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-rw-r--r--src/aggregator.c10
-rw-r--r--src/assign/assign_protein_type.c24
-rw-r--r--src/error/check_h5_error.c2
-rw-r--r--src/error/check_h5_error.h2
-rw-r--r--src/load/load_influenza_aa_dat.c12
-rw-r--r--src/load/load_influenza_faa.c12
-rw-r--r--src/updator.c4
7 files changed, 35 insertions, 31 deletions
diff --git a/src/aggregator.c b/src/aggregator.c
index 4c4ca8e..200de7d 100644
--- a/src/aggregator.c
+++ b/src/aggregator.c
@@ -9,8 +9,8 @@
9#include <stdio.h>9#include <stdio.h>
1010
11#define H5FILE "influenza.h5"11#define H5FILE "influenza.h5"
12#define INFLUENZA_AA_DAT "/home/don/exp004/genomes/INFLUENZA/influenza_aa.dat"12#define INFLUENZA_AA_DAT "/u/ac/dpellegr/Documents/exp004/genomes/INFLUENZA/influenza_aa.dat"
13#define INFLUENZA_FAA "/home/don/exp004/genomes/INFLUENZA/influenza.faa"13#define INFLUENZA_FAA "/u/ac/dpellegr/Documents/exp004/genomes/INFLUENZA/influenza.faa"
1414
15int15int
16main ()16main ()
@@ -25,14 +25,14 @@ main ()
25 {25 {
26 file_id = H5Fcreate (H5FILE, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);26 file_id = H5Fcreate (H5FILE, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
27 if (file_id < 0)27 if (file_id < 0)
28 check_h5_error (file_id, __FILE__, __LINE__);28 check_h5_error (__FILE__, __LINE__);
29 }29 }
30 else30 else
31 {31 {
32 fclose (f);32 fclose (f);
33 file_id = H5Fopen (H5FILE, H5F_ACC_RDWR, H5P_DEFAULT);33 file_id = H5Fopen (H5FILE, H5F_ACC_RDWR, H5P_DEFAULT);
34 if (file_id < 0)34 if (file_id < 0)
35 check_h5_error (file_id, __FILE__, __LINE__);35 check_h5_error (__FILE__, __LINE__);
36 }36 }
3737
38 /*38 /*
@@ -53,7 +53,7 @@ main ()
53 */53 */
54 herr_t status = H5Fclose (file_id);54 herr_t status = H5Fclose (file_id);
55 if (status < 0)55 if (status < 0)
56 check_h5_error (status, __FILE__, __LINE__);56 check_h5_error (__FILE__, __LINE__);
5757
58 return 0;58 return 0;
59}59}
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"
2323
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"
2828
29#define BUFFER_LEN 5029#define BUFFER_LEN 50
3030
@@ -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__);
7272
73 sequence_data *faa_buf = malloc (sizeof (sequence_data) * faa_nrecords);73 sequence_data *faa_buf = malloc (sizeof (sequence_data) * faa_nrecords);
7474
@@ -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__);
8585
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__);
119119
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__);
129129
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__);
133133
134 }134 }
135135
@@ -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__);
159159
160 }160 }
161161
@@ -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__);
299299
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__);
303303
304 written = i;304 written = i;
305305
@@ -326,11 +326,11 @@ assign_protein_type (hid_t file_id)
326 }326 }
327327
328 if (status < 0)328 if (status < 0)
329 check_h5_error (status, __FILE__, __LINE__);329 check_h5_error (__FILE__, __LINE__);
330330
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__);
334334
335 free (faa_buf);335 free (faa_buf);
336 free (old_buf);336 free (old_buf);
diff --git a/src/error/check_h5_error.c b/src/error/check_h5_error.c
index d90b21f..30183fe 100644
--- a/src/error/check_h5_error.c
+++ b/src/error/check_h5_error.c
@@ -3,7 +3,7 @@
3#include <stdlib.h>3#include <stdlib.h>
44
5void5void
6check_h5_error (herr_t status, const char *filename, unsigned int linenum)6check_h5_error (const char *filename, unsigned int linenum)
7{7{
8 error_at_line (EXIT_FAILURE, 0, filename, linenum,8 error_at_line (EXIT_FAILURE, 0, filename, linenum,
9 "An error has been reported by the HDF5 API.");9 "An error has been reported by the HDF5 API.");
diff --git a/src/error/check_h5_error.h b/src/error/check_h5_error.h
index e460e97..fa93c6b 100644
--- a/src/error/check_h5_error.h
+++ b/src/error/check_h5_error.h
@@ -7,6 +7,6 @@
7 * Handle errors from the HDF5 API.7 * Handle errors from the HDF5 API.
