 474 for (ptn = 0; ptn < nptn; ptn++) in optimizeOneBranch() 777 size_t nptn = aln->size()+model_factory->unobserved_ptns.size(); in computeFuncDerv() local 778 size_t maxptn = get_safe_upper_limit(nptn); in computeFuncDerv() 791 for (ptn = 0; ptn < nptn; ptn++) { in computeFuncDerv() 811 size_t all_entries = nptn*block; in computeFuncDerv() 819 if (nptn < maxptn) { in computeFuncDerv() 821 for (ptn = nptn; ptn < maxptn; ptn++) in computeFuncDerv() 849 for (ptn = 0; ptn < nptn; ptn++) { in computeFuncDerv() [all …]
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H A D | phylotree.cpp | 1451 int nptn = aln->getNPattern(); in computePatternLikelihood() local 1705 int nptn = getAlnNPattern(); in computeLogLVariance() local 1715 for (i = 0; i < nptn; i++) in computeLogLVariance() 1720 for (i = 0; i < nptn; i++) { in computeLogLVariance() 1733 int nptn = getAlnNPattern(); in computeLogLDiffVariance() local 1744 for (i = 0; i < nptn; i++) in computeLogLDiffVariance() 1748 for (i = 0; i < nptn; i++) { in computeLogLDiffVariance() 2315 size_t nptn = aln->size(); in computeBayesianBranchLength() local 4560 int nptn = getAlnNPattern(); in resampleLh() local 4565 for (i = 0; i < nptn; i++) { in resampleLh() [all …]
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H A D | phylosupertree.cpp | 739 int nptn = (*it)->aln->getNPattern(); in computePatternLikelihood() local 740 for (int j = 0; j < nptn; j++) in computePatternLikelihood() 818 int nptn = (*it)->getAlnNPattern(); in initPartitionInfo() local 1332 size_t nptn = (*it)->aln->size(); in initMarginalAncestralState() local 1335 total_size += nptn*nstates; in initMarginalAncestralState() 1336 total_ptn += nptn; in initMarginalAncestralState() 1359 size_t nptn = (*it)->getAlnNPattern(); in computeMarginalAncestralState() local 1373 ptn_ancestral_prob += nptn*nstates; in computeMarginalAncestralState() 1374 ptn_ancestral_seq += nptn; in computeMarginalAncestralState() 1394 ptn_ancestral_prob += nptn*nstates; in writeMarginalAncestralState() [all …]
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H A D | phylokernelnew.h | 1467 else if (ptn+i < nptn) in computePartialLikelihoodSIMD() 1648 } else if (ptn+x < nptn) { in computePartialLikelihoodSIMD() 1766 } else if (ptn+x < nptn) { in computePartialLikelihoodSIMD() 2041 else if (ptn+i < nptn) in computeLikelihoodBufferSIMD() 2453 lh_ptn.cutoff(nptn-ptn); in computeLikelihoodDervSIMD() 2454 df_ptn.cutoff(nptn-ptn); in computeLikelihoodDervSIMD() 2455 ddf_ptn.cutoff(nptn-ptn); in computeLikelihoodDervSIMD() 2801 else if (ptn+i < nptn) in computeLikelihoodBranchSIMD() 2873 lh_ptn.cutoff(nptn-ptn); in computeLikelihoodBranchSIMD() 3008 lh_ptn.cutoff(nptn-ptn); in computeLikelihoodBranchSIMD() [all …]
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H A D | phylokernelnonrev.cpp | 401 size_t nptn = aln->size()+model_factory->unobserved_ptns.size(); in computeNonrevLikelihoodDerv() local 426 computeBounds<Vec1d>(num_threads, nptn, limits); in computeNonrevLikelihoodDerv() 585 if (orig_nptn < nptn) { in computeNonrevLikelihoodDerv() 632 size_t nptn = aln->size()+model_factory->unobserved_ptns.size(); in computeNonrevLikelihoodBranch() local 635 computeBounds<Vec1d>(num_threads, nptn, limits); in computeNonrevLikelihoodBranch() 806 if (orig_nptn < nptn) { in computeNonrevLikelihoodBranch()
