Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/clustalo/src/squid/rk.c b/website/archive/binaries/mac/src/clustalo/src/squid/rk.c
deleted file mode 100644 (file)
index e731393..0000000
--- a/website/archive/binaries/mac/src/clustalo/src/squid/rk.c
+++ /dev/null
@@ -1,133 +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.
- *****************************************************************/
-
-/* rk.c (originally from rnabob's patsearch.c)
- * 
- * Contains a compiler and a search engine for Rabin-Karp
- * based primary sequence pattern searching on encoded
- * sequences.
- * 
- * See Sedgewick, _Algorithms_, for a general discussion of
- * the Rabin-Karp algorithm. See the rkcomp or rkexec man
- * pages for specific details.
- * 
- * RCS $Id: rk.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: rk.c,v 1.2 1998/10/09 18:07:16 eddy Exp)
- */
-
-#include <stdio.h>
-#include <string.h>
-#include <ctype.h>
-#include "squid.h"             /* seq encoding utilities and typedefs */
-#include "rk.h"
-
-
-#ifdef MEMDEBUG
-#include "dbmalloc.h"
-#endif
-
-Hashseq
-rkcomp(char *probe)               /* A,C,G,T/U, N probe string, 0-8 nt long */
-{
-  Hashseq hashprobe = 0;
-  char    coded[RK_HASHSIZE + 1];
-  int     len;
-  int     i;
-                               /* check bounds violation on probe */
-  if ((len =  strlen(probe)) > RK_HASHSIZE) return 0;
-                               /* encode the probe */
-  if (seqencode(coded, probe) == 0) return 0;
-                               /* pack the probe into a Hashseq */
-  for (i = 0; i < len; i++)
-    {
-      hashprobe <<= 4;
-      hashprobe |= (Hashseq) coded[i];
-    }
-                               /* left adjust as needed */
-  for (; i < RK_HASHSIZE; i++)
-    {
-      hashprobe <<= 4;
-      hashprobe |= (Hashseq) NTN;
-    }
-                               /* return the compiled probe */
-  return hashprobe;
-}
-  
-int
-rkseq(Hashseq   hashprobe,     /* up to 8 nt packed into the probe */
-      char     *sequence)       /* encoded sequence                 */
-{
-  long     i;
-  long     pos = 0;
-  Hashseq  target = 0;
-  
-                               /* initialize the target hashseq */
-  for (i = 0; i < RK_HASHSIZE; i++)
-    {
-      if (*(sequence + i) == NTEND)
-       break;
-      target <<= 4;
-      target |=  (Hashseq) (*(sequence + i));
-    }
-
-  while (*(sequence + pos + RK_HASHSIZE -1) != NTEND)
-    {
-#ifdef DEBUG
-      printf("hashprobe: ");
-      writehash(hashprobe);
-      printf("\ttarget: ");
-      writehash(target);
-      printf("\nhashprobe & target: ");
-      writehash(hashprobe & target);
-      printf("\n");
-#endif
-      if ((hashprobe & target) == target)
-       return ((int) pos);
-      target <<= 4;
-      target |=  (Hashseq) (*(sequence + pos + RK_HASHSIZE));
-      pos++;
-    }
-                               /* now we deal with an end effect */
-  for (i = 0; i < RK_HASHSIZE; i++)
-    {
-      target |= (Hashseq) NTN;
-      if ((hashprobe & target) == target)
-       return ((int) pos);
-      target <<=4;
-      pos++;
-    }
-
-  return(-1);
-}
-
-
-#ifdef DEBUG                   /* Debugging aids */
-
-static void
-writehash(Hashseq   hashseq)
-{
-  int idx;
-  int sym;
-
-  if (hashseq/16)
-    writehash(hashseq/16);
-  
-  sym = (int) (hashseq % 16);
-  if (sym == 0)
-    putchar('-');
-  else
-    {
-      for (idx = 0; sym != iupac[idx].code && idx < IUPACSYMNUM; idx++);
-      if (idx > IUPACSYMNUM)
-        printf("(%d)", sym);
-      else
-        putchar(iupac[idx].sym);
-    }
-}
-
-#endif