-rw-r--r-- | src/aggregator.c | 34 | ||||
-rw-r--r-- | src/assign/assign_protein_type.c | 141 | ||||
-rw-r--r-- | src/load/load_influenza_aa_dat.c | 53 | ||||
-rw-r--r-- | src/load/load_influenza_aa_dat.h | 2 | ||||
-rw-r--r-- | src/load/load_influenza_faa.c | 53 | ||||
-rw-r--r-- | src/load/load_influenza_faa.h | 2 | ||||
-rw-r--r-- | src/updator.c | 2 |
7 files changed, 201 insertions, 86 deletions
diff --git a/src/load/load_influenza_faa.c b/src/load/load_influenza_faa.c index a217989..04bf05b 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) | 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]; |
@@ -22,8 +22,7 @@ load_influenza_faa (hid_t file_id) | |||
22 | int compress = 0; | 22 | int compress = 0; |
23 | 23 | ||
24 | sequence_data p_data; | 24 | sequence_data p_data; |
25 | FILE *dat = fopen ("/home/don/exp004/genomes/INFLUENZA/influenza.faa", | 25 | FILE *dat = fopen (file_name, "r"); |
26 | "r"); | ||
27 | if (dat == NULL) | 26 | if (dat == NULL) |
28 | check_error (__FILE__, __LINE__); | 27 | check_error (__FILE__, __LINE__); |
29 | char *line = NULL; | 28 | char *line = NULL; |
@@ -62,16 +61,46 @@ load_influenza_faa (hid_t file_id) | |||
62 | 61 | ||
63 | if (current_line == 1) | 62 | if (current_line == 1) |
64 | { | 63 | { |
65 | herr_t status = H5TBmake_table ("influenza.faa", file_id, | 64 | /* |
66 | "influenza.faa", | 65 | * Dataset already exists. Purge it. |
67 | SEQUENCE_DATA_FIELD_NUM, 1, | 66 | */ |
68 | dst_size, sequence_data_field_names, | 67 | if (H5LTfind_dataset (file_id, "influenza.faa") == 1) |
69 | dst_offset, field_type, | 68 | { |
70 | chunk_size, fill_data, compress, | 69 | hsize_t nfields = 0; |
71 | &p_data); | 70 | hsize_t nrecords = 0; |
72 | if (status < 0) | 71 | herr_t status = H5TBget_table_info (file_id, "influenza.faa", &nfields, |
73 | check_h5_error (status, __FILE__, __LINE__); | 72 | &nrecords); |
73 | if (status < 0) | ||
74 | check_h5_error (status, __FILE__, __LINE__); | ||
75 | |||
76 | status = H5TBdelete_record (file_id, "influenza.faa", 0, nrecords); | ||
77 | if (status < 0) | ||
78 | check_h5_error (status, __FILE__, __LINE__); | ||
79 | |||
80 | status = | ||
81 | H5TBappend_records (file_id, "influenza.faa", 1, dst_size, | ||
82 | dst_offset, dst_sizes, &p_data); | ||
83 | if (status < 0) | ||
84 | check_h5_error (status, __FILE__, __LINE__); | ||
85 | } | ||
86 | |||
87 | /* | ||
88 | * Dataset does not exist. Create it. | ||
89 | */ | ||
90 | else | ||
91 | { | ||
92 | herr_t status = H5TBmake_table ("influenza.faa", file_id, | ||
93 | "influenza.faa", | ||
94 | SEQUENCE_DATA_FIELD_NUM, 1, | ||
95 | dst_size, sequence_data_field_names, | ||
96 | dst_offset, field_type, | ||
97 | chunk_size, fill_data, compress, | ||
98 | &p_data); | ||
99 | if (status < 0) | ||
100 | check_h5_error (status, __FILE__, __LINE__); | ||
101 | } | ||
74 | } | 102 | } |
103 | |||
75 | else | 104 | else |
76 | { | 105 | { |
77 | herr_t status = | 106 | herr_t status = |