Ran GNU indent to format the code as per GNU coding conventions.

13 files changed, 145 insertions, 148 deletions

diff --git a/src/aggregator.c b/src/aggregator.c
index 20da6df..5fb9d4a 100644
--- a/src/aggregator.c
+++ b/src/aggregator.c
@@ -11,7 +11,7 @@
 #define FILE "influenza.h5"
 
 int
-main()
+main ()
 {
   /*
    * Create the HDF5 file.
diff --git a/src/assign_protein_type.c b/src/assign_protein_type.c
index 643ea3f..54db84e 100644
--- a/src/assign_protein_type.c
+++ b/src/assign_protein_type.c
@@ -48,8 +48,8 @@ assign_protein_type (hid_t file_id)
    * Read the sequence from the database by GI.
    */
   Int4 sequence_number = readdb_gi2seq (seqdb, 453644, NULL);
-  BioseqPtr bsp = readdb_get_bioseq(seqdb, sequence_number);
-  
+  BioseqPtr bsp = readdb_get_bioseq (seqdb, sequence_number);
+
   SeqAlignPtr seqalign = BioseqBlastEngine (bsp,
                                             "blastp",
                                             REFDB,
@@ -66,8 +66,7 @@ assign_protein_type (hid_t file_id)
       Char target_id_buf[BUFFER_LEN + 1];
       SeqIdPtr target_id = SeqAlignId (seqalign, 1);
       SeqIdWrite (target_id, target_id_buf, PRINTID_FASTA_SHORT, BUFFER_LEN);
-      printf ("%s\n",
-              target_id_buf);
+      printf ("%s\n", target_id_buf);
     }
 
   // Clean up memory for the next ieration.
diff --git a/src/assign_protein_type.h b/src/assign_protein_type.h
index 1dfb8e6..221154f 100644
--- a/src/assign_protein_type.h
+++ b/src/assign_protein_type.h
@@ -10,7 +10,6 @@
  * sequence is BLASTed against this database.  The first hit is used
  * to assign a protein type to sequence.
  */
-void
-assign_protein_type (hid_t file_id);
+void assign_protein_type (hid_t file_id);
 
 #endif // ASSIGN_PROTEIN_TYPE_H
diff --git a/src/check_error.c b/src/check_error.c
index 70c62c4..4630b50 100644
--- a/src/check_error.c
+++ b/src/check_error.c
@@ -7,7 +7,7 @@ void
 check_error (const char *filename, const unsigned int linenum)
 {
   if (errno)
-    error_at_line (EXIT_FAILURE, errno, filename, linenum, 
+    error_at_line (EXIT_FAILURE, errno, filename, linenum,
                    "An error has been detected within the application.");
 
   return;
diff --git a/src/check_error.h b/src/check_error.h
index 33acc63..2250c59 100644
--- a/src/check_error.h
+++ b/src/check_error.h
@@ -5,7 +5,6 @@
  * Check the error state.  Reports and error message and exits if an
  * error has occured.
  */
-void
-check_error (const char *filename, unsigned int linenum);
+void check_error (const char *filename, unsigned int linenum);
 
 #endif // CHECK_ERROR_H
diff --git a/src/check_h5_error.c b/src/check_h5_error.c
index 30fc87c..d90b21f 100644
--- a/src/check_h5_error.c
+++ b/src/check_h5_error.c
@@ -3,7 +3,7 @@
 #include <stdlib.h>
 
 void
-check_h5_error (herr_t status, const char* filename, unsigned int linenum)
+check_h5_error (herr_t status, 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/check_h5_error.h b/src/check_h5_error.h
index 74730cd..e460e97 100644
--- a/src/check_h5_error.h
+++ b/src/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 (herr_t status, const char *filename, unsigned int linenum);
 
 #endif // CHECK_H5_ERROR_H
diff --git a/src/check_ncbi_error.c b/src/check_ncbi_error.c
index 3caa7a9..8e1c3b2 100644
--- a/src/check_ncbi_error.c
+++ b/src/check_ncbi_error.c
@@ -2,8 +2,7 @@
 
 void
 check_ncbi_error (ValNodePtr error_returns,
-                  const char* filename,
-                  unsigned int linenum)
+                  const char *filename, unsigned int linenum)
 {
   error_at_line (EXIT_FAILURE, 0, filename, linenum,
                  "An error has been reported by the NCBI Toolkit API: %s",
diff --git a/src/check_ncbi_error.h b/src/check_ncbi_error.h
index c27c56d..45ac0ca 100644
--- a/src/check_ncbi_error.h
+++ b/src/check_ncbi_error.h
@@ -8,6 +8,6 @@
  */
 void
 check_ncbi_error (ValNodePtr error_returns,
-                  const char* filename, unsigned int linenum);
+                  const char *filename, unsigned int linenum);
 
