-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 @@ | |||
8 | #include <stdlib.h> | 8 | #include <stdlib.h> |
9 | 9 | ||
10 | void | 10 | void |
11 | load_influenza_faa (hid_t file_id, const char* file_name) | 11 | load_influenza_faa (hid_t file_id, const char *file_name) |
12 | { | 12 | { |
13 | size_t dst_size; | 13 | size_t dst_size; |
14 | size_t dst_offset[SEQUENCE_DATA_FIELD_NUM]; | 14 | size_t dst_offset[SEQUENCE_DATA_FIELD_NUM]; |
@@ -16,7 +16,7 @@ load_influenza_faa (hid_t file_id, const char* file_name) | |||
16 | hid_t field_type[SEQUENCE_DATA_FIELD_NUM]; | 16 | hid_t field_type[SEQUENCE_DATA_FIELD_NUM]; |
17 | 17 | ||
18 | sequence_data_init (&dst_size, dst_offset, dst_sizes, field_type); | 18 | sequence_data_init (&dst_size, dst_offset, dst_sizes, field_type); |
19 | 19 | ||
20 | hsize_t chunk_size = 10; | 20 | hsize_t chunk_size = 10; |
21 | int *fill_data = NULL; | 21 | int *fill_data = NULL; |
22 | int compress = 0; | 22 | int compress = 0; |
@@ -31,17 +31,17 @@ load_influenza_faa (hid_t file_id, const char* file_name) | |||
31 | 31 | ||
32 | while (getline (&line, &len, dat) != -1) | 32 | while (getline (&line, &len, dat) != -1) |
33 | { | 33 | { |
34 | current_line++; | 34 | current_line++; |
35 | 35 | ||
36 | // Header line. | 36 | // Header line. |
37 | if (line[0] == '>') | 37 | if (line[0] == '>') |
38 | { | 38 | { |
39 | char *running = strdup (line); | 39 | char *running = strdup (line); |
40 | char *token = NULL; | 40 | char *token = NULL; |
41 | 41 | ||
42 | // Eat the ">gi". | 42 | // Eat the ">gi". |
43 | strsep (&running, "|"); | 43 | strsep (&running, "|"); |
44 | 44 | ||
45 | // GI value. | 45 | // GI value. |
46 | token = strsep (&running, "|"); | 46 | token = strsep (&running, "|"); |
47 | p_data.gi = atoi (token); | 47 | p_data.gi = atoi (token); |
@@ -50,13 +50,13 @@ load_influenza_faa (hid_t file_id, const char* file_name) | |||
50 | strsep (&running, "|"); | 50 | strsep (&running, "|"); |
51 | 51 | ||
52 | // GB value. | 52 | // GB value. |
53 | strncpy (p_data.gb, strsep(&running, "|"), sizeof (p_data.gb)); | 53 | strncpy (p_data.gb, strsep (&running, "|"), sizeof (p_data.gb)); |
54 | 54 | ||
55 | // Description value. | 55 | // Description value. |
56 | strncpy (p_data.description, strsep (&running, "|"), | 56 | strncpy (p_data.description, strsep (&running, "|"), |
57 | sizeof (p_data.description)); | 57 | sizeof (p_data.description)); |
58 | 58 | ||
59 | const char* sequence_data_field_names[SEQUENCE_DATA_FIELD_NUM] = | 59 | const char *sequence_data_field_names[SEQUENCE_DATA_FIELD_NUM] = |
60 | SEQUENCE_DATA_FIELD_NAMES; | 60 | SEQUENCE_DATA_FIELD_NAMES; |
61 | 61 | ||
62 | if (current_line == 1) | 62 | if (current_line == 1) |
@@ -68,12 +68,14 @@ load_influenza_faa (hid_t file_id, const char* file_name) | |||
68 | { | 68 | { |
69 | hsize_t nfields = 0; | 69 | hsize_t nfields = 0; |
70 | hsize_t nrecords = 0; | 70 | hsize_t nrecords = 0; |
71 | herr_t status = H5TBget_table_info (file_id, "influenza.faa", &nfields, | 71 | herr_t status = |
72 | &nrecords); | 72 | H5TBget_table_info (file_id, "influenza.faa", &nfields, |
73 | &nrecords); | ||
73 | if (status < 0) | 74 | if (status < 0) |
74 | check_h5_error (status, __FILE__, __LINE__); | 75 | check_h5_error (status, __FILE__, __LINE__); |
75 | 76 | ||
76 | status = H5TBdelete_record (file_id, "influenza.faa", 0, nrecords); | 77 | status = |
78 | H5TBdelete_record (file_id, "influenza.faa", 0, nrecords); | ||
77 | if (status < 0) | 79 | if (status < 0) |
78 | check_h5_error (status, __FILE__, __LINE__); | 80 | check_h5_error (status, __FILE__, __LINE__); |
79 | 81 | ||
@@ -92,9 +94,11 @@ load_influenza_faa (hid_t file_id, const char* file_name) | |||
92 | herr_t status = H5TBmake_table ("influenza.faa", file_id, | 94 | herr_t status = H5TBmake_table ("influenza.faa", file_id, |
93 | "influenza.faa", | 95 | "influenza.faa", |
94 | SEQUENCE_DATA_FIELD_NUM, 1, | 96 | SEQUENCE_DATA_FIELD_NUM, 1, |
95 | dst_size, sequence_data_field_names, | 97 | dst_size, |
98 | sequence_data_field_names, | ||
96 | dst_offset, field_type, | 99 | dst_offset, field_type, |
97 | chunk_size, fill_data, compress, | 100 | chunk_size, fill_data, |
101 | compress, | ||
98 | &p_data); | 102 | &p_data); |
99 | if (status < 0) | 103 | if (status < 0) |
100 | check_h5_error (status, __FILE__, __LINE__); | 104 | check_h5_error (status, __FILE__, __LINE__); |
@@ -114,7 +118,7 @@ load_influenza_faa (hid_t file_id, const char* file_name) | |||
114 | free (running); | 118 | free (running); |
115 | 119 | ||
116 | } | 120 | } |
117 | 121 | ||
118 | } | 122 | } |
119 | 123 | ||
120 | if (line) | 124 | if (line) |