8 */8 */
9void9void
10check_h5_error (herr_t status, const char *filename, unsigned int linenum);10check_h5_error (const char *filename, unsigned int linenum);
1111
12#endif // CHECK_H5_ERROR_H12#endif // CHECK_H5_ERROR_H
diff --git a/src/load/load_influenza_aa_dat.c b/src/load/load_influenza_aa_dat.c
index b50fcab..bbd4f8b 100644
--- a/src/load/load_influenza_aa_dat.c
+++ b/src/load/load_influenza_aa_dat.c
@@ -5,12 +5,14 @@
5 * todo: Handle NULL values occuring in numeric fields.5 * todo: Handle NULL values occuring in numeric fields.
6 */6 */
77
8#define _GNU_SOURCE
8#include "load_influenza_aa_dat.h"9#include "load_influenza_aa_dat.h"
9#include "error/check_error.h"10#include "error/check_error.h"
10#include "error/check_h5_error.h"11#include "error/check_h5_error.h"
11#include <hdf5_hl.h>12#include <hdf5_hl.h>
12#include <string.h>13#include <string.h>
13#include <stdlib.h>14#include <stdlib.h>
15#include <stdio.h>
1416
15#define NFIELDS (hsize_t) 1117#define NFIELDS (hsize_t) 11
1618
@@ -223,18 +225,18 @@ load_influenza_aa_dat (hid_t file_id, const char *file_name)
223 herr_t status = H5TBget_table_info (file_id, "influenza_aa.dat",225 herr_t status = H5TBget_table_info (file_id, "influenza_aa.dat",
224 &nfields, &nrecords);226 &nfields, &nrecords);
225 if (status < 0)227 if (status < 0)
226 check_h5_error (status, __FILE__, __LINE__);228 check_h5_error (__FILE__, __LINE__);
227229
228 status =230 status =
229 H5TBdelete_record (file_id, "influenza_aa.dat", 0, nrecords);231 H5TBdelete_record (file_id, "influenza_aa.dat", 0, nrecords);
230 if (status < 0)232 if (status < 0)
231 check_h5_error (status, __FILE__, __LINE__);233 check_h5_error (__FILE__, __LINE__);
232234
233 status =235 status =
234 H5TBappend_records (file_id, "influenza_aa.dat", 1, dst_size,236 H5TBappend_records (file_id, "influenza_aa.dat", 1, dst_size,
235 dst_offset, dst_sizes, &p_data);237 dst_offset, dst_sizes, &p_data);
236 if (status < 0)238 if (status < 0)
237 check_h5_error (status, __FILE__, __LINE__);239 check_h5_error (__FILE__, __LINE__);
238 }240 }
239241
240 /*242 /*
@@ -250,7 +252,7 @@ load_influenza_aa_dat (hid_t file_id, const char *file_name)
250 chunk_size, fill_data, compress,252 chunk_size, fill_data, compress,
251 &p_data);253 &p_data);
252 if (status < 0)254 if (status < 0)
253 check_h5_error (status, __FILE__, __LINE__);255 check_h5_error (__FILE__, __LINE__);
254 }256 }
255 }257 }
256258
@@ -260,7 +262,7 @@ load_influenza_aa_dat (hid_t file_id, const char *file_name)
260 H5TBappend_records (file_id, "influenza_aa.dat", 1, dst_size,262 H5TBappend_records (file_id, "influenza_aa.dat", 1, dst_size,
261 dst_offset, dst_sizes, &p_data);263 dst_offset, dst_sizes, &p_data);
262 if (status < 0)264 if (status < 0)
263 check_h5_error (status, __FILE__, __LINE__);265 check_h5_error (__FILE__, __LINE__);
264 }266 }
265267
266 if (running)268 if (running)
diff --git a/src/load/load_influenza_faa.c b/src/load/load_influenza_faa.c
index 80eb3ae..0026d11 100644
--- a/src/load/load_influenza_faa.c
+++ b/src/load/load_influenza_faa.c
@@ -1,3 +1,4 @@
1#define _GNU_SOURCE
