Searched refs:ptn_invar (Results 1 – 17 of 17) sorted by relevance
/dports/biology/iqtree/IQ-TREE-2.0.6/model/ |
H A D | rategammainvar.cpp | 198 double sum_rate = 0.0, sum_lh = phylo_tree->ptn_invar[i]; in computePatternRates() 200 double best_lh = phylo_tree->ptn_invar[i]; in computePatternRates() 235 double lk_ptn = phylo_tree->ptn_invar[ptn]; in optimizeWithEM() 240 ppInvar += (phylo_tree->ptn_invar[ptn]) * phylo_tree->ptn_freq[ptn] / lk_ptn; in optimizeWithEM()
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H A D | rateheterotachy.cpp | 177 double lk_ptn = phylo_tree->ptn_invar[ptn]; in optimizeWithEM()
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H A D | modelmixture.cpp | 1574 double lk_ptn = phylo_tree->ptn_invar[ptn]; in optimizeWeights() 1671 double lk_ptn = phylo_tree->ptn_invar[ptn]; in optimizeWithEM()
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H A D | ratefree.cpp | 550 double lk_ptn = phylo_tree->ptn_invar[ptn]; in optimizeWithEM()
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/dports/biology/iqtree/IQ-TREE-2.0.6/tree/ |
H A D | phylotreesse.cpp | 652 memset(ptn_invar, 0, maxptn*sizeof(double)); in computePtnInvar() 660 ptn_invar[ptn] = p_invar; in computePtnInvar() 664 ptn_invar[ptn] = p_invar * state_freq[(int) (*aln)[ptn].const_char]; in computePtnInvar() 667 ptn_invar[ptn] = 0.0; in computePtnInvar() 671 ptn_invar[ptn] += state_freq[x]; in computePtnInvar() 673 ptn_invar[ptn] *= p_invar; in computePtnInvar() 675 ptn_invar[ptn] = 0.0; in computePtnInvar() 680 ptn_invar[ptn] += state_freq[x]; in computePtnInvar() 681 ptn_invar[ptn] *= p_invar; in computePtnInvar() 690 ptn_invar[ptn] = p_invar; in computePtnInvar()
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H A D | phylokernelnonrev.h | 196 … auto underflown = ((lh_max < SCALING_THRESHOLD) & (VectorClass().load_a(&ptn_invar[ptn]) == 0.0)); 217 … auto underflown = ((lh_max < SCALING_THRESHOLD) & (VectorClass().load_a(&ptn_invar[ptn]) == 0.0)); 416 … auto underflown = ((lh_max < SCALING_THRESHOLD) & (VectorClass().load_a(&ptn_invar[ptn]) == 0.0)); 437 … auto underflown = ((lh_max < SCALING_THRESHOLD) & (VectorClass().load_a(&ptn_invar[ptn]) == 0.0)); 499 … auto underflown = ((lh_max < SCALING_THRESHOLD) & (VectorClass().load_a(&ptn_invar[ptn]) == 0.0)); 521 … auto underflown = (lh_max < SCALING_THRESHOLD) & (VectorClass().load_a(&ptn_invar[ptn]) == 0.0); 793 lh_ptn = (lh_ptn + VectorClass().load_a(&ptn_invar[ptn])); 951 lh_ptn = (lh_ptn + VectorClass().load_a(&ptn_invar[ptn])); 1239 lh_ptn = lh_ptn + VectorClass().load_a(&ptn_invar[ptn]); 1368 lh_ptn = lh_ptn + VectorClass().load_a(&ptn_invar[ptn]);
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H A D | phylokernelmixrate.h | 583 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeMixrateLikelihoodDervEigenSIMD() 655 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load(&ptn_invar[ptn]); in computeMixrateLikelihoodDervEigenSIMD() 808 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeMixrateLikelihoodBranchEigenSIMD() 852 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load(&ptn_invar[ptn]); in computeMixrateLikelihoodBranchEigenSIMD() 901 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeMixrateLikelihoodBranchEigenSIMD() 949 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load(&ptn_invar[ptn]); in computeMixrateLikelihoodBranchEigenSIMD() 1032 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeMixrateLikelihoodFromBufferEigenSIMD() 1116 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load(&ptn_invar[ptn]); in computeMixrateLikelihoodFromBufferEigenSIMD()
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H A D | phylokernelsafe.h | 310 if (ptn_invar[ptn] == 0.0) { in computePartialLikelihoodEigenSIMD() 466 if (lh_max < SCALING_THRESHOLD && ptn_invar[ptn] == 0.0 && lh_max != 0.0) { in computePartialLikelihoodEigenSIMD() 542 if (lh_max < SCALING_THRESHOLD && ptn_invar[ptn] == 0.0 && lh_max != 0.0) { in computePartialLikelihoodEigenSIMD() 746 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeLikelihoodDervEigenSIMD() 814 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load(&ptn_invar[ptn]); in computeLikelihoodDervEigenSIMD() 989 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeLikelihoodBranchEigenSIMD() 1050 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load(&ptn_invar[ptn]); in computeLikelihoodBranchEigenSIMD() 1120 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeLikelihoodBranchEigenSIMD() 1204 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load(&ptn_invar[ptn]); in computeLikelihoodBranchEigenSIMD() 1292 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeLikelihoodFromBufferEigenSIMD()
