Ran GNU indent on the code and headers.

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 ()
   /*
    * Load the FASTA protein sequence data file.
    */
-  printf ("Loading \"influenza.faa\" with contents of %s.\n",
-	  INFLUENZA_FAA);
+  printf ("Loading \"influenza.faa\" with contents of %s.\n", INFLUENZA_FAA);
   load_influenza_faa (file_id, INFLUENZA_FAA);
 
   /*
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)
   if (status < 0)
     check_h5_error (status, __FILE__, __LINE__);
 
-  sequence_data* faa_buf = malloc (sizeof(sequence_data) * faa_nrecords);
+  sequence_data *faa_buf = malloc (sizeof (sequence_data) * faa_nrecords);
 
   size_t faa_size;
   size_t faa_offset[SEQUENCE_DATA_FIELD_NUM];
@@ -86,7 +86,7 @@ assign_protein_type (hid_t file_id)
   /*
    * Allocate memory for the new table.
    */
-  gi_type_data* new_buf = malloc (sizeof (gi_type_data) * faa_nrecords);
+  gi_type_data *new_buf = malloc (sizeof (gi_type_data) * faa_nrecords);
   if (new_buf == NULL)
     check_error (__FILE__, __LINE__);
 
@@ -101,7 +101,7 @@ assign_protein_type (hid_t file_id)
   hid_t gi_field_type[GI_TYPE_DATA_FIELD_NUM];
   gi_type_data_init (&gi_size, gi_offset, gi_sizes, gi_field_type);
 
-  gi_type_data* old_buf = NULL;
+  gi_type_data *old_buf = NULL;
 
   /*
    * If the table is already present read the values into memory and
@@ -117,10 +117,11 @@ assign_protein_type (hid_t file_id)
       if (status < 0)
 	check_h5_error (status, __FILE__, __LINE__);
 
-      printf ("  Using gi_type_data cache of %i records.\n", (int)gi_nrecords);
-  
-      old_buf = malloc (sizeof(gi_type_data) * gi_nrecords);
-            
+      printf ("  Using gi_type_data cache of %i records.\n",
+	      (int) gi_nrecords);
+
+      old_buf = malloc (sizeof (gi_type_data) * gi_nrecords);
+
       status = H5TBread_table (file_id, "gi_type_data", gi_size, gi_offset,
 			       gi_sizes, old_buf);
       if (status < 0)
@@ -129,18 +130,18 @@ assign_protein_type (hid_t file_id)
       status = H5TBdelete_record (file_id, "gi_type_data", 0, gi_nrecords);
       if (status < 0)
 	check_h5_error (status, __FILE__, __LINE__);
-      
+
     }
 
   /*
    * If the table is not already present create it.
    */
   else
-    {      
+    {
 
       printf ("Creating gi_type_data.\n");
 
-      const char* gi_type_data_field_names[GI_TYPE_DATA_FIELD_NUM] =
+      const char *gi_type_data_field_names[GI_TYPE_DATA_FIELD_NUM] =
 	GI_TYPE_DATA_FIELD_NAMES;
 
       hsize_t chunk_size = 10;
@@ -152,8 +153,7 @@ assign_protein_type (hid_t file_id)
 			       GI_TYPE_DATA_FIELD_NUM, 0,
 			       gi_size, gi_type_data_field_names,
 			       gi_offset, gi_field_type,
-			       chunk_size, fill_data, compress,
-			       NULL);
+			       chunk_size, fill_data, compress, NULL);
       if (status < 0)
 	check_h5_error (status, __FILE__, __LINE__);
 
@@ -169,7 +169,7 @@ assign_protein_type (hid_t file_id)
 		   "Allocation of cache failed.");
   ENTRY e, *ep;
 
