diff options
Diffstat (limited to 'src/lib/tng_io.c')
| -rw-r--r-- | src/lib/tng_io.c | 207 |
1 files changed, 86 insertions, 121 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index f957a2f..6e52646 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -810,6 +810,48 @@ static tng_function_status tng_block_md5_hash_generate(tng_gen_block_t block) return(TNG_SUCCESS); } +/** If there is data left in the block read that to append that to the MD5 hash. + * @param tng_data is a trajectory data container. + * @param block is the data block that is being read. + * @param start_pos is the file position where the block started. + * @param md5_state is the md5 to which the md5 of the remaining block + * will be appended. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ +static tng_function_status tng_md5_remaining_append(tng_trajectory_t tng_data, + const tng_gen_block_t block, + const int64_t start_pos, + md5_state_t *md5_state) +{ + int64_t curr_file_pos; + char *temp_data; + + curr_file_pos = ftello(tng_data->input_file); + if(curr_file_pos < start_pos + block->block_contents_size) + { + temp_data = malloc(start_pos + block->block_contents_size - curr_file_pos); + if(!temp_data) + { + fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + start_pos + block->block_contents_size - curr_file_pos, __FILE__, __LINE__); + return(TNG_CRITICAL); + } + if(fread(temp_data, start_pos + block->block_contents_size - curr_file_pos, + 1, tng_data->input_file) == 0) + { + fprintf(stderr, "TNG library: Cannot read remaining part of block to generate MD5 sum. %s: %d\n", __FILE__, __LINE__); + free(temp_data); + return(TNG_CRITICAL); + } + md5_append(md5_state, (md5_byte_t *)temp_data, + start_pos + block->block_contents_size - curr_file_pos); + free(temp_data); + } + + return(TNG_SUCCESS); +} + /** Open the input file if it is not already opened. * @param tng_data is a trajectory data container. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major @@ -2193,8 +2235,8 @@ static tng_function_status tng_general_info_block_read (tng_trajectory_t tng_data, tng_gen_block_t block, const char hash_mode) { - int64_t start_pos, curr_file_pos; - char hash[TNG_MD5_HASH_LEN], *temp_data; + int64_t start_pos; + char hash[TNG_MD5_HASH_LEN]; md5_state_t md5_state; TNG_ASSERT(block != 0, "TNG library: Trying to read data to an uninitialized block (NULL pointer)"); @@ -2300,27 +2342,8 @@ static tng_function_status tng_general_info_block_read { /* If there is data left in the block that the current version of the library * cannot interpret still read that to generate the MD5 hash. */ - curr_file_pos = ftello(tng_data->input_file); - if(curr_file_pos < start_pos + block->block_contents_size) - { - temp_data = malloc(start_pos + block->block_contents_size - curr_file_pos); - if(!temp_data) - { - fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n", - start_pos + block->block_contents_size - curr_file_pos, __FILE__, __LINE__); - return(TNG_CRITICAL); - } - if(fread(temp_data, start_pos + block->block_contents_size - curr_file_pos, - 1, tng_data->input_file) == 0) - { - fprintf(stderr, "TNG library: Cannot read remaining part of block to generate MD5 sum. %s: %d\n", __FILE__, __LINE__); - free(temp_data); - return(TNG_CRITICAL); - } - md5_append(&md5_state, (md5_byte_t *)temp_data, - start_pos + block->block_contents_size - curr_file_pos); - free(temp_data); - } + tng_md5_remaining_append(tng_data, block, start_pos, &md5_state); + md5_finish(&md5_state, (md5_byte_t *)hash); if(strncmp(block->md5_hash, "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0", TNG_MD5_HASH_LEN) != 0) { @@ -2331,8 +2354,11 @@ static tng_function_status tng_general_info_block_read } } } - - fseeko(tng_data->input_file, start_pos + block->block_contents_size, SEEK_SET); + else + { + /* Seek to the end of the block */ + fseeko(tng_data->input_file, start_pos + block->block_contents_size, SEEK_SET); + } return(TNG_SUCCESS); } @@ -2871,13 +2897,13 @@ static tng_function_status tng_molecules_block_read