summaryrefslogtreecommitdiffstats
Unidiff
-rw-r--r--src/aggregator.c3
-rw-r--r--src/assign/assign_protein_type.c110
-rw-r--r--src/load/load_influenza_aa_dat.c13
-rw-r--r--src/load/load_influenza_aa_dat.h2
-rw-r--r--src/load/load_influenza_faa.c30
-rw-r--r--src/load/load_influenza_faa.h2
-rw-r--r--src/model/gi_type_data_init.c4
-rw-r--r--src/model/gi_type_data_init.h4
-rw-r--r--src/model/sequence_data_init.c18
-rw-r--r--src/model/sequence_data_init.h6
10 files changed, 99 insertions, 93 deletions
diff --git a/src/aggregator.c b/src/aggregator.c
index c9a03b5..4c4ca8e 100644
--- a/src/aggregator.c
+++ b/src/aggregator.c
@@ -45,8 +45,7 @@ main ()
45 /*45 /*
46 * Load the FASTA protein sequence data file.46 * Load the FASTA protein sequence data file.
47 */47 */
48 printf ("Loading \"influenza.faa\" with contents of %s.\n",48 printf ("Loading \"influenza.faa\" with contents of %s.\n", INFLUENZA_FAA);
49 INFLUENZA_FAA);
50 load_influenza_faa (file_id, INFLUENZA_FAA);49 load_influenza_faa (file_id, INFLUENZA_FAA);
5150
52 /*51 /*
diff --git a/src/assign/assign_protein_type.c b/src/assign/assign_protein_type.c
index 9a0717b..1df4c8d 100644
--- a/src/assign/assign_protein_type.c
+++ b/src/assign/assign_protein_type.c
@@ -70,7 +70,7 @@ assign_protein_type (hid_t file_id)
70 if (status < 0)70 if (status < 0)
71 check_h5_error (status, __FILE__, __LINE__);71 check_h5_error (status, __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
75 size_t faa_size;75 size_t faa_size;
76 size_t faa_offset[SEQUENCE_DATA_FIELD_NUM];76 size_t faa_offset[SEQUENCE_DATA_FIELD_NUM];
@@ -86,7 +86,7 @@ assign_protein_type (hid_t file_id)
86 /*86 /*
87 * Allocate memory for the new table.87 * Allocate memory for the new table.
88 */88 */
89 gi_type_data* new_buf = malloc (sizeof (gi_type_data) * faa_nrecords);89 gi_type_data *new_buf = malloc (sizeof (gi_type_data) * faa_nrecords);
90 if (new_buf == NULL)90 if (new_buf == NULL)
91 check_error (__FILE__, __LINE__);91 check_error (__FILE__, __LINE__);
9292
@@ -101,7 +101,7 @@ assign_protein_type (hid_t file_id)
101 hid_t gi_field_type[GI_TYPE_DATA_FIELD_NUM];101 hid_t gi_field_type[GI_TYPE_DATA_FIELD_NUM];
102 gi_type_data_init (&gi_size, gi_offset, gi_sizes, gi_field_type);102 gi_type_data_init (&gi_size, gi_offset, gi_sizes, gi_field_type);
103103
104 gi_type_data* old_buf = NULL;104 gi_type_data *old_buf = NULL;
105105
106 /*106 /*
107 * If the table is already present read the values into memory and107 * If the table is already present read the values into memory and
@@ -117,10 +117,11 @@ assign_protein_type (hid_t file_id)
117 if (status < 0)117 if (status < 0)
118 check_h5_error (status, __FILE__, __LINE__);118 check_h5_error (status, __FILE__, __LINE__);
119119
120 printf (" Using gi_type_data cache of %i records.\n", (int)gi_nrecords);120 printf (" Using gi_type_data cache of %i records.\n",
121 121 (int) gi_nrecords);
122 old_buf = malloc (sizeof(gi_type_data) * gi_nrecords);122
123 123 old_buf = malloc (sizeof (gi_type_data) * gi_nrecords);
124
124 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,
125 gi_sizes, old_buf);126 gi_sizes, old_buf);
126 if (status < 0)127 if (status < 0)
@@ -129,18 +130,18 @@ assign_protein_type (hid_t file_id)
129 status = H5TBdelete_record (file_id, "gi_type_data", 0, gi_nrecords);130 status = H5TBdelete_record (file_id, "gi_type_data", 0, gi_nrecords);
130 if (status < 0)131 if (status < 0)
131 check_h5_error (status, __FILE__, __LINE__);132 check_h5_error (status, __FILE__, __LINE__);
132 133
133 }134 }
134135
135 /*136 /*
136 * If the table is not already present create it.137 * If the table is not already present create it.
