-rw-r--r-- | src/aggregator.c | 10 | ||||
-rw-r--r-- | src/assign/assign_protein_type.c | 24 | ||||
-rw-r--r-- | src/error/check_h5_error.c | 2 | ||||
-rw-r--r-- | src/error/check_h5_error.h | 2 | ||||
-rw-r--r-- | src/load/load_influenza_aa_dat.c | 12 | ||||
-rw-r--r-- | src/load/load_influenza_faa.c | 12 | ||||
-rw-r--r-- | src/updator.c | 4 |
7 files changed, 35 insertions, 31 deletions
diff --git a/src/assign/assign_protein_type.c b/src/assign/assign_protein_type.c index 1df4c8d..065880f 100644 --- a/src/assign/assign_protein_type.c +++ b/src/assign/assign_protein_type.c | |||
@@ -19,12 +19,12 @@ | |||
19 | /* | 19 | /* |
20 | * BLAST database containing all of the influenza protein sequences. | 20 | * BLAST database containing all of the influenza protein sequences. |
21 | */ | 21 | */ |
22 | #define SEQDB "/home/don/exp004/influenzadb/influenzadb" | 22 | #define SEQDB "/u/ac/dpellegr/Documents/exp004/influenzadb/influenzadb" |
23 | 23 | ||
24 | /* | 24 | /* |
25 | * BLAST reference database of prototypical protein types. | 25 | * BLAST reference database of prototypical protein types. |
26 | */ | 26 | */ |
27 | #define REFDB "/home/don/exp004/influenzadb/proteinnames" | 27 | #define REFDB "/u/ac/dpellegr/Documents/exp004/influenzadb/proteinnames" |
28 | 28 | ||
29 | #define BUFFER_LEN 50 | 29 | #define BUFFER_LEN 50 |
30 | 30 | ||
@@ -68,7 +68,7 @@ assign_protein_type (hid_t file_id) | |||
68 | herr_t status = H5TBget_table_info (file_id, "influenza.faa", &faa_nfields, | 68 | herr_t status = H5TBget_table_info (file_id, "influenza.faa", &faa_nfields, |
69 | &faa_nrecords); | 69 | &faa_nrecords); |
70 | if (status < 0) | 70 | if (status < 0) |
71 | check_h5_error (status, __FILE__, __LINE__); | 71 | check_h5_error (__FILE__, __LINE__); |
72 | 72 | ||
73 | sequence_data *faa_buf = malloc (sizeof (sequence_data) * faa_nrecords); | 73 | sequence_data *faa_buf = malloc (sizeof (sequence_data) * faa_nrecords); |
74 | 74 | ||
@@ -81,7 +81,7 @@ assign_protein_type (hid_t file_id) | |||
81 | status = H5TBread_table (file_id, "influenza.faa", faa_size, faa_offset, | 81 | status = H5TBread_table (file_id, "influenza.faa", faa_size, faa_offset, |
82 | faa_sizes, faa_buf); | 82 | faa_sizes, faa_buf); |
83 | if (status < 0) | 83 | if (status < 0) |
84 | check_h5_error (status, __FILE__, __LINE__); | 84 | check_h5_error (__FILE__, __LINE__); |
85 | 85 | ||
86 | /* | 86 | /* |
87 | * Allocate memory for the new table. | 87 | * Allocate memory for the new table. |
@@ -115,7 +115,7 @@ assign_protein_type (hid_t file_id) | |||
115 | status = H5TBget_table_info (file_id, "gi_type_data", &gi_nfields, | 115 | status = H5TBget_table_info (file_id, "gi_type_data", &gi_nfields, |
116 | &gi_nrecords); | 116 | &gi_nrecords); |
117 | if (status < 0) | 117 | if (status < 0) |
118 | check_h5_error (status, __FILE__, __LINE__); | 118 | check_h5_error (__FILE__, __LINE__); |
119 | 119 | ||
120 | printf (" Using gi_type_data cache of %i records.\n", | 120 | printf (" Using gi_type_data cache of %i records.\n", |
121 | (int) gi_nrecords); | 121 | (int) gi_nrecords); |
@@ -125,11 +125,11 @@ assign_protein_type (hid_t file_id) | |||
125 | status = H5TBread_table (file_id, "gi_type_data", gi_size, gi_offset, | 125 | status = H5TBread_table (file_id, "gi_type_data", gi_size, gi_offset, |
126 | gi_sizes, old_buf); | 126 | gi_sizes, old_buf); |
127 | if (status < 0) | 127 | if (status < 0) |
128 | check_h5_error (status, __FILE__, __LINE__); | 128 | check_h5_error (__FILE__, __LINE__); |
129 | 129 | ||
130 | status = H5TBdelete_record (file_id, "gi_type_data", 0, gi_nrecords); | 130 | status = H5TBdelete_record (file_id, "gi_type_data", 0, gi_nrecords); |
131 | if (status < 0) | 131 | if (status < 0) |
132 | check_h5_error (status, __FILE__, __LINE__); | 132 | check_h5_error (__FILE__, __LINE__); |
133 | 133 | ||
134 | } | 134 | } |
135 | 135 | ||
@@ -155,7 +155,7 @@ assign_protein_type (hid_t file_id) | |||
155 | gi_offset, gi_field_type, | 155 | gi_offset, gi_field_type, |
156 | chunk_size, fill_data, compress, NULL); | 156 | chunk_size, fill_data, compress, NULL); |
157 | if (status < 0) | 157 | if (status < 0) |
158 | check_h5_error (status, __FILE__, __LINE__); | 158 | check_h5_error (__FILE__, __LINE__); |
159 | 159 | ||
160 | } | 160 | } |
161 | 161 | ||
@@ -295,11 +295,11 @@ assign_protein_type (hid_t file_id) | |||
295 | gi_size, gi_offset, gi_sizes, | 295 | gi_size, gi_offset, gi_sizes, |
296 | &new_buf[i - 1000]); | 296 | &new_buf[i - 1000]); |
297 | if (status < 0) | 297 | if (status < 0) |
298 | check_h5_error (status, __FILE__, __LINE__); | 298 | check_h5_error (__FILE__, __LINE__); |
299 | 299 | ||
300 | status = H5Fflush (file_id, H5F_SCOPE_GLOBAL); | 300 | status = H5Fflush (file_id, H5F_SCOPE_GLOBAL); |
301 | if (status < 0) | 301 | if (status < 0) |
302 | check_h5_error (status, __FILE__, __LINE__); | 302 | check_h5_error (__FILE__, __LINE__); |
303 | 303 | ||
304 | written = i; | 304 | written = i; |
305 | 305 | ||
@@ -326,11 +326,11 @@ assign_protein_type (hid_t file_id) | |||
326 | } | 326 | } |
327 | 327 | ||
328 | if (status < 0) | 328 | if (status < 0) |
329 | check_h5_error (status, __FILE__, __LINE__); | 329 | check_h5_error (__FILE__, __LINE__); |
330 | 330 | ||
331 | status = H5Fflush (file_id, H5F_SCOPE_GLOBAL); | 331 | status = H5Fflush (file_id, H5F_SCOPE_GLOBAL); |
332 | if (status < 0) | 332 | if (status < 0) |
333 | check_h5_error (status, __FILE__, __LINE__); | 333 | check_h5_error (__FILE__, __LINE__); |
334 | 334 | ||
335 | free (faa_buf); | 335 | free (faa_buf); |
336 | free (old_buf); | 336 | free (old_buf); |