-  for (int i = 0; i < (int)gi_nrecords; i++)
+  for (int i = 0; i < (int) gi_nrecords; i++)
     {
       char gi_chr[25];
       snprintf (gi_chr, 25, "%i", old_buf[i].gi);
@@ -183,14 +183,14 @@ assign_protein_type (hid_t file_id)
   /*
    * Assign protein types to records for which the field is empty.
    */
-  printf ("Records to process: %i\n", (int)faa_nrecords);
+  printf ("Records to process: %i\n", (int) faa_nrecords);
   int written = 0;
-  for (int i = 0; i < (int)faa_nrecords; i++)
+  for (int i = 0; i < (int) faa_nrecords; i++)
     {
       new_buf[i].gi = faa_buf[i].gi;
       strncpy (new_buf[i].type, "", sizeof (new_buf[i].type));
       strncpy (new_buf[i].protein, "", sizeof (new_buf[i].protein));
-      
+
       char gi_chr[25];
       snprintf (gi_chr, 25, "%i", faa_buf[i].gi);
       e.key = gi_chr;
@@ -199,24 +199,23 @@ assign_protein_type (hid_t file_id)
       /*
        * A record was not found in the cache for this gi.
        */
-      if (hsearch_r (e, FIND, &ep, &htab) == 0) 
+      if (hsearch_r (e, FIND, &ep, &htab) == 0)
 	{
-	  
+
 	  /*
 	   * Read the sequence from the database by GI.
 	   */
 	  Int4 sequence_number = readdb_gi2seq (seqdb, faa_buf[i].gi, NULL);
 	  BioseqPtr bsp = readdb_get_bioseq (seqdb, sequence_number);
-	  if (bsp == NULL) 
+	  if (bsp == NULL)
 	    {
 	      error_at_line (EXIT_FAILURE, 0, __FILE__, __LINE__,
 			     "Unable to find BLAST record for gi|%i.  Ensure "
 			     "the BLAST database is up-to-date with the HDF5 "
 			     "record set.  See the BLAST formatdb.log file "
-			     "for details.\n",
-			     faa_buf[i].gi);
+			     "for details.\n", faa_buf[i].gi);
 	    }
-	  
+
 	  SeqAlignPtr seqalign = BioseqBlastEngine (bsp,
 						    "blastp",
 						    REFDB,
@@ -224,19 +223,19 @@ assign_protein_type (hid_t file_id)
 						    NULL,
 						    &error_returns,
 						    NULL);
-	  
+
 	  /*
 	   * BLAST reported an error.  Write it out and continue processing.
 	   */
 	  if (error_returns != NULL)
 	    {
 	      CharPtr msg = BlastErrorToString (error_returns);
-	      printf ("Warning: An error has been reported by the NCBI Toolkit "
-		      "API for sequence gi|%i: %s",
-		      faa_buf[i].gi, msg);
-	      free (msg);	    
+	      printf
+		("Warning: An error has been reported by the NCBI Toolkit "
+		 "API for sequence gi|%i: %s", faa_buf[i].gi, msg);
+	      free (msg);
 	    }
-	  
+
 	  /*
 	   * A hit was found.  Record the first hit as the protein type.
 	   * Skip the first 4 characters and eat the "lcl|".
@@ -245,18 +244,18 @@ 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, 
+	      SeqIdWrite (target_id, target_id_buf, PRINTID_FASTA_SHORT,
 			  BUFFER_LEN);
 
 	      // Species Type
 	      new_buf[i].type[0] = target_id_buf[4];
 	      new_buf[i].type[1] = '\0';
-	      
+
 	      // Protein Type (Skip the underscore in the string).
-	      strncpy (new_buf[i].protein, &target_id_buf[6], 
-		       sizeof (new_buf[i].protein));	     
+	      strncpy (new_buf[i].protein, &target_id_buf[6],
+		       sizeof (new_buf[i].protein));
 	    }
-	  
+
 	  /*
 	   * BLAST did not find any hits.
 	   */
@@ -265,73 +264,74 @@ assign_protein_type (hid_t file_id)
 	      printf ("Warning: Unable to identify protein type for sequence "
 		      "gi|%i\n", faa_buf[i].gi);
 	    }
-	  
+
 	  /*
 	   * Clean up memory for the next ieration.
 	   */
 	  seqalign = SeqAlignSetFree (seqalign);
 	  bsp = BioseqFree (bsp);
-	  
-	} // End existing entry not found.
+
+	}			// End existing entry not found.
 