137 */138 */
138 else139 else
139 { 140 {
140141
141 printf ("Creating gi_type_data.\n");142 printf ("Creating gi_type_data.\n");
142143
143 const char* gi_type_data_field_names[GI_TYPE_DATA_FIELD_NUM] =144 const char *gi_type_data_field_names[GI_TYPE_DATA_FIELD_NUM] =
144 GI_TYPE_DATA_FIELD_NAMES;145 GI_TYPE_DATA_FIELD_NAMES;
145146
146 hsize_t chunk_size = 10;147 hsize_t chunk_size = 10;
@@ -152,8 +153,7 @@ assign_protein_type (hid_t file_id)
152 GI_TYPE_DATA_FIELD_NUM, 0,153 GI_TYPE_DATA_FIELD_NUM, 0,
153 gi_size, gi_type_data_field_names,154 gi_size, gi_type_data_field_names,
154 gi_offset, gi_field_type,155 gi_offset, gi_field_type,
155 chunk_size, fill_data, compress,156 chunk_size, fill_data, compress, NULL);
156 NULL);
157 if (status < 0)157 if (status < 0)
158 check_h5_error (status, __FILE__, __LINE__);158 check_h5_error (status, __FILE__, __LINE__);
159159
@@ -169,7 +169,7 @@ assign_protein_type (hid_t file_id)
169 "Allocation of cache failed.");169 "Allocation of cache failed.");
170 ENTRY e, *ep;170 ENTRY e, *ep;
171171
172 for (int i = 0; i < (int)gi_nrecords; i++)172 for (int i = 0; i < (int) gi_nrecords; i++)
173 {173 {
174 char gi_chr[25];174 char gi_chr[25];
175 snprintf (gi_chr, 25, "%i", old_buf[i].gi);175 snprintf (gi_chr, 25, "%i", old_buf[i].gi);
@@ -183,14 +183,14 @@ assign_protein_type (hid_t file_id)
183 /*183 /*
184 * Assign protein types to records for which the field is empty.184 * Assign protein types to records for which the field is empty.
185 */185 */
186 printf ("Records to process: %i\n", (int)faa_nrecords);186 printf ("Records to process: %i\n", (int) faa_nrecords);
187 int written = 0;187 int written = 0;
188 for (int i = 0; i < (int)faa_nrecords; i++)188 for (int i = 0; i < (int) faa_nrecords; i++)
189 {189 {
190 new_buf[i].gi = faa_buf[i].gi;190 new_buf[i].gi = faa_buf[i].gi;
191 strncpy (new_buf[i].type, "", sizeof (new_buf[i].type));191 strncpy (new_buf[i].type, "", sizeof (new_buf[i].type));
192 strncpy (new_buf[i].protein, "", sizeof (new_buf[i].protein));192 strncpy (new_buf[i].protein, "", sizeof (new_buf[i].protein));
193 193
194 char gi_chr[25];194 char gi_chr[25];
195 snprintf (gi_chr, 25, "%i", faa_buf[i].gi);195 snprintf (gi_chr, 25, "%i", faa_buf[i].gi);
196 e.key = gi_chr;196 e.key = gi_chr;
@@ -199,24 +199,23 @@ assign_protein_type (hid_t file_id)
199 /*199 /*
200 * A record was not found in the cache for this gi.200 * A record was not found in the cache for this gi.
201 */201 */
202 if (hsearch_r (e, FIND, &ep, &htab) == 0) 202 if (hsearch_r (e, FIND, &ep, &htab) == 0)
203 {203 {
204 204
205 /*205 /*
206 * Read the sequence from the database by GI.206 * Read the sequence from the database by GI.
