Index

C

car_to_block() (in module procars.utils.util_adjacency_functions) change_adj_discarded_files() (in module procars.step_modules.compute_resolved_conflicts) check_potential_cars_neighbors() (in module procars.step_modules.compute_conserved_adjacencies) commons_read_blocks() (in module procars.step_modules.compute_initialpqtree) commons_read_cars() (in module procars.step_modules.compute_conserved_adjacencies) commons_read_tree() (in module procars.step_modules.compute_initialpqtree) compute_adjacencies() (in module procars.utils.util_adjacency_functions) compute_adjacencymatrix_from_adjacency_array() (in module procars.step_modules.compute_dcj_adjacencies) compute_adjacencymatrix_from_neighbor_arrays() (in module procars.step_modules.compute_conserved_adjacencies) compute_blocks_cars() (in module procars.step_modules.compute_conserved_adjacencies) compute_blocks_neighbors() (in module procars.step_modules.compute_initialpqtree)

compute_cars_neighbors() (in module procars.step_modules.compute_conserved_adjacencies) compute_conserved_adjacencies() (in module procars.step_modules.compute_conserved_adjacencies) compute_cost() (in module procars.step_modules.compute_resolved_conflicts) compute_extremity() (in module procars.step_modules.compute_conserved_adjacencies) compute_extremity_pair() (in module procars.utils.util_adjacency_functions) compute_neighbor() (in module procars.step_modules.compute_dcj_adjacencies) compute_parameters_from_tree() (in module procars.step_modules.compute_initialpqtree) compute_partition_and_species_id() (in module procars.step_modules.compute_initialpqtree) compute_potential_cars_neighbors() (in module procars.step_modules.compute_conserved_adjacencies) conservation_status() (in module procars.utils.util_adjacency_functions)

D

diff_nc_matrix_m() (in module procars.step_modules.compute_conserved_adjacencies)

F

fill_conserved_arrays() (in module procars.step_modules.compute_conserved_adjacencies) find_adj_info() (in module procars.utils.util_adjacency_functions) find_adjacency_sets() (in module procars.step_modules.compute_conserved_adjacencies) find_cars() (in module procars.step_modules.compute_pqtree) find_conflicts_couples() (in module procars.step_modules.compute_resolved_conflicts)

find_independant_sets() (in module procars.step_modules.compute_resolved_conflicts) find_info_and_write_adjs() (in module procars.step_modules.compute_conserved_adjacencies) find_mincost_set() (in module procars.step_modules.compute_resolved_conflicts) find_possible_dcj_adjs() (in module procars.step_modules.compute_dcj_adjacencies)

G

get_adjacencies_costs() (in module procars.step_modules.compute_resolved_conflicts)

I

init_read_from_block_in_cycle() (in module procars.step_modules.compute_pqtree) is_adjacency_in_car() (in module procars.step_modules.compute_dcj_adjacencies) is_car_adjacency() (in module procars.step_modules.compute_dcj_adjacencies)

is_dcj_reliable() (in module procars.step_modules.compute_dcj_adjacencies) is_dcj_reliable_conserved() (in module procars.step_modules.compute_dcj_adjacencies)

L

list_leaves_internals() (in module procars.step_modules.compute_initialpqtree)

M

main() (in module procars.step_modules.compute_conserved_adjacencies) (in module procars.step_modules.compute_dcj_adjacencies) (in module procars.step_modules.compute_initialpqtree) (in module procars.step_modules.compute_pqtree) (in module procars.step_modules.compute_resolved_conflicts)

mark_ancestors() (in module procars.step_modules.compute_initialpqtree)

P

pairs() (procars.utils.util_classes.SparseMatrix method) partition_species() (in module procars.step_modules.compute_initialpqtree) procars.procars_steps (module) procars.step_modules.compute_conserved_adjacencies (module) procars.step_modules.compute_dcj_adjacencies (module) procars.step_modules.compute_initialpqtree (module)

procars.step_modules.compute_pqtree (module) procars.step_modules.compute_resolved_conflicts (module) procars.utils.initial_files_reader (module) procars.utils.util_adjacency_functions (module) procars.utils.util_classes (module) procars.utils.utils_IO (module)

R

read_adjacency_file() (in module procars.utils.utils_IO) read_binary_file() (in module procars.utils.utils_IO) read_block_file() (in module procars.utils.initial_files_reader) read_block_line() (in module procars.utils.initial_files_reader) read_car_file() (in module procars.utils.utils_IO) read_conflict_adj_file() (in module procars.utils.utils_IO) read_from_block() (in module procars.step_modules.compute_pqtree)

read_from_block_in_cycle() (in module procars.step_modules.compute_pqtree) read_treefile() (in module procars.utils.initial_files_reader) remove_adjacency_from_file() (in module procars.step_modules.compute_pqtree) reverse() (in module procars.step_modules.compute_conserved_adjacencies) run_step_a() (in module procars.procars_steps) run_step_b() (in module procars.procars_steps) run_step_c() (in module procars.procars_steps)

S

save_binary_information() (in module procars.utils.utils_IO) segment_car_common_extremity() (in module procars.step_modules.compute_conserved_adjacencies)

SparseMatrix (class in procars.utils.util_classes) split_adjacencymatrix() (in module procars.utils.util_adjacency_functions)

W

write_adjacency() (in module procars.utils.utils_IO) write_car_file() (in module procars.utils.utils_IO) write_discarded_adjs() (in module procars.step_modules.compute_conserved_adjacencies)

write_init_cars_file() (in module procars.step_modules.compute_initialpqtree) write_retained_adjs() (in module procars.step_modules.compute_conserved_adjacencies) (in module procars.step_modules.compute_dcj_adjacencies) (in module procars.step_modules.compute_resolved_conflicts) write_retained_conflict_adjs() (in module procars.utils.utils_IO)