       /*
        * Hash table entry found.  Keep the old value.
        */
       else
 	{
-	  gi_type_data* old_value = (gi_type_data*)ep->data;
+	  gi_type_data *old_value = (gi_type_data *) ep->data;
 	  new_buf[i].gi = old_value->gi;
-	  strncpy (new_buf[i].type, old_value->type, sizeof (new_buf[i].type));
-	  strncpy (new_buf[i].protein, old_value->protein, sizeof (new_buf[i].protein));
+	  strncpy (new_buf[i].type, old_value->type,
+		   sizeof (new_buf[i].type));
+	  strncpy (new_buf[i].protein, old_value->protein,
+		   sizeof (new_buf[i].protein));
 	}
-      
+
       /*
        * Write the data out to the file.
        */
-      if ( (i % 1000 == 0) && (i > 0) )
+      if ((i % 1000 == 0) && (i > 0))
 	{
 	  status = H5TBappend_records (file_id, "gi_type_data", 1000,
-				      gi_size, gi_offset, gi_sizes, 
-				      &new_buf[i-1000]);
+				       gi_size, gi_offset, gi_sizes,
+				       &new_buf[i - 1000]);
 	  if (status < 0)
 	    check_h5_error (status, __FILE__, __LINE__);
-	  
+
 	  status = H5Fflush (file_id, H5F_SCOPE_GLOBAL);
 	  if (status < 0)
 	    check_h5_error (status, __FILE__, __LINE__);
 
 	  written = i;
 
-	  printf ("Processed %i of %i records.\n", i, (int)faa_nrecords);
+	  printf ("Processed %i of %i records.\n", i, (int) faa_nrecords);
 	}
-      
+
     }
 
   /*
    * Write out records from the last bin if it was less than 1000
    * records in size.
    */
-  if ((int)faa_nrecords < 1000) 
+  if ((int) faa_nrecords < 1000)
     {
       status = H5TBappend_records (file_id, "gi_type_data", faa_nrecords,
-				  gi_size, gi_offset, gi_sizes,
-				  new_buf);
+				   gi_size, gi_offset, gi_sizes, new_buf);
     }
 
   else
     {
-      status = H5TBappend_records (file_id, "gi_type_data", faa_nrecords - written,
-				  gi_size, gi_offset, gi_sizes, 
-				   &new_buf[written]);
+      status =
+	H5TBappend_records (file_id, "gi_type_data", faa_nrecords - written,
+			    gi_size, gi_offset, gi_sizes, &new_buf[written]);
     }
 
   if (status < 0)
     check_h5_error (status, __FILE__, __LINE__);
-  
+
   status = H5Fflush (file_id, H5F_SCOPE_GLOBAL);
   if (status < 0)
     check_h5_error (status, __FILE__, __LINE__);
-  
+
   free (faa_buf);
   free (old_buf);
   free (new_buf);
@@ -339,6 +339,6 @@ assign_protein_type (hid_t file_id)
 
   options = BLASTOptionDelete (options);
   readdb_destruct (seqdb);
-  
+
   return;
 }
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 @@
 #define NFIELDS (hsize_t) 11
 
 void
-load_influenza_aa_dat (hid_t file_id, const char* file_name)
+load_influenza_aa_dat (hid_t file_id, const char *file_name)
 {
   /*
    * Model the data using native types.
@@ -225,7 +225,8 @@ load_influenza_aa_dat (hid_t file_id, const char* file_name)
 	      if (status < 0)
 		check_h5_error (status, __FILE__, __LINE__);
 