207 */207 */
208 Int4 sequence_number = readdb_gi2seq (seqdb, faa_buf[i].gi, NULL);208 Int4 sequence_number = readdb_gi2seq (seqdb, faa_buf[i].gi, NULL);
209 BioseqPtr bsp = readdb_get_bioseq (seqdb, sequence_number);209 BioseqPtr bsp = readdb_get_bioseq (seqdb, sequence_number);
210 if (bsp == NULL) 210 if (bsp == NULL)
211 {211 {
212 error_at_line (EXIT_FAILURE, 0, __FILE__, __LINE__,212 error_at_line (EXIT_FAILURE, 0, __FILE__, __LINE__,
213 "Unable to find BLAST record for gi|%i. Ensure "213 "Unable to find BLAST record for gi|%i. Ensure "
214 "the BLAST database is up-to-date with the HDF5 "214 "the BLAST database is up-to-date with the HDF5 "
215 "record set. See the BLAST formatdb.log file "215 "record set. See the BLAST formatdb.log file "
216 "for details.\n",216 "for details.\n", faa_buf[i].gi);
217 faa_buf[i].gi);
218 }217 }
219 218
220 SeqAlignPtr seqalign = BioseqBlastEngine (bsp,219 SeqAlignPtr seqalign = BioseqBlastEngine (bsp,
221 "blastp",220 "blastp",
222 REFDB,221 REFDB,
@@ -224,19 +223,19 @@ assign_protein_type (hid_t file_id)
224 NULL,223 NULL,
225 &error_returns,224 &error_returns,
226 NULL);225 NULL);
227 226
228 /*227 /*
229 * BLAST reported an error. Write it out and continue processing.228 * BLAST reported an error. Write it out and continue processing.
230 */229 */
231 if (error_returns != NULL)230 if (error_returns != NULL)
232 {231 {
233 CharPtr msg = BlastErrorToString (error_returns);232 CharPtr msg = BlastErrorToString (error_returns);
234 printf ("Warning: An error has been reported by the NCBI Toolkit "233 printf
235 "API for sequence gi|%i: %s",234 ("Warning: An error has been reported by the NCBI Toolkit "
236 faa_buf[i].gi, msg);235 "API for sequence gi|%i: %s", faa_buf[i].gi, msg);
237 free (msg); 236 free (msg);
238 }237 }
239 238
240 /*239 /*
241 * A hit was found. Record the first hit as the protein type.240 * A hit was found. Record the first hit as the protein type.
242 * Skip the first 4 characters and eat the "lcl|".241 * Skip the first 4 characters and eat the "lcl|".
@@ -245,18 +244,18 @@ assign_protein_type (hid_t file_id)
245 {244 {
246 Char target_id_buf[BUFFER_LEN + 1];245 Char target_id_buf[BUFFER_LEN + 1];
247 SeqIdPtr target_id = SeqAlignId (seqalign, 1);246 SeqIdPtr target_id = SeqAlignId (seqalign, 1);
248 SeqIdWrite (target_id, target_id_buf, PRINTID_FASTA_SHORT, 247 SeqIdWrite (target_id, target_id_buf, PRINTID_FASTA_SHORT,
249 BUFFER_LEN);248 BUFFER_LEN);
250249
251 // Species Type250 // Species Type
252 new_buf[i].type[0] = target_id_buf[4];251 new_buf[i].type[0] = target_id_buf[4];
253 new_buf[i].type[1] = '\0';252 new_buf[i].type[1] = '\0';
254 253
255 // Protein Type (Skip the underscore in the string).254 // Protein Type (Skip the underscore in the string).
256 strncpy (new_buf[i].protein, &target_id_buf[6], 255 strncpy (new_buf[i].protein, &target_id_buf[6],
257 sizeof (new_buf[i].protein)); 256 sizeof (new_buf[i].protein));
258 }257 }
259 258
260 /*259 /*
261 * BLAST did not find any hits.260 * BLAST did not find any hits.
262 */261 */
@@ -265,73 +264,74 @@ assign_protein_type (hid_t file_id)
265 printf ("Warning: Unable to identify protein type for sequence "264 printf ("Warning: Unable to identify protein type for sequence "
266 "gi|%i\n", faa_buf[i].gi);265 "gi|%i\n", faa_buf[i].gi);
267 }266 }
268 267
269 /*268 /*
270 * Clean up memory for the next ieration.269 * Clean up memory for the next ieration.
271 */270 */
272 seqalign = SeqAlignSetFree (seqalign);271 seqalign = SeqAlignSetFree (seqalign);
273 bsp = BioseqFree (bsp);272 bsp = BioseqFree (bsp);
274 273
275 } // End existing entry not found.274 } // End existing entry not found.
276275
277 /*276 /*
278 * Hash table entry found. Keep the old value.277 * Hash table entry found. Keep the old value.
