From e57116f25523fc6e27c7b49f9241dd7e20fb2789 Mon Sep 17 00:00:00 2001
From: Don Pellegrino <don@drexel.edu>
Date: Tue, 19 Jan 2010 20:49:49 +0000
Subject: Cleaned up some of the documentation.

---
diff --git a/src/assign/assign_protein_type.c b/src/assign/assign_protein_type.c
index 3947800..9a0717b 100644
--- a/src/assign/assign_protein_type.c
+++ b/src/assign/assign_protein_type.c
@@ -42,6 +42,7 @@ assign_protein_type (hid_t file_id)
    * Make BLAST messages reportable.
    */
   ErrSetMessageLevel (SEV_WARNING);
+  ValNodePtr error_returns = NULL;
 
   /*
    * Open the BLAST sequence database.
@@ -59,8 +60,6 @@ assign_protein_type (hid_t file_id)
   options->window_size = 0;
   options->multiple_hits_only = false;
 
-  ValNodePtr error_returns = NULL;
-
   /*
    * Read the data from HDF5 influenza.faa.
    */
@@ -240,7 +239,7 @@ assign_protein_type (hid_t file_id)
 	  
 	  /*
 	   * A hit was found.  Record the first hit as the protein type.
-	   * Skip the first 6 characters and eat the "lcl|x_".
+	   * Skip the first 4 characters and eat the "lcl|".
 	   */
 	  else if (seqalign != NULL)
 	    {
@@ -253,7 +252,7 @@ assign_protein_type (hid_t file_id)
 	      new_buf[i].type[0] = target_id_buf[4];
 	      new_buf[i].type[1] = '\0';
 	      
-	      // Protein Type
+	      // Protein Type (Skip the underscore in the string).
 	      strncpy (new_buf[i].protein, &target_id_buf[6], 
 		       sizeof (new_buf[i].protein));	     
 	    }
--
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