-	      status = H5TBdelete_record (file_id, "influenza_aa.dat", 0, nrecords);
+	      status =
+		H5TBdelete_record (file_id, "influenza_aa.dat", 0, nrecords);
 	      if (status < 0)
 		check_h5_error (status, __FILE__, __LINE__);
 
@@ -233,7 +234,7 @@ 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 (status, __FILE__, __LINE__);
 	    }
 
 	  /*
@@ -242,8 +243,10 @@ load_influenza_aa_dat (hid_t file_id, const char* file_name)
 	  else
 	    {
 	      herr_t status = H5TBmake_table ("influenza_aa.dat", file_id,
-					      "influenza_aa.dat", NFIELDS, 1, dst_size,
-					      field_names, dst_offset, field_type,
+					      "influenza_aa.dat", NFIELDS, 1,
+					      dst_size,
+					      field_names, dst_offset,
+					      field_type,
 					      chunk_size, fill_data, compress,
 					      &p_data);
 	      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 @@
  * Load the supplementary protein data from the NCBI influenza_aa.dat
  * file.
  */
-void load_influenza_aa_dat (hid_t file_id, const char* file_name);
+void load_influenza_aa_dat (hid_t file_id, const char *file_name);
 
 #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 @@
 #include <stdlib.h>
 
 void
-load_influenza_faa (hid_t file_id, const char* file_name)
+load_influenza_faa (hid_t file_id, const char *file_name)
 {
   size_t dst_size;
   size_t dst_offset[SEQUENCE_DATA_FIELD_NUM];
@@ -16,7 +16,7 @@ load_influenza_faa (hid_t file_id, const char* file_name)
   hid_t field_type[SEQUENCE_DATA_FIELD_NUM];
 
   sequence_data_init (&dst_size, dst_offset, dst_sizes, field_type);
-  
+
   hsize_t chunk_size = 10;
   int *fill_data = NULL;
   int compress = 0;
@@ -31,17 +31,17 @@ load_influenza_faa (hid_t file_id, const char* file_name)
 
   while (getline (&line, &len, dat) != -1)
     {
-      current_line++;      
+      current_line++;
 
       // Header line.
       if (line[0] == '>')
 	{
 	  char *running = strdup (line);
 	  char *token = NULL;
-	  
+
 	  // Eat the ">gi".
 	  strsep (&running, "|");
-	  
+
 	  // GI value.
 	  token = strsep (&running, "|");
 	  p_data.gi = atoi (token);
@@ -50,13 +50,13 @@ load_influenza_faa (hid_t file_id, const char* file_name)
 	  strsep (&running, "|");
 
 	  // GB value.
-	  strncpy (p_data.gb, strsep(&running, "|"), sizeof (p_data.gb));
+	  strncpy (p_data.gb, strsep (&running, "|"), sizeof (p_data.gb));
 
 	  // Description value.
 	  strncpy (p_data.description, strsep (&running, "|"),
 		   sizeof (p_data.description));
 
-	  const char* sequence_data_field_names[SEQUENCE_DATA_FIELD_NUM] =
+	  const char *sequence_data_field_names[SEQUENCE_DATA_FIELD_NUM] =
 	    SEQUENCE_DATA_FIELD_NAMES;
 
 	  if (current_line == 1)
@@ -68,12 +68,14 @@ load_influenza_faa (hid_t file_id, const char* file_name)
 		{
 		  hsize_t nfields = 0;
 		  hsize_t nrecords = 0;
-		  herr_t status = H5TBget_table_info (file_id, "influenza.faa", &nfields,
-						      &nrecords);
+		  herr_t status =
+		    H5TBget_table_info (file_id, "influenza.faa", &nfields,
+					&nrecords);
 		  if (status < 0)
 		    check_h5_error (status, __FILE__, __LINE__);
 
