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Searched refs:p_lk_tip_r (Results 1 – 13 of 13) sorted by relevance

/dports/biology/phyml/phyml-3.3.20200621/src/
H A Dancestral.c184 else for(i=0;i<ns;++i) probs[i] = b->p_lk_tip_r[site*ns+i]; in Sample_Ancestral_Seq_Pre()
245 else if(d == b->rght) for(i=0;i<ns;++i) probs[i] = b->p_lk_tip_r[site*ns+i]; in Sample_Ancestral_Seq_Core()
292 r += tree->e_root->p_lk_tip_r[site*dim2+j] * Pij[r_cat*dim3+i*dim2+j]; in Sample_Ancestral_Seq_Core()
718 p0 += v0->b[0]->p_lk_tip_r[csite*ns+j] * Pij0[catg*nsns+i*ns+j]; in Ancestral_Sequences_One_Node()
724 v0->b[0]->p_lk_tip_r[csite*ns+j], in Ancestral_Sequences_One_Node()
755 p1 += v1->b[0]->p_lk_tip_r[csite*ns+j] * Pij1[catg*nsns+i*ns+j]; in Ancestral_Sequences_One_Node()
761 v1->b[0]->p_lk_tip_r[csite*ns+j], in Ancestral_Sequences_One_Node()
791 p2 += v2->b[0]->p_lk_tip_r[csite*ns+j] * Pij2[catg*nsns+i*ns+j]; in Ancestral_Sequences_One_Node()
H A Dmake.c80 tree->n_root->b[1]->p_lk_tip_r = tree->e_root->p_lk_tip_l; in Make_Tree_For_Lk()
81 tree->n_root->b[2]->p_lk_tip_r = tree->e_root->p_lk_tip_r; in Make_Tree_For_Lk()
361 b->p_lk_tip_r = NULL; in Make_Edge_Lk_Rght()
367 …if(posix_memalign((void **)&b->p_lk_tip_r,BYTE_ALIGN,(size_t)tree->data->crunch_len*tree->mod->ns*… in Make_Edge_Lk_Rght()
369 … b->p_lk_tip_r = _aligned_malloc(tree->data->crunch_len*tree->mod->ns*sizeof(phydbl),BYTE_ALIGN); in Make_Edge_Lk_Rght()
372 b->p_lk_tip_r = (phydbl *)mCalloc(tree->data->crunch_len*tree->mod->ns,sizeof(phydbl)); in Make_Edge_Lk_Rght()
380 b->p_lk_tip_r = NULL; in Make_Edge_Lk_Rght()
H A Dlk.c609 p_lk_rght = b->rght->tax ? b->p_lk_tip_r : b->p_lk_rght; in Lk()
1070 if(b->rght->tax == YES) p_lk_rght = b->p_lk_tip_r; in Update_Eigen_Lr()
1460 … p1_lk1 += Pij1[catg*nsns+i*ns+j] * (phydbl)n_v1->b[0]->p_lk_tip_r[site*ns+j]; in Update_Partial_Lk_Generic()
1497 … p2_lk2 += Pij2[catg*nsns+i*ns+j] * (phydbl)n_v2->b[0]->p_lk_tip_r[site*ns+j]; in Update_Partial_Lk_Generic()
2082 tree->a_nodes[i]->b[0]->p_lk_tip_r); in Init_Partial_Lk_Tips_Double()
2086 tree->a_nodes[i]->b[0]->p_lk_tip_r); in Init_Partial_Lk_Tips_Double()
2093 tree->a_nodes[i]->b[0]->p_lk_tip_r); in Init_Partial_Lk_Tips_Double()
2129 tree->a_nodes[i]->b[0]->p_lk_tip_r); in Init_Partial_Lk_Tips_Int()
2137 tree->a_nodes[i]->b[0]->p_lk_tip_r); in Init_Partial_Lk_Tips_Int()
2148 tree->a_nodes[i]->b[0]->p_lk_tip_r); in Init_Partial_Lk_Tips_Int()
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H A Dutilities.c1382 n_e->b[j]->p_lk_tip_r = n_f->b[j]->p_lk_tip_r; in Share_Lk_Struct()
1409 n_e->b[0]->p_lk_tip_r = n_f->b[0]->p_lk_tip_r; in Share_Lk_Struct()
5187 b1->p_lk_tip_r = b2->p_lk_tip_r; in Prune_Subtree()
5505 residual->p_lk_tip_r = target->p_lk_tip_r; in Graft_Subtree()
5686 tree->n_root->b[2]->p_lk_tip_r = tree->e_root->p_lk_tip_r; in Graft_Subtree()
6734 buff_p_lk_tip = b->p_lk_tip_r; in Swap_Partial_Lk()
6735 b->p_lk_tip_r = a->p_lk_tip_l; in Swap_Partial_Lk()
6784 b->p_lk_tip_l = a->p_lk_tip_r; in Swap_Partial_Lk()
6785 a->p_lk_tip_r = buff_p_lk_tip; in Swap_Partial_Lk()
6833 b->p_lk_tip_r = a->p_lk_tip_r; in Swap_Partial_Lk()
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H A Dbeagle_utils.c151 …double* tip = short_to_double(tree->a_nodes[i]->b[0]->p_lk_tip_r, tree->n_pattern*tree->mod->ns); … in create_beagle_instance()
H A Dm4.c583 tree->a_nodes[i]->b[0]->p_lk_tip_r[curr_site*dim2 + j*dim3+k] = in M4_Init_Partial_Lk_Tips_Int()
584 tree->a_nodes[i]->b[0]->p_lk_tip_r[curr_site*dim2 + 0*dim3+k]; in M4_Init_Partial_Lk_Tips_Int()
699 b->p_lk_tip_r[tree->curr_site*dim2 + l] * in M4_Post_Prob_H_Class_Edge_Site()
H A Dfree.c517 if(b->p_lk_tip_r) Free(b->p_lk_tip_r); in Free_Edge_Lk_Rght()
H A Dsse.c82 p_lk_rght = b->rght->tax ? b->p_lk_tip_r : b->p_lk_rght; in SSE_Update_Eigen_Lr()
H A Davx.c82 p_lk_rght = b->rght->tax ? b->p_lk_tip_r : b->p_lk_rght; in AVX_Update_Eigen_Lr()
H A Dmixt.c916 b->p_lk_tip_r + site*ns, in MIXT_Lk()
2686 p0 += v0->b[0]->p_lk_tip_r[csite*Ns+j] * Pij0[catg*NsNs+i*Ns+j]; in MIXT_Ancestral_Sequences_One_Node()
2707 p1 += v1->b[0]->p_lk_tip_r[csite*Ns+j] * Pij1[catg*NsNs+i*Ns+j]; in MIXT_Ancestral_Sequences_One_Node()
2731 p2 += v2->b[0]->p_lk_tip_r[csite*Ns+j] * Pij2[catg*NsNs+i*Ns+j]; in MIXT_Ancestral_Sequences_One_Node()
H A Dutilities.h638 phydbl *p_lk_tip_r, *p_lk_tip_l; member
H A Dio.c3300 int tip_partial = d->b[0]->p_lk_tip_r[site*tree->mod->ns + i]; in Print_Tip_Partials()
3399 fprintf(stdout,"[%d,%d]%.1f ",site,j,b->p_lk_tip_r[site*tree->mod->ns + j]); in Print_Edge_Likelihoods()
/dports/biology/seaview/seaview/csrc/
H A Dphyml_util.h203 short int **p_lk_tip_r,**p_lk_tip_l; member