Searched refs:_pattern_lh_cat (Results 1 – 14 of 14) sorted by relevance
/dports/biology/iqtree/IQ-TREE-2.0.6/model/ |
H A D | rateheterotachy.cpp | 168 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 D | rategammainvar.cpp | 196 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 D | modelmixture.cpp | 1565 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 D | ratekategory.cpp | 109 double *lh_cat = phylo_tree->_pattern_lh_cat; in computePatternRates()
|
H A D | ratefree.cpp | 549 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 D | rategamma.cpp | 268 double *lh_cat = phylo_tree->_pattern_lh_cat; in computePatternRates()
|
/dports/biology/iqtree/IQ-TREE-2.0.6/tree/ |
H A D | phylokernelnonrev.cpp | 692 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 D | phylosupertreeplen.cpp | 116 (*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 D | phylotree.cpp | 91 _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 D | phylokernelnonrev.h | 1146 … 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 D | phylokernelsitemodel.cpp | 593 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 D | phylotreemixlen.cpp | 452 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 D | phylotree.h | 2066 double *getPatternLhCatPointer() { return _pattern_lh_cat; } in getPatternLhCatPointer() 2173 double *_pattern_lh_cat; variable
|
H A D | phylokernelnew.h | 2762 … 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()
|