diff options
author | Magnus Lundborg <magnus.lundborg@scilifelab.se> | 2012-12-03 16:57:57 (GMT) |
---|---|---|
committer | Magnus Lundborg <magnus.lundborg@scilifelab.se> | 2012-12-03 16:57:57 (GMT) |
commit | fa78b5bab2b7884a294de10fdbfca8a380823d79 (patch) | |
tree | f75345ecb10d6dc74225c247179895f7ae1dac60 /src/lib/tng_io.c | |
parent | 2742db93246135f910c74255dbd935bcf8438650 (diff) |
Typedef tng_trajectory to restrict data access to the API.
Diffstat (limited to 'src/lib/tng_io.c')
-rw-r--r-- | src/lib/tng_io.c | 132 |
1 files changed, 66 insertions, 66 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 73a92c1..57cd31f 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -37,7 +37,7 @@ /* This function swaps the byte order of a 32 bit numerical variable. It does not only work with integer, but e.g. floats need casting */ static inline tng_function_status tng_swap_byte_order_32 - (const struct tng_trajectory *tng_data, int32_t *v) + (const tng_trajectory_t tng_data, int32_t *v) { switch(tng_data->endianness_32) { @@ -68,7 +68,7 @@ static inline tng_function_status tng_swap_byte_order_32 The byte order swapping routine can convert five different byte orders to big endian. */ static inline tng_function_status tng_swap_byte_order_64 - (const struct tng_trajectory *tng_data, int64_t *v) + (const tng_trajectory_t tng_data, int64_t *v) { switch(tng_data->endianness_64) { @@ -158,7 +158,7 @@ static tng_function_status tng_verify_hash_match(struct tng_gen_block *block, } -static tng_function_status tng_init_input_file(struct tng_trajectory *tng_data, +static tng_function_status tng_init_input_file(tng_trajectory_t tng_data, const tng_bool update_read_pos) { if(!tng_data->input_file) @@ -195,7 +195,7 @@ static tng_function_status tng_init_input_file(struct tng_trajectory *tng_data, } static tng_function_status tng_init_output_file - (struct tng_trajectory *tng_data, + (tng_trajectory_t tng_data, const tng_bool update_write_pos) { if(!tng_data->output_file) @@ -240,7 +240,7 @@ static tng_function_status tng_init_output_file } static tng_function_status tng_read_block_header - (struct tng_trajectory *tng_data, struct tng_gen_block *block) + (tng_trajectory_t tng_data, struct tng_gen_block *block) { int len, offset = 0; @@ -369,7 +369,7 @@ static tng_function_status tng_read_block_header } static tng_function_status tng_write_block_header - (struct tng_trajectory *tng_data, + (tng_trajectory_t tng_data, struct tng_gen_block *block, write_mode mode) { int name_len, offset = 0; @@ -511,7 +511,7 @@ static tng_function_status tng_write_block_header static tng_function_status tng_read_general_info_block - (struct tng_trajectory *tng_data, struct tng_gen_block *block) + (tng_trajectory_t tng_data, struct tng_gen_block *block) { int len, offset = 0; tng_bool same_hash; @@ -694,7 +694,7 @@ static tng_function_status tng_read_general_info_block } static tng_function_status tng_write_general_info_block - (struct tng_trajectory *tng_data, + (tng_trajectory_t tng_data, struct tng_gen_block *block, write_mode mode) { @@ -948,7 +948,7 @@ static tng_function_status tng_write_general_info_block /* FIXME: Update this according to the new specs */ static tng_function_status tng_read_molecules_block - (struct tng_trajectory *tng_data, + (tng_trajectory_t tng_data, struct tng_gen_block *block) { int i, j, k, l, len, offset = 0; @@ -1361,7 +1361,7 @@ static tng_function_status tng_read_molecules_block /* FIXME: Update this according to the new specs */ static tng_function_status tng_write_molecules_block - (struct tng_trajectory *tng_data, + (tng_trajectory_t tng_data, struct tng_gen_block *block, write_mode mode) { @@ -1830,7 +1830,7 @@ static tng_function_status tng_write_molecules_block static tng_function_status tng_read_frame_set_block - (struct tng_trajectory *tng_data, + (tng_trajectory_t tng_data, struct tng_gen_block *block) { int i, file_pos, offset = 0; @@ -2060,7 +2060,7 @@ static tng_function_status tng_read_frame_set_block } static tng_function_status tng_write_frame_set_block - (struct tng_trajectory *tng_data, + (tng_trajectory_t tng_data, struct tng_gen_block *block, write_mode mode) { @@ -2267,7 +2267,7 @@ static tng_function_status tng_write_frame_set_block } static tng_function_status tng_read_trajectory_toc_block - (struct tng_trajectory *tng_data, + (tng_trajectory_t tng_data, struct tng_gen_block *block) { int64_t i, old_n_blocks; @@ -2381,7 +2381,7 @@ static tng_function_status tng_read_trajectory_toc_block } static tng_function_status tng_write_trajectory_toc_block - (struct tng_trajectory *tng_data, + (tng_trajectory_t tng_data, struct tng_gen_block *block, write_mode mode) { @@ -2503,7 +2503,7 @@ static tng_function_status tng_write_trajectory_toc_block } static tng_function_status tng_read_trajectory_mapping_block - (struct tng_trajectory *tng_data, + (tng_trajectory_t tng_data, struct tng_gen_block *block) { int64_t i, old_n_particles; @@ -2643,7 +2643,7 @@ static tng_function_status tng_read_trajectory_mapping_block } static tng_function_status tng_write_trajectory_mapping_block - (struct tng_trajectory *tng_data, + (tng_trajectory_t tng_data, struct tng_gen_block *block, int mapping_block_nr, write_mode mode) @@ -2793,7 +2793,7 @@ static tng_function_status tng_write_trajectory_mapping_block } static tng_function_status tng_create_particle_data_block - (struct tng_trajectory *tng_data, + (tng_trajectory_t tng_data, const tng_block_type block_type_flag) { struct tng_trajectory_frame_set *frame_set = @@ -2911,7 +2911,7 @@ tng_function_status tng_allocate_particle_data_mem } static tng_function_status tng_read_particle_data - (struct tng_trajectory *tng_data, + (tng_trajectory_t tng_data, struct tng_gen_block *block, int *offset, const char datatype, @@ -3135,7 +3135,7 @@ static tng_function_status tng_read_particle_data static tng_function_status tng_write_particle_data_block - (struct tng_trajectory *tng_data, + (tng_trajectory_t tng_data, struct tng_gen_block *block, const int block_index, const struct tng_particle_mapping *mapping, @@ -3511,7 +3511,7 @@ static tng_function_status tng_write_particle_data_block /* UNTESTED */ static tng_function_status tng_create_data_block - (struct tng_trajectory *tng_data, + (tng_trajectory_t tng_data, const tng_block_type block_type_flag) { struct tng_trajectory_frame_set *frame_set = @@ -3616,7 +3616,7 @@ tng_function_status tng_allocate_data_mem return(TRG_SUCCESS); } -static tng_function_status tng_read_data(struct tng_trajectory *tng_data, +static tng_function_status tng_read_data(tng_trajectory_t tng_data, struct tng_gen_block *block, int *offset, const char datatype, @@ -3819,7 +3819,7 @@ static tng_function_status tng_read_data(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -static tng_function_status tng_write_data_block(struct tng_trajectory *tng_data, +static tng_function_status tng_write_data_block(tng_trajectory_t tng_data, struct tng_gen_block *block, const int block_index, const write_mode mode) @@ -4140,7 +4140,7 @@ static tng_function_status tng_write_data_block(struct tng_trajectory *tng_data, } static tng_function_status tng_read_data_block_contents - (struct tng_trajectory *tng_data, + (tng_trajectory_t tng_data, struct tng_gen_block *block) { int64_t n_values, codec_id, n_frames, first_frame_with_data; @@ -4362,7 +4362,7 @@ static tng_function_status tng_read_data_block_contents } } -static tng_function_status tng_update_md5_hash(struct tng_trajectory *tng_data, +static tng_function_status tng_update_md5_hash(tng_trajectory_t tng_data, struct tng_gen_block *block, int64_t header_start_pos, int64_t contents_start_pos) @@ -4392,7 +4392,7 @@ static tng_function_status tng_update_md5_hash(struct tng_trajectory *tng_data, static tng_function_status tng_update_header_pointers - (struct tng_trajectory *tng_data) + (tng_trajectory_t tng_data) { struct