3 #include "libhmsbeagle/beagle.h"
5 typedef std::vector<int> CodedSequence;
6 typedef std::vector<double> PartialVector;
26 void abort(std::string msg);
30 void updateBrlen(
unsigned brlen_index);
31 void defineOperations();
32 double calcLnL(
int return_value);
37 unsigned like_root_node;
38 unsigned like_parent_index;
39 unsigned like_child_index;
40 unsigned transmat_index;
41 std::string data_file_name;
51 std::vector<std::string> taxon_name;
52 std::vector<CodedSequence> data;
53 std::vector<PartialVector> partial;
54 std::vector<int> transition_matrix_index;
55 std::vector<double> brlens;
56 std::vector<int> operations;
57 std::vector<int> scaleIndices;
60 bool use_tip_partials;
61 bool accumulate_on_the_fly;
65 int calculate_derivatives;
66 bool empirical_derivatives;
67 bool sse_vectorization;