279 */278 */
280 else279 else
281 {280 {
282 gi_type_data* old_value = (gi_type_data*)ep->data;281 gi_type_data *old_value = (gi_type_data *) ep->data;
283 new_buf[i].gi = old_value->gi;282 new_buf[i].gi = old_value->gi;
284 strncpy (new_buf[i].type, old_value->type, sizeof (new_buf[i].type));283 strncpy (new_buf[i].type, old_value->type,
285 strncpy (new_buf[i].protein, old_value->protein, sizeof (new_buf[i].protein));284 sizeof (new_buf[i].type));
285 strncpy (new_buf[i].protein, old_value->protein,
286 sizeof (new_buf[i].protein));
286 }287 }
287 288
288 /*289 /*
289 * Write the data out to the file.290 * Write the data out to the file.
290 */291 */
291 if ( (i % 1000 == 0) && (i > 0) )292 if ((i % 1000 == 0) && (i > 0))
292 {293 {
293 status = H5TBappend_records (file_id, "gi_type_data", 1000,294 status = H5TBappend_records (file_id, "gi_type_data", 1000,
294 gi_size, gi_offset, gi_sizes, 295 gi_size, gi_offset, gi_sizes,
295 &new_buf[i-1000]);296 &new_buf[i - 1000]);
296 if (status < 0)297 if (status < 0)
297 check_h5_error (status, __FILE__, __LINE__);298 check_h5_error (status, __FILE__, __LINE__);
298 299
299 status = H5Fflush (file_id, H5F_SCOPE_GLOBAL);300 status = H5Fflush (file_id, H5F_SCOPE_GLOBAL);
300 if (status < 0)301 if (status < 0)
301 check_h5_error (status, __FILE__, __LINE__);302 check_h5_error (status, __FILE__, __LINE__);
302303
303 written = i;304 written = i;
304305
305 printf ("Processed %i of %i records.\n", i, (int)faa_nrecords);306 printf ("Processed %i of %i records.\n", i, (int) faa_nrecords);
306 }307 }
307 308
308 }309 }
309310
310 /*311 /*
311 * Write out records from the last bin if it was less than 1000312 * Write out records from the last bin if it was less than 1000
312 * records in size.313 * records in size.
313 */314 */
314 if ((int)faa_nrecords < 1000) 315 if ((int) faa_nrecords < 1000)
315 {316 {
316 status = H5TBappend_records (file_id, "gi_type_data", faa_nrecords,317 status = H5TBappend_records (file_id, "gi_type_data", faa_nrecords,
317 gi_size, gi_offset, gi_sizes,318 gi_size, gi_offset, gi_sizes, new_buf);
318 new_buf);
319 }319 }
320320
321 else321 else
322 {322 {
323 status = H5TBappend_records (file_id, "gi_type_data", faa_nrecords - written,323 status =
324 gi_size, gi_offset, gi_sizes, 324 H5TBappend_records (file_id, "gi_type_data", faa_nrecords - written,
325 &new_buf[written]);325 gi_size, gi_offset, gi_sizes, &new_buf[written]);
326 }326 }
327327
328 if (status < 0)328 if (status < 0)
329 check_h5_error (status, __FILE__, __LINE__);329 check_h5_error (status, __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 (status, __FILE__, __LINE__);
334 334
335 free (faa_buf);335 free (faa_buf);
336 free (old_buf);336 free (old_buf);
337 free (new_buf);337 free (new_buf);
@@ -339,6 +339,6 @@ assign_protein_type (hid_t file_id)
339339
340 options = BLASTOptionDelete (options);340 options = BLASTOptionDelete (options);
341 readdb_destruct (seqdb);341 readdb_destruct (seqdb);
342 342
343 return;343 return;
344}344}
diff --git a/src/load/load_influenza_aa_dat.c b/src/load/load_influenza_aa_dat.c
index 3826349..b50fcab 100644
--- a/src/load/load_influenza_aa_dat.c
+++ b/src/load/load_influenza_aa_dat.c
@@ -15,7 +15,7 @@
15#define NFIELDS (hsize_t) 1115#define NFIELDS (hsize_t) 11
1616
17void17void
18load_influenza_aa_dat (hid_t file_id, const char* file_name)18load_influenza_aa_dat (hid_t file_id, const char *file_name)
19{19{
20 /*20 /*
21 * Model the data using native types.21 * Model the data using native types.