-		  status = H5TBdelete_record (file_id, "influenza.faa", 0, nrecords);
+		  status =
+		    H5TBdelete_record (file_id, "influenza.faa", 0, nrecords);
 		  if (status < 0)
 		    check_h5_error (status, __FILE__, __LINE__);
 
@@ -92,9 +94,11 @@ load_influenza_faa (hid_t file_id, const char* file_name)
 		  herr_t status = H5TBmake_table ("influenza.faa", file_id,
 						  "influenza.faa",
 						  SEQUENCE_DATA_FIELD_NUM, 1,
-						  dst_size, sequence_data_field_names,
+						  dst_size,
+						  sequence_data_field_names,
 						  dst_offset, field_type,
-						  chunk_size, fill_data, compress,
+						  chunk_size, fill_data,
+						  compress,
 						  &p_data);
 		  if (status < 0)
 		    check_h5_error (status, __FILE__, __LINE__);
@@ -114,7 +118,7 @@ load_influenza_faa (hid_t file_id, const char* file_name)
 	    free (running);
 
 	}
-      
+
     }
 
   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 @@
 /*
  * Load the protein sequence data from the NCBI influenza.faa file.
  */
-void load_influenza_faa (hid_t file_id, const char* file_name);
+void load_influenza_faa (hid_t file_id, const char *file_name);
 
 #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 @@
  * struct.  Perhaps an HDF5 precompiler could do such a thing.
  */
 void
-gi_type_data_init (size_t *dst_size, size_t *dst_offset, size_t *dst_sizes,
-		   hid_t *field_type)
+gi_type_data_init (size_t * dst_size, size_t * dst_offset, size_t * dst_sizes,
+		   hid_t * field_type)
 {
   *dst_size = sizeof (gi_type_data);
 
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 @@
  * structures are used by the HDF5 API.
  */
 void
-gi_type_data_init (size_t *dst_size, size_t *dst_offset, size_t *dst_sizes,
-		   hid_t *field_type);
+gi_type_data_init (size_t * dst_size, size_t * dst_offset, size_t * dst_sizes,
+		   hid_t * field_type);
 
 #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 @@
 #include "sequence_data_init.h"
 #include "sequence_data.h"
 
-void 
-sequence_data_init (size_t *dst_size, size_t *dst_offset, size_t *dst_sizes,
-		    hid_t *field_type)
+void
+sequence_data_init (size_t * dst_size, size_t * dst_offset,
+		    size_t * dst_sizes, hid_t * field_type)
 {
   *dst_size = sizeof (sequence_data);
-  
+
   dst_offset[0] = HOFFSET (sequence_data, gi);
   dst_offset[1] = HOFFSET (sequence_data, gb);
   dst_offset[2] = HOFFSET (sequence_data, description);
-  
+
   sequence_data dst_buf[1];
-  
+
   dst_sizes[0] = sizeof (dst_buf[0].gi);
   dst_sizes[1] = sizeof (dst_buf[0].gb);
   dst_sizes[2] = sizeof (dst_buf[0].description);
-  
+
   field_type[0] = H5T_NATIVE_INT;
-  
+
   hid_t gb_type = H5Tcopy (H5T_C_S1);
   H5Tset_size (gb_type, 9);
   field_type[1] = gb_type;
-  
+
   hid_t description_type = H5Tcopy (H5T_C_S1);
   H5Tset_size (description_type, 196);
   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 @@
  * Initialize the structures describing sequence_data.  These
  * descriptive structures are used by the HDF5 API.
  */
-void 
-sequence_data_init (size_t *dst_size, size_t *dst_offset, size_t *dst_sizes,
-		    hid_t *field_type);
+void
+sequence_data_init (size_t * dst_size, size_t * dst_offset,
+		    size_t * dst_sizes, hid_t * field_type);
 
 #endif // SEQUENCE_DATA_INIT_H