tng_gen_block_t block, const char hash_mode) { - int64_t start_pos, curr_file_pos, i, j, k, l; + int64_t start_pos, i, j, k, l; tng_molecule_t molecule; tng_chain_t chain; tng_residue_t residue; tng_atom_t atom; tng_bond_t bond; - char hash[TNG_MD5_HASH_LEN], *temp_data; + char hash[TNG_MD5_HASH_LEN]; md5_state_t md5_state; if(tng_input_file_init(tng_data) != TNG_SUCCESS) @@ -3224,27 +3250,8 @@ static tng_function_status tng_molecules_block_read { /* If there is data left in the block that the current version of the library * cannot interpret still read that to generate the MD5 hash. */ - curr_file_pos = ftello(tng_data->input_file); - if(curr_file_pos < start_pos + block->block_contents_size) - { - temp_data = malloc(start_pos + block->block_contents_size - curr_file_pos); - if(!temp_data) - { - fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n", - start_pos + block->block_contents_size - curr_file_pos, __FILE__, __LINE__); - return(TNG_CRITICAL); - } - if(fread(temp_data, start_pos + block->block_contents_size - curr_file_pos, - 1, tng_data->input_file) == 0) - { - fprintf(stderr, "TNG library: Cannot read remaining part of block to generate MD5 sum. %s: %d\n", __FILE__, __LINE__); - free(temp_data); - return(TNG_CRITICAL); - } - md5_append(&md5_state, (md5_byte_t *)temp_data, - start_pos + block->block_contents_size - curr_file_pos); - free(temp_data); - } + tng_md5_remaining_append(tng_data, block, start_pos, &md5_state); + md5_finish(&md5_state, (md5_byte_t *)hash); if(strncmp(block->md5_hash, "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0", TNG_MD5_HASH_LEN) != 0) { @@ -3256,7 +3263,11 @@ static tng_function_status tng_molecules_block_read } } - fseeko(tng_data->input_file, start_pos + block->block_contents_size, SEEK_SET); + else + { + /* Seek to the end of the block */ + fseeko(tng_data->input_file, start_pos + block->block_contents_size, SEEK_SET); + } return(TNG_SUCCESS); } @@ -3521,7 +3532,7 @@ static tng_function_status tng_frame_set_block_read int64_t file_pos, start_pos, i, prev_n_particles; tng_trajectory_frame_set_t frame_set = &tng_data->current_trajectory_frame_set; - char hash[TNG_MD5_HASH_LEN], *temp_data; + char hash[TNG_MD5_HASH_LEN]; md5_state_t md5_state; if(tng_input_file_init(tng_data) != TNG_SUCCESS) @@ -3663,27 +3674,8 @@ static tng_function_status tng_frame_set_block_read { /* If there is data left in the block that the current version of the library * cannot interpret still read that to generate the MD5 hash. */ - file_pos = ftello(tng_data->input_file); - if(file_pos < start_pos + block->block_contents_size) - { - temp_data = malloc(start_pos + block->block_contents_size - file_pos); - if(!temp_data) - { - fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n", - start_pos + block->block_contents_size - file_pos, __FILE__, __LINE__); - return(TNG_CRITICAL); - } - if(fread(temp_data, start_pos + block->block_contents_size - file_pos, - 1, tng_data->input_file) == 0) - { - fprintf(stderr, "TNG library: Cannot read remaining part of block to generate MD5 sum. %s: %d\n", __FILE__, __LINE__); - free(temp_data); - return(TNG_CRITICAL); - } - md5_append(&md5_state, (md5_byte_t *)temp_data, - start_pos + block->block_contents_size - file_pos); - free(temp_data); - } + tng_md5_remaining_append(tng_data, block, start_pos, &md5_state); + md5_finish(&md5_state, (md5_byte_t *)hash); if(strncmp(block->md5_hash, "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0", TNG_MD5_HASH_LEN) != 0) { @@ -3694,6 +3686,11 @@ static tng_function_status tng_frame_set_block_read } } } + else + { + /* Seek to the end of the block */ + fseeko(tng_data->input_file, start_pos + block->block_contents_size, SEEK_SET); + } /* If the output file and the input files are the same the number of * frames in the file are the same number as has just been read. @@ -3897,11 +3894,11 @@ static tng_function_status tng_trajectory_mapping_block_read tng_gen_block_t block, const char hash_mode) { - int64_t start_pos, curr_file_pos, i; + int64_t