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H A D | upperbounds.cpp | 662 int nptn = tree->aln->getNPattern(); in getBestNNIForBranUB() local 700 for(i = 0; i<nptn; i++){ in getBestNNIForBranUB() 860 int nptn = tree->aln->getNPattern(); in sumFraction() local 869 for(i = 0; i<nptn; i++){ in sumFraction()
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H A D | iqtree.cpp | 361 size_t nptn = get_safe_upper_limit_float(orig_nptn); in initSettings() local 363 size_t nptn = get_safe_upper_limit(orig_nptn); in initSettings() local 368 boot_samples[i] = mem + i*nptn; in initSettings() 417 boot_samples_int[i].resize(nptn, 0); in initSettings() 3501 int nptn = getAlnNPattern(); in saveCurrentTree() local 3504 int maxnptn = get_safe_upper_limit_float(nptn); in saveCurrentTree() 3509 for (int i = 0; i < nptn; i++) in saveCurrentTree() 3512 int maxnptn = get_safe_upper_limit(nptn); in saveCurrentTree() 4175 size_t nptn = getAlnNPattern(); in warnNumThreads() local 4176 if (nptn < num_threads*vector_size) in warnNumThreads() [all …]
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/dports/biology/iqtree/IQ-TREE-2.0.6/model/ |
H A D | ratemeyerdiscrete.cpp | 415 int nptn = size(); in normalizeRates() local 418 for (i = 0; i < nptn; i++) { in normalizeRates() 438 int nptn = size(); in classifyRatesKMeans() local 442 double *points = new double[nptn]; in classifyRatesKMeans() 443 int *weights = new int[nptn]; in classifyRatesKMeans() 445 if (!ptn_cat) ptn_cat = new int[nptn]; in classifyRatesKMeans() 446 for (i = 0; i < nptn; i++) { in classifyRatesKMeans() 456 double cost = RunKMeans1D(nptn, ncategory, points, weights, rates, ptn_cat); in classifyRatesKMeans() 512 int nptn = phylo_tree->aln->getNPattern(); in classifyRates() local 513 rates = new double[nptn]; in classifyRates() [all …]
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H A D | rateheterotachy.cpp | 154 size_t nptn = phylo_tree->aln->getNPattern(); in optimizeWithEM() local 167 for (ptn = 0; ptn < nptn; ptn++) { in optimizeWithEM() 175 for (ptn = 0; ptn < nptn; ptn++) { in optimizeWithEM()
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H A D | modelmixture.cpp | 1551 size_t nptn = phylo_tree->aln->getNPattern(); in optimizeWeights() local 1564 for (ptn = 0; ptn < nptn; ptn++) { in optimizeWeights() 1572 for (ptn = 0; ptn < nptn; ptn++) { in optimizeWeights() 1622 size_t nptn = phylo_tree->aln->getNPattern(); in optimizeWithEM() local 1669 for (ptn = 0; ptn < nptn; ptn++) { in optimizeWithEM() 1745 for (ptn = 0; ptn < nptn; ptn++) in optimizeWithEM()
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H A D | rategammainvar.cpp | 225 size_t nptn = phylo_tree->aln->getNPattern(); in optimizeWithEM() local 233 for (size_t ptn = 0; ptn < nptn; ptn++) { in optimizeWithEM()
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H A D | ratefree.cpp | 489 size_t nptn = phylo_tree->aln->getNPattern(); in optimizeWithEM() local 548 for (ptn = 0; ptn < nptn; ptn++) { in optimizeWithEM() 630 for (ptn = 0; ptn < nptn; ptn++) in optimizeWithEM()
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/dports/misc/vxl/vxl-3.3.2/core/vgl/tests/ |
