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Searched refs:_pattern_lh_cat (Results 1 – 14 of 14) sorted by relevance

/dports/biology/iqtree/IQ-TREE-2.0.6/model/
H A Drateheterotachy.cpp168 double *this_lk_cat = phylo_tree->_pattern_lh_cat + ptn*nmix; in optimizeWithEM()
176 double *this_lk_cat = phylo_tree->_pattern_lh_cat + ptn*nmix; in optimizeWithEM()
H A Drategammainvar.cpp196 double *lh_cat = phylo_tree->_pattern_lh_cat; in computePatternRates()
234 double *this_lk_cat = phylo_tree->_pattern_lh_cat + ptn * ncat; in optimizeWithEM()
H A Dmodelmixture.cpp1565 double *this_lk_cat = phylo_tree->_pattern_lh_cat + ptn*nmix; in optimizeWeights()
1573 double *this_lk_cat = phylo_tree->_pattern_lh_cat + ptn*nmix; in optimizeWeights()
1670 double *this_lk_cat = phylo_tree->_pattern_lh_cat + ptn*nmix; in optimizeWithEM()
1744 double *this_lk_cat = phylo_tree->_pattern_lh_cat+c; in optimizeWithEM()
H A Dratekategory.cpp109 double *lh_cat = phylo_tree->_pattern_lh_cat; in computePatternRates()
H A Dratefree.cpp549 double *this_lk_cat = phylo_tree->_pattern_lh_cat + ptn*nmix; in optimizeWithEM()
629 double *this_lk_cat = phylo_tree->_pattern_lh_cat+c; in optimizeWithEM()
H A Drategamma.cpp268 double *lh_cat = phylo_tree->_pattern_lh_cat; in computePatternRates()
/dports/biology/iqtree/IQ-TREE-2.0.6/tree/
H A Dphylokernelnonrev.cpp692 memset(_pattern_lh_cat+ptn_lower*ncat, 0, (ptn_upper-ptn_lower)*ncat*sizeof(double)); in computeNonrevLikelihoodBranch()
696 double *lh_cat = _pattern_lh_cat + ptn*ncat; in computeNonrevLikelihoodBranch()
742 memset(_pattern_lh_cat+ptn_lower*ncat, 0, (ptn_upper-ptn_lower)*ncat*sizeof(double)); in computeNonrevLikelihoodBranch()
746 double *lh_cat = _pattern_lh_cat + ptn*ncat; in computeNonrevLikelihoodBranch()
H A Dphylosupertreeplen.cpp116 (*it)->_pattern_lh_cat = NULL; in deleteAllPartialLh()
138 (*it)->_pattern_lh_cat = NULL; in ~PhyloSuperTreePlen()
1655 if (!_pattern_lh_cat) in initializeAllPartialLh()
1656 _pattern_lh_cat = aligned_alloc<double>(total_lh_cat_size); in initializeAllPartialLh()
1657 at(part_order[0])->_pattern_lh_cat = _pattern_lh_cat; in initializeAllPartialLh()
1697 (*it)->_pattern_lh_cat = (*prev_it)->_pattern_lh_cat + lh_cat_size[part]; in initializeAllPartialLh()
H A Dphylotree.cpp91 _pattern_lh_cat = NULL; in init()
231 if (_pattern_lh_cat) in ~PhyloTree()
232 aligned_free(_pattern_lh_cat); in ~PhyloTree()
233 _pattern_lh_cat = NULL; in ~PhyloTree()
868 if (!_pattern_lh_cat) in initializeAllPartialLh()
928 if (_pattern_lh_cat) in deleteAllPartialLh()
929 aligned_free(_pattern_lh_cat); in deleteAllPartialLh()
943 _pattern_lh_cat = NULL; in deleteAllPartialLh()
1389 double *lh_cat = _pattern_lh_cat; in computePatternStateFreq()
1527 double *lh_cat = _pattern_lh_cat; in computePatternLikelihood()
[all …]
H A Dphylokernelnonrev.h1146 … memset(_pattern_lh_cat+ptn_lower*ncat_mix, 0, sizeof(double)*(ptn_upper-ptn_lower)*ncat_mix);
1153 VectorClass *lh_cat = (VectorClass*)(_pattern_lh_cat + ptn*ncat_mix);
1218 double *this_lh_cat = &_pattern_lh_cat[ptn*ncat_mix + i];
1288 … memset(_pattern_lh_cat+ptn_lower*ncat_mix, 0, (ptn_upper-ptn_lower)*ncat_mix*sizeof(double));
1293 VectorClass *lh_cat = (VectorClass*)(_pattern_lh_cat + ptn*ncat_mix);
1348 double *this_lh_cat = &_pattern_lh_cat[ptn*ncat_mix + i];
H A Dphylokernelsitemodel.cpp593 memset(_pattern_lh_cat, 0, sizeof(double)*nptn*ncat); in computeSitemodelLikelihoodBranchEigen()
604 double *lh_cat = _pattern_lh_cat + ptn*ncat; in computeSitemodelLikelihoodBranchEigen()
634 double *lh_cat = _pattern_lh_cat + ptn*ncat; in computeSitemodelLikelihoodBranchEigen()
H A Dphylotreemixlen.cpp452 double *this_lk_cat = _pattern_lh_cat + ptn*nmix; in optimizeOneBranch()
473 double *this_lk_cat = _pattern_lh_cat+cur_mixture; in optimizeOneBranch()
H A Dphylotree.h2066 double *getPatternLhCatPointer() { return _pattern_lh_cat; } in getPatternLhCatPointer()
2173 double *_pattern_lh_cat; variable
H A Dphylokernelnew.h2762 … memset(_pattern_lh_cat + ptn_lower*ncat_mix, 0, sizeof(double)*(ptn_upper-ptn_lower)*ncat_mix); in computeLikelihoodBranchSIMD()
2773 VectorClass *lh_cat = (VectorClass*)(_pattern_lh_cat + ptn*ncat_mix); in computeLikelihoodBranchSIMD()
2842 double *this_lh_cat = &_pattern_lh_cat[ptn*ncat_mix + i]; in computeLikelihoodBranchSIMD()
2915 … memset(_pattern_lh_cat + ptn_lower*ncat_mix, 0, sizeof(double)*(ptn_upper-ptn_lower)*ncat_mix); in computeLikelihoodBranchSIMD()
2924 VectorClass *lh_cat = (VectorClass*)(_pattern_lh_cat + ptn*ncat_mix); in computeLikelihoodBranchSIMD()
2977 double *this_lh_cat = &_pattern_lh_cat[ptn*ncat_mix + i]; in computeLikelihoodBranchSIMD()