Wrapper for Clustal Omega.

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

diff --git a/binaries/src/clustalo/src/squid/revcomp.c b/binaries/src/clustalo/src/squid/revcomp.c
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+/*****************************************************************
+ * 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