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Searched refs:ptn_invar (Results 1 – 17 of 17) sorted by relevance

/dports/biology/iqtree/IQ-TREE-2.0.6/model/
H A Drategammainvar.cpp198 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()
H A Drateheterotachy.cpp177 double lk_ptn = phylo_tree->ptn_invar[ptn]; in optimizeWithEM()
H A Dmodelmixture.cpp1574 double lk_ptn = phylo_tree->ptn_invar[ptn]; in optimizeWeights()
1671 double lk_ptn = phylo_tree->ptn_invar[ptn]; in optimizeWithEM()
H A Dratefree.cpp550 double lk_ptn = phylo_tree->ptn_invar[ptn]; in optimizeWithEM()
/dports/biology/iqtree/IQ-TREE-2.0.6/tree/
H A Dphylotreesse.cpp652 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()
H A Dphylokernelnonrev.h196 … 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]);
H A Dphylokernelmixrate.h583 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()
H A Dphylokernelsafe.h310 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()
H A Dphylokernelmixture.h614 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()
H A Dphylokernelnonrev.cpp478 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()
H A Dphylokernelsitemodel.cpp521 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()
H A Dphylosupertreeplen.cpp123 (*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()
H A Dphylokernelsitemodel.h501 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()
H A Dphylokernelnew.h1523 … 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 …]
H A Dphylotreemixlen.cpp453 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()
H A Dphylotree.cpp100 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()
H A Dphylotree.h1480 double *ptn_invar; variable