start_pos, i; tng_trajectory_frame_set_t frame_set = &tng_data->current_trajectory_frame_set; tng_particle_mapping_t mapping, mappings; - char hash[TNG_MD5_HASH_LEN], *temp_data; + char hash[TNG_MD5_HASH_LEN]; md5_state_t md5_state; if(tng_input_file_init(tng_data) != TNG_SUCCESS) @@ -3991,27 +3988,8 @@ static tng_function_status tng_trajectory_mapping_block_read { /* If there is data left in the block that the current version of the library * cannot interpret still read that to generate the MD5 hash. */ - curr_file_pos = ftello(tng_data->input_file); - if(curr_file_pos < start_pos + block->block_contents_size) - { - temp_data = malloc(start_pos + block->block_contents_size - curr_file_pos); - if(!temp_data) - { - fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n", - start_pos + block->block_contents_size - curr_file_pos, __FILE__, __LINE__); - return(TNG_CRITICAL); - } - if(fread(temp_data, start_pos + block->block_contents_size - curr_file_pos, - 1, tng_data->input_file) == 0) - { - fprintf(stderr, "TNG library: Cannot read remaining part of block to generate MD5 sum. %s: %d\n", __FILE__, __LINE__); - free(temp_data); - return(TNG_CRITICAL); - } - md5_append(&md5_state, (md5_byte_t *)temp_data, - start_pos + block->block_contents_size - curr_file_pos); - free(temp_data); - } + tng_md5_remaining_append(tng_data, block, start_pos, &md5_state); + md5_finish(&md5_state, (md5_byte_t *)hash); if(strncmp(block->md5_hash, "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0", TNG_MD5_HASH_LEN) != 0) { @@ -4022,8 +4000,11 @@ static tng_function_status tng_trajectory_mapping_block_read } } } - - fseeko(tng_data->input_file, start_pos + block->block_contents_size, SEEK_SET); + else + { + /* Seek to the end of the block */ + fseeko(tng_data->input_file, start_pos + block->block_contents_size, SEEK_SET); + } return(TNG_SUCCESS); } @@ -6377,12 +6358,12 @@ static tng_function_status tng_data_block_contents_read tng_gen_block_t block, const char hash_mode) { - int64_t start_pos, curr_file_pos, n_values, codec_id, n_frames, first_frame_with_data; + int64_t start_pos, n_values, codec_id, n_frames, first_frame_with_data; int64_t remaining_len, stride_length, block_n_particles, num_first_particle; double multiplier; char datatype, dependency, sparse_data; tng_function_status stat = TNG_SUCCESS; - char hash[TNG_MD5_HASH_LEN], *temp_data; + char hash[TNG_MD5_HASH_LEN]; md5_state_t md5_state; if(tng_input_file_init(tng_data) != TNG_SUCCESS) @@ -6435,27 +6416,8 @@ static tng_function_status tng_data_block_contents_read { /* If there is data left in the block that the current version of the library * cannot interpret still read that to generate the MD5 hash. */ - curr_file_pos = ftello(tng_data->input_file); - if(curr_file_pos < start_pos + block->block_contents_size) - { - temp_data = malloc(start_pos + block->block_contents_size - curr_file_pos); - if(!temp_data) - { - fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n", - start_pos + block->block_contents_size - curr_file_pos, __FILE__, __LINE__); - return(TNG_CRITICAL); - } - if(fread(temp_data, start_pos + block->block_contents_size - curr_file_pos, - 1, tng_data->input_file) == 0) - { - fprintf(stderr, "TNG library: Cannot read remaining part of block to generate MD5 sum. %s: %d\n", __FILE__, __LINE__); - free(temp_data); - return(TNG_CRITICAL); - } - md5_append(&md5_state, (md5_byte_t *)temp_data, - start_pos + block->block_contents_size - curr_file_pos); - free(temp_data); - } + tng_md5_remaining_append(tng_data, block, start_pos, &md5_state); + md5_finish(&md5_state, (md5_byte_t *)hash); if(strncmp(block->md5_hash, "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0", TNG_MD5_HASH_LEN) != 0) { @@ -6466,8 +6428,11 @@ static tng_function_status tng_data_block_contents_read } } } - - fseeko(tng_data->input_file, start_pos + block->block_contents_size, SEEK_SET); + else + { + /* Seek to the end of the block */ + fseeko(tng_data->input_file, start_pos + block->block_contents_size, SEEK_SET); + } return(stat); } |