--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clustalomega/clustal-omega-0.2.0/src/squid/getopt.c	Tue Jun 07 17:04:25 2011 -0400
@@ -0,0 +1,250 @@
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ * 
+ *     This source code is freely distributed under the terms of the
+ *     GNU General Public License. See the files COPYRIGHT and LICENSE
+ *     for details.
+ *****************************************************************/
+
+/* RCS $Id: getopt.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: getopt.c,v 1.7 2001/02/21 21:09:10 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+
+#include "squid.h"
+
+/* Function: Getopt()
+ * 
+ * Purpose:  Portable command line option parsing with abbreviated
+ *           option switches. Replaces UNIX getopt(). Using UNIX getopt()
+ *           hinders portability to non-UNIX platforms, and getopt()
+ *           is also limited to single letter options.
+ *
+ *           Getopt() implements a superset of UNIX getopt().
+ *           All of getopt()'s single-character switch behavior
+ *           is emulated, and "--" by itself terminates the options.
+ *           Additionally, Getopt() provides extended switches
+ *           like "--youroptionhere", and Getopt() type checks
+ *           arguments.  
+ * 
+ *           Extended options must start with "--", as in "--option1".
+ *           Normal options must start with "-", as in "-o".
+ *           Normal options may be concatenated, as in "-a -b" == "-ab".
+ *           
+ *           See bottom of this .c file after #fdef GETOPT_TESTDRIVER
+ *           for an example of calling Getopt().
+ *           
+ * Args:     argc  - from main(). number of elems in argv.
+ *           argv  - from main(). argv[0] is the name of the command.
+ *           opt   - array of opt_s structures, defining option switches
+ *           nopts - number of switches in opt
+ *           usage - a (possibly long) string to print if usage error.
+ *           ret_optind - RETURN: the index in argv[] of the next 
+ *                        valid command-line token.
+ *           ret_optname- RETURN: ptr to the name of option switch 
+ *                        seen, or NULL if no option was seen.
+ *           ret_optarg - RETURN: ptr to the optional argument, if any;
+ *                        NULL if option takes no argument.
+ *                        
+ * Return:   1 if a valid option was parsed.
+ *           0 if no option was found, and command-line parsing is complete.
+ *           Die()'s here if an error is detected.
+ */
+int
+Getopt(int argc, char **argv, struct opt_s *opt, int nopts, char *usage,
+       int *ret_optind, char **ret_optname, char **ret_optarg)
+{
+  int i;
+  int arglen;
+  int nmatch;
+  static int optind   = 1;        /* init to 1 on first call  */
+  static char *optptr = NULL;     /* ptr to next valid switch */
+  int opti = 0;			  /* init only to silence gcc uninit warnings */
+
+  /* Check to see if we've run out of options.
+   * A '-' by itself is an argument (e.g. "read from stdin")
+   * not an option.
+   */
+  if (optind >= argc || argv[optind][0] != '-' || strcmp(argv[optind], "-") == 0)
+    { 
+      *ret_optind  = optind; 
+      *ret_optarg  = NULL; 
+      *ret_optname = NULL; 
+      return 0; 
+    }
+
+  /* Check to see if we're being told that this is the end
+   * of the options with the special "--" flag.
+   */
+  if (strcmp(argv[optind], "--") == 0)
+    { 
+      optind++;
+      *ret_optind  = optind; 
+      *ret_optname = NULL;
+      *ret_optarg  = NULL; 
+      return 0; 
+    }
+
+  /* We have a real option. Find which one it is.
+   * We handle single letter switches "-o" separately
+   * from full switches "--option", based on the "-" vs. "--"
+   * prefix -- single letter switches can be concatenated
+   * as long as they don't have arguments.
