Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalo / src / squid / revcomp.c

diff --git a/website/archive/binaries/mac/src/clustalo/src/squid/revcomp.c b/website/archive/binaries/mac/src/clustalo/src/squid/revcomp.c
deleted file mode 100644 (file)
index fed4981..0000000
--- a/website/archive/binaries/mac/src/clustalo/src/squid/revcomp.c
+++ /dev/null
@@ -1,87 +0,0 @@
-/*****************************************************************
- * 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.
- *****************************************************************/
-
-/* revcomp.c
- * 
- * Reverse complement of a IUPAC character string
- * RCS $Id: revcomp.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: revcomp.c,v 1.5 2002/06/25 20:06:06 eddy Exp)
- */
-
-#include <stdio.h>
-#include <string.h>
-#include <ctype.h>
-#include "squid.h"
-
-/* Function: revcomp()
- *
- * Purpose:  Reverse complement seq; store in comp.
- *           Can revcomp "in place" (revcomp(seq, seq)).
- *
- * Args:     comp  - destination for reverse complement of seq
- *           seq   - sequence to reverse complement
- *
- * Returns:  NULL on failure; or a (useless) pointer to comp.
- */
-char *
-revcomp(char *comp, char *seq)
-{
-  char *s;
-  char  c;
-
-  if (comp == NULL) return NULL;
-  if (seq == NULL)  return NULL;
-
-  StrReverse(comp, seq);
-  for (s = comp; *s != '\0'; s++)
-    {
-      c = *s;
-      c = sre_toupper(c);
-      switch (c) {
-      case 'A': c = 'T'; break;
-      case 'C': c = 'G'; break;
-      case 'G': c = 'C'; break;
-      case 'T': c = 'A'; break;
-      case 'U': c = 'A'; break;
-      case 'R': c = 'Y'; break;
-      case 'Y': c = 'R'; break;
-      case 'M': c = 'K'; break;
-      case 'K': c = 'M'; break;
-      case 'S': c = 'S'; break;
-      case 'W': c = 'W'; break;
-      case 'H': c = 'D'; break;
-      case 'D': c = 'H'; break;
-      case 'B': c = 'V'; break;
-      case 'V': c = 'B'; break;
-      default:  break;         /* anything else? leave it; it's prob a gap or an X */
-      }
-      if (islower((int) *s)) c = (char) sre_tolower((int) c);
-      *s = c;
-    }
-  return comp;
-}
-  
-#ifdef REVCOMP_TESTDRIVER
-/* gcc -g -DREVCOMP_TESTDRIVER revcomp.c sre_string.c shuffle.c sre_math.c sre_ctype.c sqerror.c -lm
-*/
-int
-main(void)
-{
-  float p[4]     = {0.25, 0.25, 0.25, 0.25};
-  char *alphabet = "ACGT";
-  int   len      = 10;
-  char *seq;
-
-  seq = RandomSequence(alphabet, p, 4, len);
-  printf("%s\n", seq);
-  revcomp(seq, seq);
-  printf("%s\n", seq);
-  free(seq);
-  exit(0);
-}
-#endif