Removed the need for the -F command line option when a single input file is...

Removed the need for the -F command line option when a single input file is used. If blixem is called with one input file, it is assumed to contain both alignment data and the reference sequence. If it is called with two files, the first is assumed to contain the reference sequence and the second the alignment data. The -F option has been left in for now for backwards compatibility.

blxmain.c

@@ -27,7 +27,7 @@
  * Last edited: May 26 17:13 2009 (edgrif)
  * * Aug 26 16:57 1999 (fw): added this header
  * Created: Thu Aug 26 16:56:45 1999 (fw)
- * CVS info:   $Id: blxmain.c,v 1.22 2010-08-06 13:08:34 gb10 Exp $
+ * CVS info:   $Id: blxmain.c,v 1.23 2010-08-27 13:14:07 gb10 Exp $
  *-------------------------------------------------------------------
  */
 
@@ -54,11 +54,13 @@ static char *usageText ="\n\
  Copyright (c) 2009-2010: Genome Research Ltd.\n\
 \n\
 \n\
-  Usage: blixem [options] <sequencefile> <datafile> [X options] \n\
+  Usage: blixem [options] [<sequencefile>] <datafile> [X options] \n\
 \n\
  Both <sequencefile> and <datafile> can be substituted by \"-\"\n\
  for reading from stdin (pipe).  If <sequencefile> is piped, the first\n\
  line should contain the sequence name and the second the sequence itself.\n\
+ If <sequencefile> is ommitted, <datafile> should contain the reference\n\
+ sequence in FASTA format.\n\
 \n\
  Options:\n\
  -s <mode>  Sorting mode at startup.\n\
@@ -76,7 +78,6 @@ static char *usageText ="\n\
  -c <file>  Read configuration options from 'file'.\n\
  -k <file>  Read color/style options from key-value file 'file'. (See GLib Key-value-file-parser documentation.)\n\
  -S <n>     Start display at position n.\n\
- -F <file>  Read in query sequence and data from <file> (replaces sequencefile).\n\
  -h         Help and more options.\n\
  -o <optstring>\n\
             Blixem options, e.g. -o \"MBr\". You'll have to read the source code for details.\n\
@@ -251,8 +252,6 @@ int main(int argc, char **argv)
   int displayStart = 0;
   int qOffset = 0;
   int install = 1;
-  gboolean singleFile = FALSE;        /* if true, there is a single file containing both the query 
-                                         sequence and the alignment data */
   
   int          optc;
   extern int   optind;
@@ -308,7 +307,6 @@ int main(int argc, char **argv)
 	  key_file = strnew(optarg, 0) ;
           break;
 	case 'F': 
-	  singleFile = TRUE;        
 	  strcpy(FSfilename, optarg);
 	  break;
 	case 'h': 
@@ -383,10 +381,11 @@ int main(int argc, char **argv)
 	}
     }
 
-  if (argc-optind < 2 && !singleFile)
+  /* We expect one or two input files, or 0 input files if the FSfilename was already set with the -F option */
+  const int numFiles = argc - optind;
+  if (!(numFiles == 1 || numFiles == 2 || (numFiles == 0 && *FSfilename != '\0')))
     {
       fprintf(stderr, "%s\n", usage); 
-
       exit(EXIT_FAILURE);
     }
 
@@ -410,11 +409,15 @@ int main(int argc, char **argv)
   /* Read in the key file, if there is one */
   GSList *styles = blxReadStylesFile(key_file, &error);
   reportAndClearIfError(&error, G_LOG_LEVEL_CRITICAL);
-  
-  if (!singleFile)
+
+  if (numFiles == 1)
     {
-      /* The query sequence is in a separate file. */
-      
+      /* We have a single file containing both the aligments and the ref seq */
+      strcpy(FSfilename, argv[optind]);
+    }
+  else if (numFiles == 2)
+    {
+      /* The ref seq is in a separate file. Read it in now. */
       strcpy(seqfilename, argv[optind]);
       strcpy(FSfilename, argv[optind+1]);