10 files changed, 99 insertions, 93 deletions

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;
 }