@@ -225,7 +225,8 @@ load_influenza_aa_dat (hid_t file_id, const char* file_name)
225 if (status < 0)225 if (status < 0)
226 check_h5_error (status, __FILE__, __LINE__);226 check_h5_error (status, __FILE__, __LINE__);
227227
228 status = H5TBdelete_record (file_id, "influenza_aa.dat", 0, nrecords);228 status =
229 H5TBdelete_record (file_id, "influenza_aa.dat", 0, nrecords);
229 if (status < 0)230 if (status < 0)
230 check_h5_error (status, __FILE__, __LINE__);231 check_h5_error (status, __FILE__, __LINE__);
231232
@@ -233,7 +234,7 @@ load_influenza_aa_dat (hid_t file_id, const char* file_name)
233 H5TBappend_records (file_id, "influenza_aa.dat", 1, dst_size,234 H5TBappend_records (file_id, "influenza_aa.dat", 1, dst_size,
234 dst_offset, dst_sizes, &p_data);235 dst_offset, dst_sizes, &p_data);
235 if (status < 0)236 if (status < 0)
236 check_h5_error (status, __FILE__, __LINE__); 237 check_h5_error (status, __FILE__, __LINE__);
237 }238 }
238239
239 /*240 /*
@@ -242,8 +243,10 @@ load_influenza_aa_dat (hid_t file_id, const char* file_name)
242 else243 else
243 {244 {
244 herr_t status = H5TBmake_table ("influenza_aa.dat", file_id,245 herr_t status = H5TBmake_table ("influenza_aa.dat", file_id,
245 "influenza_aa.dat", NFIELDS, 1, dst_size,246 "influenza_aa.dat", NFIELDS, 1,
246 field_names, dst_offset, field_type,247 dst_size,
248 field_names, dst_offset,
249 field_type,
247 chunk_size, fill_data, compress,250 chunk_size, fill_data, compress,
248 &p_data);251 &p_data);
249 if (status < 0)252 if (status < 0)
diff --git a/src/load/load_influenza_aa_dat.h b/src/load/load_influenza_aa_dat.h
index 97e36f8..c4ce152 100644
--- a/src/load/load_influenza_aa_dat.h
+++ b/src/load/load_influenza_aa_dat.h
@@ -7,6 +7,6 @@
7 * Load the supplementary protein data from the NCBI influenza_aa.dat7 * Load the supplementary protein data from the NCBI influenza_aa.dat
8 * file.8 * file.
9 */9 */
10void load_influenza_aa_dat (hid_t file_id, const char* file_name);10void load_influenza_aa_dat (hid_t file_id, const char *file_name);
1111
12#endif // LOAD_INFLUENZA_AA_DAT_H12#endif // LOAD_INFLUENZA_AA_DAT_H
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>
99
10void10void
11load_influenza_faa (hid_t file_id, const char* file_name)11load_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];
1717
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)
3131
32 while (getline (&line, &len, dat) != -1)32 while (getline (&line, &len, dat) != -1)
33 {33 {
34 current_line++; 34 current_line++;
3535
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, "|");
5151
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));
5454
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));
5858
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;
6161
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__);
7576
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__);
7981
@@ -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);
115119
116 }120 }
117 121
118 }122 }
119123
120 if (line)124 if (line)
diff --git a/src/load/load_influenza_faa.h b/src/load/load_influenza_faa.h
index 1ad5797..070bdea 100644
--- a/src/load/load_influenza_faa.h
+++ b/src/load/load_influenza_faa.h
@@ -6,6 +6,6 @@
6/*6/*
7 * Load the protein sequence data from the NCBI influenza.faa file.7 * Load the protein sequence data from the NCBI influenza.faa file.
8 */8 */
9void load_influenza_faa (hid_t file_id, const char* file_name);9void load_influenza_faa (hid_t file_id, const char *file_name);
1010
11#endif // LOAD_INFLUENZA_FAA_H11#endif // LOAD_INFLUENZA_FAA_H
diff --git a/src/model/gi_type_data_init.c b/src/model/gi_type_data_init.c
index 4a161c7..54f47a7 100644
--- a/src/model/gi_type_data_init.c
+++ b/src/model/gi_type_data_init.c
@@ -7,8 +7,8 @@
7 * struct. Perhaps an HDF5 precompiler could do such a thing.7 * struct. Perhaps an HDF5 precompiler could do such a thing.