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H A D | phylokernelmixture.h | 614 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeMixtureLikelihoodDervEigenSIMD() 685 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load(&ptn_invar[ptn]); in computeMixtureLikelihoodDervEigenSIMD() 865 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeMixtureLikelihoodBranchEigenSIMD() 935 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load(&ptn_invar[ptn]); in computeMixtureLikelihoodBranchEigenSIMD() 983 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeMixtureLikelihoodBranchEigenSIMD() 1031 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load(&ptn_invar[ptn]); in computeMixtureLikelihoodBranchEigenSIMD() 1117 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeMixtureLikelihoodFromBufferEigenSIMD() 1201 lh_ptn = horizontal_add(vc_ptn) + VectorClass().load(&ptn_invar[ptn]); in computeMixtureLikelihoodFromBufferEigenSIMD()
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H A D | phylokernelnonrev.cpp | 478 double lh_ptn = ptn_invar[ptn], df_ptn = 0.0, ddf_ptn = 0.0; in computeNonrevLikelihoodDerv() 532 double lh_ptn = ptn_invar[ptn], df_ptn = 0.0, ddf_ptn = 0.0; in computeNonrevLikelihoodDerv() 695 double lh_ptn = ptn_invar[ptn]; in computeNonrevLikelihoodBranch() 745 double lh_ptn = ptn_invar[ptn]; in computeNonrevLikelihoodBranch()
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H A D | phylokernelsitemodel.cpp | 521 double lh_ptn = ptn_invar[ptn], df_ptn = 0.0, ddf_ptn = 0.0; in computeSitemodelLikelihoodDervEigen() 603 double lh_ptn = ptn_invar[ptn]; in computeSitemodelLikelihoodBranchEigen() 633 double lh_ptn = ptn_invar[ptn]; in computeSitemodelLikelihoodBranchEigen() 708 double lh_ptn = ptn_invar[ptn]; in computeSitemodelLikelihoodFromBufferEigen()
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H A D | phylosupertreeplen.cpp | 123 (*it)->ptn_invar = NULL; in deleteAllPartialLh() 145 (*it)->ptn_invar = NULL; in ~PhyloSuperTreePlen() 1676 if (!ptn_invar) in initializeAllPartialLh() 1677 ptn_invar = aligned_alloc<double>(total_mem_size); in initializeAllPartialLh() 1678 at(part_order[0])->ptn_invar = ptn_invar; in initializeAllPartialLh() 1704 (*it)->ptn_invar = (*prev_it)->ptn_invar + mem_size[part]; in initializeAllPartialLh()
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H A D | phylokernelsitemodel.h | 501 VectorClass inv_lh_ptn = horizontal_add(lh_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeSitemodelLikelihoodDervEigenSIMD() 613 VectorClass lh_ptn_sum = horizontal_add(lh_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeSitemodelLikelihoodBranchEigenSIMD() 671 VectorClass lh_ptn_sum = horizontal_add(lh_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeSitemodelLikelihoodBranchEigenSIMD() 780 VectorClass lh_ptn_sum = horizontal_add(lh_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeSitemodelLikelihoodFromBufferEigenSIMD()
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H A D | phylokernelnew.h | 1523 … auto underflown = ((lh_max < SCALING_THRESHOLD) & (VectorClass().load_a(&ptn_invar[ptn]) == 0.0)); in computePartialLikelihoodSIMD() 1542 … auto underflown = (lh_max < SCALING_THRESHOLD) & (VectorClass().load_a(&ptn_invar[ptn]) == 0.0); in computePartialLikelihoodSIMD() 1823 … auto underflown = (lh_max < SCALING_THRESHOLD) & (VectorClass().load_a(&ptn_invar[ptn]) == 0.0); in computePartialLikelihoodSIMD() 1926 … auto underflown = ((lh_max < SCALING_THRESHOLD) & (VectorClass().load_a(&ptn_invar[ptn]) == 0.0)); in computePartialLikelihoodSIMD() 1948 … auto underflown = (lh_max < SCALING_THRESHOLD) & (VectorClass().load_a(&ptn_invar[ptn]) == 0.0); in computePartialLikelihoodSIMD() 2356 lh_ptn = abs(lh_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeLikelihoodDervSIMD() 2437 lh_ptn = abs(lh_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeLikelihoodDervSIMD() 2864 lh_ptn = abs(lh_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeLikelihoodBranchSIMD() 2998 lh_ptn = abs(lh_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeLikelihoodBranchSIMD() 3226 lh_ptn = abs(lh_ptn) + VectorClass().load_a(&ptn_invar[ptn]); in computeLikelihoodFromBufferSIMD() [all …]
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H A D | phylotreemixlen.cpp | 453 double lk_ptn = ptn_invar[ptn]; in optimizeOneBranch() 850 double lh_ptn = ptn_invar[ptn], df_ptn = 0.0, ddf_ptn = 0.0; in computeFuncDerv()
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H A D | phylotree.cpp | 100 ptn_invar = NULL; in init() 255 if (ptn_invar) in ~PhyloTree() 256 aligned_free(ptn_invar); in ~PhyloTree() 257 ptn_invar = NULL; in ~PhyloTree() 883 if (!ptn_invar) in initializeAllPartialLh() 884 ptn_invar = aligned_alloc<double>(mem_size); in initializeAllPartialLh() 916 if (ptn_invar) in deleteAllPartialLh() 917 aligned_free(ptn_invar); in deleteAllPartialLh() 936 ptn_invar = NULL; in deleteAllPartialLh()
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H A D | phylotree.h | 1480 double *ptn_invar; variable
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