| -rw-r--r-- | src/aggregator.c | 3 | ||||
| -rw-r--r-- | src/assign/assign_protein_type.c | 110 | ||||
| -rw-r--r-- | src/load/load_influenza_aa_dat.c | 13 | ||||
| -rw-r--r-- | src/load/load_influenza_aa_dat.h | 2 | ||||
| -rw-r--r-- | src/load/load_influenza_faa.c | 30 | ||||
| -rw-r--r-- | src/load/load_influenza_faa.h | 2 | ||||
| -rw-r--r-- | src/model/gi_type_data_init.c | 4 | ||||
| -rw-r--r-- | src/model/gi_type_data_init.h | 4 | ||||
| -rw-r--r-- | src/model/sequence_data_init.c | 18 | ||||
| -rw-r--r-- | src/model/sequence_data_init.h | 6 |
10 files changed, 99 insertions, 93 deletions
diff --git a/src/load/load_influenza_faa.c b/src/load/load_influenza_faa.c index 04bf05b..80eb3ae 100644 --- a/src/load/load_influenza_faa.c +++ b/src/load/load_influenza_faa.c @@ -8,7 +8,7 @@ #include <stdlib.h> void -load_influenza_faa (hid_t file_id, const char* file_name) +load_influenza_faa (hid_t file_id, const char *file_name) { size_t dst_size; size_t dst_offset[SEQUENCE_DATA_FIELD_NUM]; @@ -16,7 +16,7 @@ load_influenza_faa (hid_t file_id, const char* file_name) hid_t field_type[SEQUENCE_DATA_FIELD_NUM]; sequence_data_init (&dst_size, dst_offset, dst_sizes, field_type); - + hsize_t chunk_size = 10; int *fill_data = NULL; int compress = 0; @@ -31,17 +31,17 @@ load_influenza_faa (hid_t file_id, const char* file_name) while (getline (&line, &len, dat) != -1) { - current_line++; + current_line++; // Header line. if (line[0] == '>') { char *running = strdup (line); char *token = NULL; - + // Eat the ">gi". strsep (&running, "|"); - + // GI value. token = strsep (&running, "|"); p_data.gi = atoi (token); @@ -50,13 +50,13 @@ load_influenza_faa (hid_t file_id, const char* file_name) strsep (&running, "|"); // GB value. - strncpy (p_data.gb, strsep(&running, "|"), sizeof (p_data.gb)); + strncpy (p_data.gb, strsep (&running, "|"), sizeof (p_data.gb)); // Description value. strncpy (p_data.description, strsep (&running, "|"), sizeof (p_data.description)); - const char* sequence_data_field_names[SEQUENCE_DATA_FIELD_NUM] = + const char *sequence_data_field_names[SEQUENCE_DATA_FIELD_NUM] = SEQUENCE_DATA_FIELD_NAMES; if (current_line == 1) @@ -68,12 +68,14 @@ load_influenza_faa (hid_t file_id, const char* file_name) { hsize_t nfields = 0; hsize_t nrecords = 0; - herr_t status = H5TBget_table_info (file_id, "influenza.faa", &nfields, - &nrecords); + herr_t status = + H5TBget_table_info (file_id, "influenza.faa", &nfields, + &nrecords); if (status < 0) check_h5_error (status, __FILE__, __LINE__); - status = H5TBdelete_record (file_id, "influenza.faa", 0, nrecords); + status = + H5TBdelete_record (file_id, "influenza.faa", 0, nrecords); if (status < 0) check_h5_error (status, __FILE__, __LINE__); @@ -92,9 +94,11 @@ load_influenza_faa (hid_t file_id, const char* file_name) herr_t status = H5TBmake_table ("influenza.faa", file_id, "influenza.faa", SEQUENCE_DATA_FIELD_NUM, 1, - dst_size, sequence_data_field_names, + dst_size, + sequence_data_field_names, dst_offset, field_type, - chunk_size, fill_data, compress, + chunk_size, fill_data, + compress, &p_data); if (status < 0) check_h5_error (status, __FILE__, __LINE__); @@ -114,7 +118,7 @@ load_influenza_faa (hid_t file_id, const char* file_name) free (running); } - + } if (line) |