tng_gen_block block; FILE *temp = tng_data->input_file; @@ -4480,7 +4480,7 @@ static tng_function_status tng_update_header_pointers } static tng_function_status tng_update_frame_set_pointers - (struct tng_trajectory *tng_data) + (tng_trajectory_t tng_data) { struct tng_gen_block block; struct tng_trajectory_frame_set *frame_set; @@ -4603,7 +4603,7 @@ static tng_function_status tng_update_frame_set_pointers } -tng_function_status tng_set_block_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_block_name(tng_trajectory_t tng_data, struct tng_gen_block *block, const char *new_name) { @@ -4683,7 +4683,7 @@ tng_function_status tng_destroy_block(struct tng_gen_block *block) return(TRG_SUCCESS); } -tng_function_status tng_set_atom_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_atom_name(tng_trajectory_t tng_data, struct tng_atom *atom, const char *new_name) { @@ -4712,7 +4712,7 @@ tng_function_status tng_set_atom_name(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_set_atom_type(struct tng_trajectory *tng_data, +tng_function_status tng_set_atom_type(tng_trajectory_t tng_data, struct tng_atom *atom, const char *new_type) { @@ -4765,7 +4765,7 @@ tng_function_status tng_destroy_atom(struct tng_atom *atom) return(TRG_SUCCESS); } -tng_function_status tng_add_molecule(struct tng_trajectory *tng_data, +tng_function_status tng_add_molecule(tng_trajectory_t tng_data, const char *name, struct tng_molecule **molecule) { @@ -4835,7 +4835,7 @@ tng_function_status tng_add_molecule(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_set_molecule_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_molecule_name(tng_trajectory_t tng_data, struct tng_molecule *molecule, const char *new_name) { @@ -4864,7 +4864,7 @@ tng_function_status tng_set_molecule_name(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_get_molecule_cnt(struct tng_trajectory *tng_data, +tng_function_status tng_get_molecule_cnt(tng_trajectory_t tng_data, struct tng_molecule *molecule, int64_t *cnt) { @@ -4887,7 +4887,7 @@ tng_function_status tng_get_molecule_cnt(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_set_molecule_cnt(struct tng_trajectory *tng_data, +tng_function_status tng_set_molecule_cnt(tng_trajectory_t tng_data, struct tng_molecule *molecule, const int64_t cnt) { @@ -4914,7 +4914,7 @@ tng_function_status tng_set_molecule_cnt(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_add_chain_to_molecule(struct tng_trajectory *tng_data, +tng_function_status tng_add_chain_to_molecule(tng_trajectory_t tng_data, struct tng_molecule *molecule, const char *name, struct tng_chain **chain) @@ -4949,7 +4949,7 @@ tng_function_status tng_add_chain_to_molecule(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_set_chain_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_chain_name(tng_trajectory_t tng_data, struct tng_chain *chain, const char *new_name) { @@ -4978,7 +4978,7 @@ tng_function_status tng_set_chain_name(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_add_residue_to_chain(struct tng_trajectory *tng_data, +tng_function_status tng_add_residue_to_chain(tng_trajectory_t tng_data, struct tng_chain *chain, const char *name, struct tng_residue **residue) @@ -5055,7 +5055,7 @@ tng_function_status tng_add_residue_to_chain(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_set_residue_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_residue_name(tng_trajectory_t tng_data, struct tng_residue *residue, const char *new_name) { @@ -5084,7 +5084,7 @@ tng_function_status tng_set_residue_name(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_add_atom_to_residue(struct tng_trajectory *tng_data, +tng_function_status tng_add_atom_to_residue(tng_trajectory_t tng_data, struct tng_residue *residue, const char *atom_name, const char *atom_type, @@ -5238,7 +5238,7 @@ tng_function_status tng_destroy_molecule(struct tng_molecule *molecule) return(TRG_SUCCESS); } -tng_function_status