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Searched refs:nptn (Results 1 – 25 of 34) sorted by relevance

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/dports/biology/iqtree/IQ-TREE-2.0.6/tree/
H A Dphylokernelsitemodel.h34 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
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H A Dphylotreesse.cpp383 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
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H A Dphylokernelmixrate.h210 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()
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H A Dphylokernelsitemodel.cpp25 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
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H A Dphylokernelmixture.h221 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()
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H A Dphylokernelsafe.h114 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()
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H A Dphylokernelnonrev.h139 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)
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H A Dphylotreemixlen.cpp432 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()
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H A Dphylotree.cpp1451 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()
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H A Dphylosupertree.cpp739 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()
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H A Dphylokernelnew.h1467 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()
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H A Dphylokernelnonrev.cpp401 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()
H A Dupperbounds.cpp662 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()
H A Diqtree.cpp361 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()
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/dports/biology/iqtree/IQ-TREE-2.0.6/model/
H A Dratemeyerdiscrete.cpp415 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()
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H A Drateheterotachy.cpp154 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()
H A Dmodelmixture.cpp1551 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()
H A Drategammainvar.cpp225 size_t nptn = phylo_tree->aln->getNPattern(); in optimizeWithEM() local
233 for (size_t ptn = 0; ptn < nptn; ptn++) { in optimizeWithEM()
H A Dratefree.cpp489 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()
/dports/misc/vxl/vxl-3.3.2/core/vgl/tests/
H A Dtest_plane_3d.cxx25 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()
/dports/biology/iqtree/IQ-TREE-2.0.6/alignment/
H A Dalignmentpairwise.cpp109 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()
H A Dsuperalignment.cpp1036 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()
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H A Dalignment.cpp989 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
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/dports/biology/iqtree/IQ-TREE-2.0.6/main/
H A Dtreetesting.cpp80 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()
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/dports/math/octave/octave-6.4.0/scripts/strings/
H A Derase.m101 nptn = ifelse (ischar (ptn), 1, numel (ptn)); variable
102 if (nptn == 1)

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