+   */
+				/* full option */
+  if (optptr == NULL && strncmp(argv[optind], "--", 2) == 0)
+    {
+      /* Use optptr to parse argument in options of form "--foo=666"
+       */
+      if ((optptr = strchr(argv[optind], '=')) != NULL)
+	{ *optptr = '\0'; optptr++; }
+
+      arglen = strlen(argv[optind]);
+      nmatch = 0;
+      for (i = 0; i < nopts; i++)
+	if (opt[i].single == FALSE && 
+	    strncmp(opt[i].name, argv[optind], arglen) == 0)
+	  { 
+	    nmatch++;
+	    opti = i;
+	    if (arglen == strlen(opt[i].name)) break; /* exact match, stop now */
+	  }
+      if (nmatch > 1 && arglen != strlen(opt[i].name)) 
+	Die("Option \"%s\" is ambiguous; please be more specific.\n%s",
+	    argv[optind], usage);
+      if (nmatch == 0)
+	Die("No such option \"%s\".\n%s", argv[optind], usage);
+
+      *ret_optname = opt[opti].name;
+
+      /* Set the argument, if there is one
+       */
+      if (opt[opti].argtype != sqdARG_NONE) 
+	{
+	  if (optptr != NULL)
+	    {			/* --foo=666 style */
+	      *ret_optarg = optptr;
+	      optptr = NULL;
+	      optind++;
+	    }
+	  else if (optind+1 >= argc)
+	    Die("Option %s requires an argument\n%s", opt[opti].name, usage);
+	  else			/* "--foo 666" style */
+	    {
+	      *ret_optarg = argv[optind+1];
+	      optind+=2;
+	    }
+	}
+      else  /* sqdARG_NONE */
+	{
+	  if (optptr != NULL) 
+	    Die("Option %s does not take an argument\n%s", opt[opti].name, usage);
+	  *ret_optarg = NULL;
+	  optind++;
+	}
+    }
+  else				/* else, a single letter option "-o" */
+    {
+				/* find the option */
+      if (optptr == NULL) 
+	optptr = argv[optind]+1;
+      for (opti = -1, i = 0; i < nopts; i++)
+	if (opt[i].single == TRUE && *optptr == opt[i].name[1])
+	  { opti = i; break; }
+      if (opti == -1)
+	Die("No such option \"%c\".\n%s", *optptr, usage);
+      *ret_optname = opt[opti].name;
+
+				/* set the argument, if there is one */
+      if (opt[opti].argtype != sqdARG_NONE) 
+	{
+	  if (*(optptr+1) != '\0')   /* attached argument */
+	    {
+	      *ret_optarg = optptr+1;
+	      optind++;
+	    }
+	  else if (optind+1 < argc) /* unattached argument */
+	    {
+	      *ret_optarg = argv[optind+1];
+	      optind+=2;	      
+	    }
+	  else Die("Option %s requires an argument\n%s", opt[opti].name, usage);
+
+	  optptr = NULL;	/* can't concatenate after an argument */
+	}
+      else  /* sqdARG_NONE */
+	{
+	  *ret_optarg = NULL;
+	  if (*(optptr+1) != '\0')   /* concatenation */
+	    optptr++; 
+	  else
+	    {
+	      optind++;                /* move to next field */
+	      optptr = NULL;
+	    }
+	}
+
+    }
+
+  /* Type check the argument, if there is one
+   */
+  if (opt[opti].argtype != sqdARG_NONE) 
+    {
+      if (opt[opti].argtype == sqdARG_INT && ! IsInt(*ret_optarg))
+	Die("Option %s requires an integer argument\n%s",
+	    opt[opti].name, usage);
+      else if (opt[opti].argtype == sqdARG_FLOAT && ! IsReal(*ret_optarg))
+	Die("Option %s requires a numerical argument\n%s",
+	    opt[opti].name, usage);
+      else if (opt[opti].argtype == sqdARG_CHAR && strlen(*ret_optarg) != 1)
+	Die("Option %s requires a single-character argument\n%s",
+	    opt[opti].name, usage);
+      /* sqdARG_STRING is always ok, no type check necessary */
+    }
+
+  *ret_optind = optind;
+  return 1;
+}
+
+
+
+#ifdef GETOPT_TESTDRIVER 
+/* cc -DGETOPT_TESTDRIVER -L ~/lib/squid.linux/ getopt.c -lsquid
+ */
+struct opt_s OPTIONS[] = {
+  { "--test1", FALSE, sqdARG_INT    },
+  { "--test2", FALSE, sqdARG_FLOAT  },
+  { "--test3", FALSE, sqdARG_STRING },
+  { "--test4", FALSE, sqdARG_CHAR   },
+  { "-a",      TRUE,  sqdARG_NONE   },
+  { "-b",      TRUE,  sqdARG_INT    },
+};
+#define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s))
+    
+int
+main(int argc, char **argv)
+{
+  int   optind;
+  char *optarg;
+  char *optname;
+
+  while (Getopt(argc, argv, OPTIONS, NOPTIONS, "Usage/help here",
+		&optind, &optname, &optarg))
+    {
+      printf("Option:   index: %d name: %s argument: %s\n",
+	     optind, optname, optarg);
+    }
+  while (optind < argc)
+    {
+      printf("Argument: index: %d name: %s\n", optind, argv[optind]);
+      optind++;
+    }
+
+
+}
+
+
+#endif /*GETOPT_TESTDRIVER*/