8 */8 */
9void9void
10gi_type_data_init (size_t *dst_size, size_t *dst_offset, size_t *dst_sizes,10gi_type_data_init (size_t * dst_size, size_t * dst_offset, size_t * dst_sizes,
11 hid_t *field_type)11 hid_t * field_type)
12{12{
13 *dst_size = sizeof (gi_type_data);13 *dst_size = sizeof (gi_type_data);
1414
diff --git a/src/model/gi_type_data_init.h b/src/model/gi_type_data_init.h
index 5c45cba..080f035 100644
--- a/src/model/gi_type_data_init.h
+++ b/src/model/gi_type_data_init.h
@@ -8,7 +8,7 @@
8 * structures are used by the HDF5 API.8 * structures are used by the HDF5 API.
9 */9 */
10void10void
11gi_type_data_init (size_t *dst_size, size_t *dst_offset, size_t *dst_sizes,11gi_type_data_init (size_t * dst_size, size_t * dst_offset, size_t * dst_sizes,
12 hid_t *field_type);12 hid_t * field_type);
1313
14#endif // GI_TYPE_DATA_INIT_H14#endif // GI_TYPE_DATA_INIT_H
diff --git a/src/model/sequence_data_init.c b/src/model/sequence_data_init.c
index f6b3b1f..21881bf 100644
--- a/src/model/sequence_data_init.c
+++ b/src/model/sequence_data_init.c
@@ -1,28 +1,28 @@
1#include "sequence_data_init.h"1#include "sequence_data_init.h"
2#include "sequence_data.h"2#include "sequence_data.h"
33
4void 4void
5sequence_data_init (size_t *dst_size, size_t *dst_offset, size_t *dst_sizes,5sequence_data_init (size_t * dst_size, size_t * dst_offset,
6 hid_t *field_type)6 size_t * dst_sizes, hid_t * field_type)
7{7{
8 *dst_size = sizeof (sequence_data);8 *dst_size = sizeof (sequence_data);
9 9
10 dst_offset[0] = HOFFSET (sequence_data, gi);10 dst_offset[0] = HOFFSET (sequence_data, gi);
11 dst_offset[1] = HOFFSET (sequence_data, gb);11 dst_offset[1] = HOFFSET (sequence_data, gb);
12 dst_offset[2] = HOFFSET (sequence_data, description);12 dst_offset[2] = HOFFSET (sequence_data, description);
13 13
14 sequence_data dst_buf[1];14 sequence_data dst_buf[1];
15 15
16 dst_sizes[0] = sizeof (dst_buf[0].gi);16 dst_sizes[0] = sizeof (dst_buf[0].gi);
17 dst_sizes[1] = sizeof (dst_buf[0].gb);17 dst_sizes[1] = sizeof (dst_buf[0].gb);
18 dst_sizes[2] = sizeof (dst_buf[0].description);18 dst_sizes[2] = sizeof (dst_buf[0].description);
19 19
20 field_type[0] = H5T_NATIVE_INT;20 field_type[0] = H5T_NATIVE_INT;
21 21
22 hid_t gb_type = H5Tcopy (H5T_C_S1);22 hid_t gb_type = H5Tcopy (H5T_C_S1);
23 H5Tset_size (gb_type, 9);23 H5Tset_size (gb_type, 9);
24 field_type[1] = gb_type;24 field_type[1] = gb_type;
25 25
26 hid_t description_type = H5Tcopy (H5T_C_S1);26 hid_t description_type = H5Tcopy (H5T_C_S1);
27 H5Tset_size (description_type, 196);27 H5Tset_size (description_type, 196);
28 field_type[2] = description_type;28 field_type[2] = description_type;
diff --git a/src/model/sequence_data_init.h b/src/model/sequence_data_init.h
index c87e7e6..1a2c75c 100644
--- a/src/model/sequence_data_init.h
+++ b/src/model/sequence_data_init.h
@@ -7,8 +7,8 @@
7 * Initialize the structures describing sequence_data. These7 * Initialize the structures describing sequence_data. These
8 * descriptive structures are used by the HDF5 API.8 * descriptive structures are used by the HDF5 API.
9 */9 */
10void 10void
11sequence_data_init (size_t *dst_size, size_t *dst_offset, size_t *dst_sizes,11sequence_data_init (size_t * dst_size, size_t * dst_offset,
12 hid_t *field_type);12 size_t * dst_sizes, hid_t * field_type);
1313
14#endif // SEQUENCE_DATA_INIT_H14#endif // SEQUENCE_DATA_INIT_H

Valid XHTML 1.0 Strict

Copyright © 2009 Don Pellegrino All Rights Reserved.