H A D | test_plane_3d.cxx | 25 vgl_vector_3d<double> nabcd = plane_abcd.normal(), nptn = plane_ptn.normal(); in test_constructor() local 26 double dist = std::fabs(1.0 - dot_product(nabcd, nptn)); in test_constructor() 33 dist = std::fabs(1.0 - dot_product(ncoin, nptn)); in test_constructor() 39 dist = std::fabs(1.0 - dot_product(npara, nptn)); in test_constructor()
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/dports/biology/iqtree/IQ-TREE-2.0.6/alignment/ |
H A D | alignmentpairwise.cpp | 109 int nptn = tree->aln->getNPattern(); in computeFunction() local 114 for (i = 0; i < nptn; i++) { in computeFunction() 126 for (i = 0; i < nptn; i++) { in computeFunction() 180 int nptn = tree->aln->getNPattern(); in computeFuncDerv() local 186 for (i = 0; i < nptn; i++) { in computeFuncDerv() 206 for (i = 0; i < nptn; i++) { in computeFuncDerv()
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H A D | superalignment.cpp | 1036 int nptn = 0; in getSitePatternIndex() local 1041 pattern_index[i] += nptn; in getSitePatternIndex() 1042 nptn += (*it)->getNPattern(); in getSitePatternIndex() 1295 int nptn = 0; in createBootstrapAlignment() local 1297 nptn += (*it)->getNPattern(); in createBootstrapAlignment() 1300 int *internal_freq = new int[nptn]; in createBootstrapAlignment() 1302 pattern_freq.insert(pattern_freq.end(), internal_freq, internal_freq + nptn); in createBootstrapAlignment() 1314 int nptn = 0; in createBootstrapAlignment() local 1317 part_pos.push_back(nptn); in createBootstrapAlignment() 1318 nptn += (*it)->getNPattern(); in createBootstrapAlignment() [all …]
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H A D | alignment.cpp | 989 int nptn = getNPattern(); in orderPatternByNumChars() local 991 int *num_chars = new int[nptn]; in orderPatternByNumChars() 992 int *ptn_order = new int[nptn]; in orderPatternByNumChars() 1003 for (ptn = 0; ptn < nptn; ptn++) { in orderPatternByNumChars() 3313 int nptn = getNPattern(); in createBootstrapAlignment() local 3405 int nptn = getNPattern(); in createBootstrapAlignment() local 3406 pattern_freq.resize(nptn, 0); in createBootstrapAlignment() 3409 for (int i = 0; i < nptn; i++) in createBootstrapAlignment() 3433 int nptn = getNPattern(); in createBootstrapAlignment() local 4810 int nptn = size(); in computeUnconstrainedLogL() local [all …]
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/dports/biology/iqtree/IQ-TREE-2.0.6/main/ |
H A D | treetesting.cpp | 80 size_t nptn = stree->at(part)->getAlnNPattern(); in printPartitionLh() local 82 for (i = 0; i < nptn; i++) in printPartitionLh() 84 pattern_lh_ptr += nptn; in printPartitionLh() 773 size_t nptn = tree->getAlnNPattern(); in performAUTest() local 774 size_t maxnptn = get_safe_upper_limit(nptn); in performAUTest() 825 for (ptn = 0; ptn < nptn; ptn++) in performAUTest() 1084 size_t nptn = tree->getAlnNPattern(); in evaluateTrees() local 1085 size_t maxnptn = get_safe_upper_limit(nptn); in evaluateTrees() 1100 #pragma omp parallel private(boot) if(nptn > 10000) in evaluateTrees() 1216 int *this_boot_sample = boot_samples + (boot*nptn); in evaluateTrees() [all …]
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/dports/math/octave/octave-6.4.0/scripts/strings/ |
H A D | erase.m | 101 nptn = ifelse (ischar (ptn), 1, numel (ptn)); variable 102 if (nptn == 1)
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