tng_init_trajectory(struct tng_trajectory *tng_data) +tng_function_status tng_init_trajectory(tng_trajectory_t tng_data) { time_t seconds; struct tng_trajectory_frame_set *frame_set = @@ -5394,7 +5394,7 @@ tng_function_status tng_init_trajectory(struct tng_trajectory *tng_data) return(TRG_SUCCESS); } -tng_function_status tng_destroy_trajectory(struct tng_trajectory *tng_data) +tng_function_status tng_destroy_trajectory(tng_trajectory_t tng_data) { int64_t n_frames, n_particles; int i, j, k, l; @@ -5718,7 +5718,7 @@ tng_function_status tng_destroy_trajectory(struct tng_trajectory *tng_data) return(TRG_SUCCESS); } -tng_function_status tng_set_input_file(struct tng_trajectory *tng_data, +tng_function_status tng_set_input_file(tng_trajectory_t tng_data, const char *file_name) { int len; @@ -5750,7 +5750,7 @@ tng_function_status tng_set_input_file(struct tng_trajectory *tng_data, return(tng_init_input_file(tng_data, FALSE)); } -tng_function_status tng_set_output_file(struct tng_trajectory *tng_data, +tng_function_status tng_set_output_file(tng_trajectory_t tng_data, const char *file_name) { int len; @@ -5783,7 +5783,7 @@ tng_function_status tng_set_output_file(struct tng_trajectory *tng_data, } -tng_function_status tng_set_program_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_program_name(tng_trajectory_t tng_data, const char *new_name) { int len; @@ -5811,7 +5811,7 @@ tng_function_status tng_set_program_name(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_set_forcefield_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_forcefield_name(tng_trajectory_t tng_data, const char *new_name) { int len; @@ -5839,7 +5839,7 @@ tng_function_status tng_set_forcefield_name(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_set_user_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_user_name(tng_trajectory_t tng_data, const char *new_name) { int len; @@ -5867,7 +5867,7 @@ tng_function_status tng_set_user_name(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_set_computer_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_computer_name(tng_trajectory_t tng_data, const char *new_name) { int len; @@ -5895,7 +5895,7 @@ tng_function_status tng_set_computer_name(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_set_signature(struct tng_trajectory *tng_data, +tng_function_status tng_set_signature(tng_trajectory_t tng_data, const char *signature) { int len; @@ -5923,7 +5923,7 @@ tng_function_status tng_set_signature(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_read_file_headers(struct tng_trajectory *tng_data, +tng_function_status tng_read_file_headers(tng_trajectory_t tng_data, tng_close_file_flag close_file) { int i, cnt = 0, prev_pos = 0; @@ -5997,7 +5997,7 @@ tng_function_status tng_read_file_headers(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_write_file_headers(struct tng_trajectory *tng_data, +tng_function_status tng_write_file_headers(tng_trajectory_t tng_data, tng_close_file_flag close_file) { int i; @@ -6072,7 +6072,7 @@ tng_function_status tng_write_file_headers(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_read_next_block(struct tng_trajectory *tng_data, +tng_function_status tng_read_next_block(tng_trajectory_t tng_data, struct tng_gen_block *block, tng_close_file_flag close_file) { @@ -6110,7 +6110,7 @@ tng_function_status tng_read_next_block(struct tng_trajectory *tng_data, } } -// tng_function_status tng_write_block(struct tng_trajectory *tng_data, +// tng_function_status tng_write_block(tng_trajectory_t tng_data, // struct tng_gen_block *block, // tng_close_file_flag close_file) // { @@ -6168,7 +6168,7 @@ tng_function_status tng_read_next_block(struct tng_trajectory *tng_data, // return(TRG_SUCCESS); // } -tng_function_status tng_read_next_frame_set(struct tng_trajectory *tng_data, +tng_function_status tng_read_next_frame_set(tng_trajectory_t tng_data, tng_close_file_flag close_file) { long