 #endif // CHECK_NCBI_ERROR_H
diff --git a/src/load_influenza_aa_dat.c b/src/load_influenza_aa_dat.c
index 91ef415..9ee3c46 100644
--- a/src/load_influenza_aa_dat.c
+++ b/src/load_influenza_aa_dat.c
@@ -46,60 +46,63 @@ load_influenza_aa_dat (hid_t file_id)
    * memory."
    */
   size_t dst_size = sizeof (supplementary_data);
-  size_t dst_offset[NFIELDS] = { HOFFSET ( supplementary_data, genbank_accession_number ),
-                                 HOFFSET ( supplementary_data, host ),
-                                 HOFFSET ( supplementary_data, genome_segment_number ),
-                                 HOFFSET ( supplementary_data, subtype ),
-                                 HOFFSET ( supplementary_data, country ),
-                                 HOFFSET ( supplementary_data, year ),
-                                 HOFFSET ( supplementary_data, sequence_length ),
-                                 HOFFSET ( supplementary_data, virus_name ),
-                                 HOFFSET ( supplementary_data, age ),
-                                 HOFFSET ( supplementary_data, gender ),
-                                 HOFFSET ( supplementary_data, full_length_indicator )};
+  size_t dst_offset[NFIELDS] =
+    { HOFFSET (supplementary_data, genbank_accession_number),
+    HOFFSET (supplementary_data, host),
+    HOFFSET (supplementary_data, genome_segment_number),
+    HOFFSET (supplementary_data, subtype),
+    HOFFSET (supplementary_data, country),
+    HOFFSET (supplementary_data, year),
+    HOFFSET (supplementary_data, sequence_length),
+    HOFFSET (supplementary_data, virus_name),
+    HOFFSET (supplementary_data, age),
+    HOFFSET (supplementary_data, gender),
+    HOFFSET (supplementary_data, full_length_indicator)
+  };
 
   supplementary_data dst_buf[1];
 
-  size_t dst_sizes[NFIELDS] = { sizeof ( dst_buf[0].genbank_accession_number ),
-                                sizeof ( dst_buf[0].host ),
-                                sizeof ( dst_buf[0].genome_segment_number ),
-                                sizeof ( dst_buf[0].subtype ),
-                                sizeof ( dst_buf[0].country ),
-                                sizeof ( dst_buf[0].year ),
-                                sizeof ( dst_buf[0].sequence_length ),
-                                sizeof ( dst_buf[0].virus_name ),
-                                sizeof ( dst_buf[0].age ),
-                                sizeof ( dst_buf[0].gender ),
-                                sizeof ( dst_buf[0].full_length_indicator)};
+  size_t dst_sizes[NFIELDS] = { sizeof (dst_buf[0].genbank_accession_number),
+    sizeof (dst_buf[0].host),
+    sizeof (dst_buf[0].genome_segment_number),
+    sizeof (dst_buf[0].subtype),
+    sizeof (dst_buf[0].country),
+    sizeof (dst_buf[0].year),
+    sizeof (dst_buf[0].sequence_length),
+    sizeof (dst_buf[0].virus_name),
+    sizeof (dst_buf[0].age),
+    sizeof (dst_buf[0].gender),
+    sizeof (dst_buf[0].full_length_indicator)
+  };
 
   /*
    * Map the native types to HDF5 types for each field.
    */
   hid_t field_type[NFIELDS];
 
-  hid_t genbank_accession_number_type = H5Tcopy ( H5T_C_S1 );
-  H5Tset_size ( genbank_accession_number_type, 9 );
+  hid_t genbank_accession_number_type = H5Tcopy (H5T_C_S1);
+  H5Tset_size (genbank_accession_number_type, 9);
   field_type[0] = genbank_accession_number_type;
 
-  hid_t host_type = H5Tcopy ( H5T_C_S1 );
-  H5Tset_size ( host_type, 15 );
+  hid_t host_type = H5Tcopy (H5T_C_S1);
+  H5Tset_size (host_type, 15);
   field_type[1] = host_type;
-  
+
   field_type[2] = H5T_NATIVE_INT;
 
-  hid_t subtype_type = H5Tcopy ( H5T_C_S1 );
-  H5Tset_size (subtype_type, 7 );
+  hid_t subtype_type = H5Tcopy (H5T_C_S1);
+  H5Tset_size (subtype_type, 7);
   field_type[3] = subtype_type;
 
