From 6bfe5755d6a9b3d88032287e97681c65b7f32f0f Mon Sep 17 00:00:00 2001 From: Donald Pellegrino Date: Thu, 21 Jan 2010 19:00:00 +0000 Subject: Removed unused status variable from check_h5_error function. --- 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 @@ #include #define H5FILE "influenza.h5" -#define INFLUENZA_AA_DAT "/home/don/exp004/genomes/INFLUENZA/influenza_aa.dat" -#define INFLUENZA_FAA "/home/don/exp004/genomes/INFLUENZA/influenza.faa" +#define INFLUENZA_AA_DAT "/u/ac/dpellegr/Documents/exp004/genomes/INFLUENZA/influenza_aa.dat" +#define INFLUENZA_FAA "/u/ac/dpellegr/Documents/exp004/genomes/INFLUENZA/influenza.faa" int main () @@ -25,14 +25,14 @@ main () { file_id = H5Fcreate (H5FILE, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT); if (file_id < 0) - check_h5_error (file_id, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); } else { fclose (f); file_id = H5Fopen (H5FILE, H5F_ACC_RDWR, H5P_DEFAULT); if (file_id < 0) - check_h5_error (file_id, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); } /* @@ -53,7 +53,7 @@ main () */ herr_t status = H5Fclose (file_id); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); return 0; } 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 @@ /* * BLAST database containing all of the influenza protein sequences. */ -#define SEQDB "/home/don/exp004/influenzadb/influenzadb" +#define SEQDB "/u/ac/dpellegr/Documents/exp004/influenzadb/influenzadb" /* * BLAST reference database of prototypical protein types. */ -#define REFDB "/home/don/exp004/influenzadb/proteinnames" +#define REFDB "/u/ac/dpellegr/Documents/exp004/influenzadb/proteinnames" #define BUFFER_LEN 50 @@ -68,7 +68,7 @@ assign_protein_type (hid_t file_id) herr_t status = H5TBget_table_info (file_id, "influenza.faa", &faa_nfields, &faa_nrecords); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); sequence_data *faa_buf = malloc (sizeof (sequence_data) * faa_nrecords); @@ -81,7 +81,7 @@ assign_protein_type (hid_t file_id) status = H5TBread_table (file_id, "influenza.faa", faa_size, faa_offset, faa_sizes, faa_buf); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); /* * Allocate memory for the new table. @@ -115,7 +115,7 @@ assign_protein_type (hid_t file_id) status = H5TBget_table_info (file_id, "gi_type_data", &gi_nfields, &gi_nrecords); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); printf (" Using gi_type_data cache of %i records.\n", (int) gi_nrecords); @@ -125,11 +125,11 @@ assign_protein_type (hid_t file_id) status = H5TBread_table (file_id, "gi_type_data", gi_size, gi_offset, gi_sizes, old_buf); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); status = H5TBdelete_record (file_id, "gi_type_data", 0, gi_nrecords); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); } @@ -155,7 +155,7 @@ assign_protein_type (hid_t file_id) gi_offset, gi_field_type, chunk_size, fill_data, compress, NULL); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); } @@ -295,11 +295,11 @@ assign_protein_type (hid_t file_id) gi_size, gi_offset, gi_sizes, &new_buf[i - 1000]); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); status = H5Fflush (file_id, H5F_SCOPE_GLOBAL); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); written = i; @@ -326,11 +326,11 @@ assign_protein_type (hid_t file_id) } if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); status = H5Fflush (file_id, H5F_SCOPE_GLOBAL); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); free (faa_buf); 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 @@ #include void -check_h5_error (herr_t status, const char *filename, unsigned int linenum) +check_h5_error (const char *filename, unsigned int linenum) { error_at_line (EXIT_FAILURE, 0, filename, linenum, "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 @@ * Handle errors from the HDF5 API. */ void -check_h5_error (herr_t status, const char *filename, unsigned int linenum); +check_h5_error (const char *filename, unsigned int linenum); #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 @@ * todo: Handle NULL values occuring in numeric fields. */ +#define _GNU_SOURCE #include "load_influenza_aa_dat.h" #include "error/check_error.h" #include "error/check_h5_error.h" #include #include #include +#include #define NFIELDS (hsize_t) 11 @@ -223,18 +225,18 @@ load_influenza_aa_dat (hid_t file_id, const char *file_name) herr_t status = H5TBget_table_info (file_id, "influenza_aa.dat", &nfields, &nrecords); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); status = H5TBdelete_record (file_id, "influenza_aa.dat", 0, nrecords); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); status = H5TBappend_records (file_id, "influenza_aa.dat", 1, dst_size, dst_offset, dst_sizes, &p_data); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); } /* @@ -250,7 +252,7 @@ load_influenza_aa_dat (hid_t file_id, const char *file_name) chunk_size, fill_data, compress, &p_data); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); } } @@ -260,7 +262,7 @@ load_influenza_aa_dat (hid_t file_id, const char *file_name) H5TBappend_records (file_id, "influenza_aa.dat", 1, dst_size, dst_offset, dst_sizes, &p_data); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); } 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 @@ +#define _GNU_SOURCE #include "error/check_error.h" #include "error/check_h5_error.h" #include "load_influenza_faa.h" @@ -6,6 +7,7 @@ #include #include #include +#include void load_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) H5TBget_table_info (file_id, "influenza.faa", &nfields, &nrecords); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); status = H5TBdelete_record (file_id, "influenza.faa", 0, nrecords); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); status = H5TBappend_records (file_id, "influenza.faa", 1, dst_size, dst_offset, dst_sizes, &p_data); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); } /* @@ -101,7 +103,7 @@ load_influenza_faa (hid_t file_id, const char *file_name) compress, &p_data); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); } } @@ -111,7 +113,7 @@ load_influenza_faa (hid_t file_id, const char *file_name) H5TBappend_records (file_id, "influenza.faa", 1, dst_size, dst_offset, dst_sizes, &p_data); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); } 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 () */ hid_t file_id = H5Fopen (FILE, H5F_ACC_RDWR, H5P_DEFAULT); if (file_id < 0) - check_h5_error (file_id, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); /* * Assign protein type values to the sequence records. @@ -29,7 +29,7 @@ main () */ herr_t status = H5Fclose (file_id); if (status < 0) - check_h5_error (status, __FILE__, __LINE__); + check_h5_error (__FILE__, __LINE__); return 0; } -- cgit v0.8.3.1-22-g547a