int file_pos; @@ -6256,7 +6256,7 @@ tng_function_status tng_read_next_frame_set(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_write_frame_set(struct tng_trajectory *tng_data, +tng_function_status tng_write_frame_set(tng_trajectory_t tng_data, tng_close_file_flag close_file) { int i, j; @@ -6342,7 +6342,7 @@ tng_function_status tng_write_frame_set(struct tng_trajectory *tng_data, return(stat); } -tng_function_status tng_new_frame_set(struct tng_trajectory *tng_data, +tng_function_status tng_new_frame_set(tng_trajectory_t tng_data, const int64_t first_frame, const int64_t n_frames) { @@ -6477,7 +6477,7 @@ tng_function_status tng_new_frame_set(struct tng_trajectory *tng_data, } /* UNTESTED */ -tng_function_status tng_add_data_block(struct tng_trajectory *tng_data, +tng_function_status tng_add_data_block(tng_trajectory_t tng_data, const int64_t id, const char *block_name, const char datatype, @@ -6651,7 +6651,7 @@ tng_function_status tng_add_data_block(struct tng_trajectory *tng_data, } -tng_function_status tng_add_particle_data_block(struct tng_trajectory *tng_data, +tng_function_status tng_add_particle_data_block(tng_trajectory_t tng_data, const int64_t id, const char *block_name, const char datatype, @@ -6844,21 +6844,21 @@ tng_function_status tng_add_particle_data_block(struct tng_trajectory *tng_data, } -tng_function_status tng_read_next_traj_block(struct tng_trajectory *tng_data, +tng_function_status tng_read_next_traj_block(tng_trajectory_t tng_data, tng_close_file_flag close_file) { /* STUB */ return(TRG_SUCCESS); } -tng_function_status tng_write_next_traj_block(struct tng_trajectory *tng_data, +tng_function_status tng_write_next_traj_block(tng_trajectory_t tng_data, tng_close_file_flag close_file) { /* STUB */ return(TRG_SUCCESS); } -tng_function_status tng_read_traj_block(struct tng_trajectory *tng_data, +tng_function_status tng_read_traj_block(tng_trajectory_t tng_data, int64_t block_id, tng_close_file_flag close_file) { @@ -6866,7 +6866,7 @@ tng_function_status tng_read_traj_block(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_write_traj_block(struct tng_trajectory *tng_data, +tng_function_status tng_write_traj_block(tng_trajectory_t tng_data, int64_t block_id, tng_close_file_flag close_file) { @@ -6874,7 +6874,7 @@ tng_function_status tng_write_traj_block(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_read_frame_nr(struct tng_trajectory *tng_data, +tng_function_status tng_read_frame_nr(tng_trajectory_t tng_data, int64_t frame_nr, tng_close_file_flag close_file) { @@ -6882,7 +6882,7 @@ tng_function_status tng_read_frame_nr(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_write_frame_nr(struct tng_trajectory *tng_data, +tng_function_status tng_write_frame_nr(tng_trajectory_t tng_data, int64_t frame_nr, tng_close_file_flag close_file) { @@ -6890,7 +6890,7 @@ tng_function_status tng_write_frame_nr(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_read_frame_nrs(struct tng_trajectory *tng_data, +tng_function_status tng_read_frame_nrs(tng_trajectory_t tng_data, int64_t start_frame_nr, int64_t end_frame_nr, tng_close_file_flag close_file) @@ -6899,7 +6899,7 @@ tng_function_status tng_read_frame_nrs(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_write_frame_nrs(struct tng_trajectory *tng_data, +tng_function_status tng_write_frame_nrs(tng_trajectory_t tng_data, int64_t start_frame_nr, int64_t end_frame_nr, tng_close_file_flag close_file) @@ -6908,14 +6908,14 @@ tng_function_status tng_write_frame_nrs(struct tng_trajectory *tng_data, return(TRG_SUCCESS); } -tng_function_status tng_read_frame_set_nr(struct tng_trajectory *tng_data, +tng_function_status tng_read_frame_set_nr(tng_trajectory_t tng_data, int64_t frame_set_nr) { return(TRG_SUCCESS); } -tng_function_status tng_get_time_str(struct tng_trajectory *tng_data, +tng_function_status tng_get_time_str(tng_trajectory_t tng_data, char *time) { struct tm *time_data; |