-  hid_t country_type = H5Tcopy ( H5T_C_S1 );
-  H5Tset_size (country_type, 25 );
+  hid_t country_type = H5Tcopy (H5T_C_S1);
+  H5Tset_size (country_type, 25);
   field_type[4] = country_type;
 
   field_type[5] = H5T_NATIVE_INT;
 
   field_type[6] = H5T_NATIVE_INT;
 
-  hid_t virus_name_type = H5Tcopy ( H5T_C_S1 );
+  hid_t virus_name_type = H5Tcopy (H5T_C_S1);
   H5Tset_size (virus_name_type, 196);
   field_type[7] = virus_name_type;
 
@@ -118,18 +121,18 @@ load_influenza_aa_dat (hid_t file_id)
   /*
    * Labels used for the fields in the table.
    */
-  const char *field_names[NFIELDS] =
-    { "GenBank accession number",
-      "Host",
-      "Genome segment number",
-      "Subtype",
-      "Country",
-      "Year",
-      "Sequence length",
-      "Virus name",
-      "Age",
-      "Gender",
-      "Full-length Indicator" };
+  const char *field_names[NFIELDS] = { "GenBank accession number",
+    "Host",
+    "Genome segment number",
+    "Subtype",
+    "Country",
+    "Year",
+    "Sequence length",
+    "Virus name",
+    "Age",
+    "Gender",
+    "Full-length Indicator"
+  };
 
   /*
    * Table storage options.
@@ -142,7 +145,7 @@ load_influenza_aa_dat (hid_t file_id)
    * Insert the records.
    */
   supplementary_data p_data;
-  FILE* dat = fopen ("/home/don/exp004/genomes/INFLUENZA/influenza_aa.dat",
+  FILE *dat = fopen ("/home/don/exp004/genomes/INFLUENZA/influenza_aa.dat",
                      "r");
   if (dat == NULL)
     check_error (__FILE__, __LINE__);
@@ -150,89 +153,89 @@ load_influenza_aa_dat (hid_t file_id)
   size_t len = 0;
   int current_line = 0;
 