1#include "error/check_error.h"2#include "error/check_error.h"
2#include "error/check_h5_error.h"3#include "error/check_h5_error.h"
3#include "load_influenza_faa.h"4#include "load_influenza_faa.h"
@@ -6,6 +7,7 @@
6#include <hdf5_hl.h>7#include <hdf5_hl.h>
7#include <string.h>8#include <string.h>
8#include <stdlib.h>9#include <stdlib.h>
10#include <stdio.h>
911
10void12void
11load_influenza_faa (hid_t file_id, const char *file_name)13load_influenza_faa (hid_t file_id, const char *file_name)
@@ -72,18 +74,18 @@ load_influenza_faa (hid_t file_id, const char *file_name)
72 H5TBget_table_info (file_id, "influenza.faa", &nfields,74 H5TBget_table_info (file_id, "influenza.faa", &nfields,
73 &nrecords);75 &nrecords);
74 if (status < 0)76 if (status < 0)
75 check_h5_error (status, __FILE__, __LINE__);77 check_h5_error (__FILE__, __LINE__);
7678
77 status =79 status =
78 H5TBdelete_record (file_id, "influenza.faa", 0, nrecords);80 H5TBdelete_record (file_id, "influenza.faa", 0, nrecords);
79 if (status < 0)81 if (status < 0)
80 check_h5_error (status, __FILE__, __LINE__);82 check_h5_error (__FILE__, __LINE__);
8183
82 status =84 status =
83 H5TBappend_records (file_id, "influenza.faa", 1, dst_size,85 H5TBappend_records (file_id, "influenza.faa", 1, dst_size,
84 dst_offset, dst_sizes, &p_data);86 dst_offset, dst_sizes, &p_data);
85 if (status < 0)87 if (status < 0)
86 check_h5_error (status, __FILE__, __LINE__);88 check_h5_error (__FILE__, __LINE__);
87 }89 }
8890
89 /*91 /*
@@ -101,7 +103,7 @@ load_influenza_faa (hid_t file_id, const char *file_name)
101 compress,103 compress,
102 &p_data);104 &p_data);
103 if (status < 0)105 if (status < 0)
104 check_h5_error (status, __FILE__, __LINE__);106 check_h5_error (__FILE__, __LINE__);
105 }107 }
106 }108 }
107109
@@ -111,7 +113,7 @@ load_influenza_faa (hid_t file_id, const char *file_name)
111 H5TBappend_records (file_id, "influenza.faa", 1, dst_size,113 H5TBappend_records (file_id, "influenza.faa", 1, dst_size,
112 dst_offset, dst_sizes, &p_data);114 dst_offset, dst_sizes, &p_data);
113 if (status < 0)115 if (status < 0)
114 check_h5_error (status, __FILE__, __LINE__);116 check_h5_error (__FILE__, __LINE__);
115 }117 }
116118
117 if (running)119 if (running)
diff --git a/src/updator.c b/src/updator.c
index 9a5ad18..f93e205 100644
--- a/src/updator.c
+++ b/src/updator.c
@@ -17,7 +17,7 @@ main ()
17 */17 */
18 hid_t file_id = H5Fopen (FILE, H5F_ACC_RDWR, H5P_DEFAULT);18 hid_t file_id = H5Fopen (FILE, H5F_ACC_RDWR, H5P_DEFAULT);
19 if (file_id < 0)19 if (file_id < 0)
20 check_h5_error (file_id, __FILE__, __LINE__);20 check_h5_error (__FILE__, __LINE__);
2121
22 /*22 /*
23 * Assign protein type values to the sequence records.23 * Assign protein type values to the sequence records.
@@ -29,7 +29,7 @@ main ()
29 */29 */
30 herr_t status = H5Fclose (file_id);30 herr_t status = H5Fclose (file_id);
31 if (status < 0)31 if (status < 0)
32 check_h5_error (status, __FILE__, __LINE__);32 check_h5_error (__FILE__, __LINE__);
3333
34 return 0;34 return 0;
35}35}

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