-  while (getline (&line, &len, dat) != -1) {
-
-    current_line++;
-    char *running = strdup (line);
-    char *token;
-    
-    /*
-     * Parse the line, handling the case of empty fields represented
-     * by sequential delimiters.
-     */
-    strncpy(p_data.genbank_accession_number, strsep (&running, "\t"),
-            sizeof(p_data.genbank_accession_number));
-    
-    strncpy(p_data.host, strsep (&running, "\t"),
-            sizeof(p_data.host));
-    
-    token = strsep (&running, "\t");
-    if (strcmp (token, "\0") == 0)
-      p_data.genome_segment_number = 0;
-    else
-      p_data.genome_segment_number = atoi(token);
-    
-    strncpy(p_data.subtype, strsep (&running, "\t"),
-            sizeof(p_data.subtype));
-    
-    strncpy(p_data.country, strsep (&running, "\t"),
-            sizeof(p_data.country));
-    
-    /*
-     * Convert the year field from text to numeric.  Unknown and empty
-     * values are assigned a numeric value of zero.
-     */
-    token = strsep (&running, "\t");
-    if (strcmp (token, "\0") == 0)
-      p_data.year = 0;
-    else if (strcmp (token, "unknown") == 0)
-      p_data.year = 0;
-    else if (strcmp (token, "NON") == 0)
-      p_data.year = 0;
-    else
-      p_data.year = atoi(token);
-
-    token = strsep (&running, "\t");
-    if (strcmp (token, "\0") == 0)
-      p_data.sequence_length = 0;
-    else
-      p_data.sequence_length = atoi(token);
-    
-    strncpy(p_data.virus_name, strsep (&running, "\t"),
-            sizeof(p_data.virus_name));
-    
-    strncpy(p_data.age, strsep (&running, "\t"),
-            sizeof(p_data.age));
-    
-    strncpy(p_data.gender, strsep (&running, "\t"),
-            sizeof(p_data.gender));
-    
-    strncpy(p_data.full_length_indicator, strsep (&running, "\t"),
-            sizeof(p_data.full_length_indicator));
-
-    if (current_line == 1) 
-      {
-        herr_t status = H5TBmake_table ("influenza_aa.dat", file_id,
-                                                TABLE_NAME, NFIELDS, 1,dst_size,
-                                        field_names, dst_offset, field_type,
-                                        chunk_size, fill_data, compress,
-                                        &p_data);
-        if (status < 0)
-          check_h5_error (status, __FILE__, __LINE__);
-      }
-    else
-      {
-        herr_t status = H5TBappend_records (file_id, TABLE_NAME, 1, dst_size,
-                                            dst_offset, dst_sizes, &p_data);
-        if (status < 0)
-          check_h5_error (status, __FILE__, __LINE__);
-      }
-
-    if (running)
-      free (running);
-   
-  }
-  
+  while (getline (&line, &len, dat) != -1)
+    {
+
+      current_line++;
+      char *running = strdup (line);
+      char *token;
+
+      /*
+       * Parse the line, handling the case of empty fields represented
+       * by sequential delimiters.
+       */
+      strncpy (p_data.genbank_accession_number, strsep (&running, "\t"),
+               sizeof (p_data.genbank_accession_number));
+
+      strncpy (p_data.host, strsep (&running, "\t"), sizeof (p_data.host));
+
+      token = strsep (&running, "\t");
+      if (strcmp (token, "\0") == 0)
+        p_data.genome_segment_number = 0;
+      else
+        p_data.genome_segment_number = atoi (token);
+
+      strncpy (p_data.subtype, strsep (&running, "\t"),
+               sizeof (p_data.subtype));
+
+      strncpy (p_data.country, strsep (&running, "\t"),
+               sizeof (p_data.country));
+
+      /*
+       * Convert the year field from text to numeric.  Unknown and empty
+       * values are assigned a numeric value of zero.
+       */
+      token = strsep (&running, "\t");
+      if (strcmp (token, "\0") == 0)
+        p_data.year = 0;
+      else if (strcmp (token, "unknown") == 0)
+        p_data.year = 0;
+      else if (strcmp (token, "NON") == 0)
+        p_data.year = 0;
+      else
+        p_data.year = atoi (token);
+
+      token = strsep (&running, "\t");
+      if (strcmp (token, "\0") == 0)
+        p_data.sequence_length = 0;
+      else
+        p_data.sequence_length = atoi (token);
+
+      strncpy (p_data.virus_name, strsep (&running, "\t"),
+               sizeof (p_data.virus_name));
+
+      strncpy (p_data.age, strsep (&running, "\t"), sizeof (p_data.age));
+
+      strncpy (p_data.gender, strsep (&running, "\t"),
+               sizeof (p_data.gender));
+
+      strncpy (p_data.full_length_indicator, strsep (&running, "\t"),
+               sizeof (p_data.full_length_indicator));
+
+      if (current_line == 1)
+        {
+          herr_t status = H5TBmake_table ("influenza_aa.dat", file_id,
+                                          TABLE_NAME, NFIELDS, 1, dst_size,
+                                          field_names, dst_offset, field_type,
+                                          chunk_size, fill_data, compress,
+                                          &p_data);
+          if (status < 0)
+            check_h5_error (status, __FILE__, __LINE__);
+        }
+      else
+        {
+          herr_t status =
+            H5TBappend_records (file_id, TABLE_NAME, 1, dst_size,
+                                dst_offset, dst_sizes, &p_data);
+          if (status < 0)
+            check_h5_error (status, __FILE__, __LINE__);
+        }
+
+      if (running)
+        free (running);
+
+    }
+
   if (line)
     free (line);
 
diff --git a/src/load_influenza_aa_dat.h b/src/load_influenza_aa_dat.h
index c431e67..f6c60be 100644
--- a/src/load_influenza_aa_dat.h
+++ b/src/load_influenza_aa_dat.h
@@ -7,7 +7,6 @@
  * Load the supplementary protein data from the NCBI influenza_aa.dat
  * file.
  */
-void 
-load_influenza_aa_dat (hid_t file_id);
+void load_influenza_aa_dat (hid_t file_id);
 
 #endif // LOAD_INFLUENZA_AA_DAT_H
diff --git a/src/load_influenza_faa.c b/src/load_influenza_faa.c
index 8c43992..8fd0cd7 100644
--- a/src/load_influenza_faa.c
+++ b/src/load_influenza_faa.c
@@ -3,7 +3,7 @@
 void
 load_influenza_faa (hid_t file_id)
 {
-  
+
 
   return;
 }
diff --git a/src/load_influenza_faa.h b/src/load_influenza_faa.h
index 4b1dbdd..569c411 100644
--- a/src/load_influenza_faa.h
+++ b/src/load_influenza_faa.h
@@ -6,7 +6,6 @@
 /*
  * Load the protein sequence data from the NCBI influenza.faa file.
  */
-void
-load_influenza_faa (hid_t file_id);
+void load_influenza_faa (hid_t file_id);
 
 #endif // LOAD_INFLUENZA_FAA_H