Mac binaries

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

diff --git a/website/archive/binaries/mac/src/clustalo/src/squid/seqencode.c b/website/archive/binaries/mac/src/clustalo/src/squid/seqencode.c
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+++ b/website/archive/binaries/mac/src/clustalo/src/squid/seqencode.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.
+ *****************************************************************/
+
+/* seqencode.c
+ * 
+ * Routines for creating and manipulating encoded sequence strings.
+ * RCS $Id: seqencode.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: seqencode.c,v 1.3 1999/05/02 21:55:27 eddy Exp)
+ */
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+#include "squid.h"
+
+                       
+#ifdef MEMDEBUG
+#include "dbmalloc.h"
+#endif
+                               /* seqcmp()
+                                  returns 0 if s1 == s2
+                                  mismatch number otherwise */
+int
+seqcmp(char *s1, char *s2, int allow)
+{
+  int mmat = 0;
+
+  while ((*s1 != NTEND) && (*s2 != NTEND) && (mmat <= allow)) 
+    {
+      if (!(ntmatch(*s1, *s2)))
+       mmat++;;
+      s1++;
+      s2++;
+    }
+  while ((*s1++ != NTEND) && (mmat <= allow))
+    mmat++;
+  return(mmat);
+}
+                               /* seqncmp()
+                                  same as seqcmp but it looks at,
+                                  at most, n positions */
+int
+seqncmp(char *s1, char *s2, int n, int allow)
+{
+  int mmat = 0;
+
+  while ((*s2 != NTEND) &&
+        (n-- != 0))
+    {
+      if ((!(ntmatch(*s1, *s2))) &&
+         (++mmat > allow))
+       return(mmat);
+      s1++;
+      s2++;
+    }
+  while ((n-- != 0) && (*s1++ != NTEND) && (mmat <= allow))
+    mmat++;
+  return (mmat);
+}
+      
+                               /* seqencode()
+                                  given a character text string str (A,C,G,T),
+                                  convert to an encoded seq string;
+                                  return 1 for success, 0 if fail */
+int
+seqencode(char *codeseq, /* pre-allocated space for answer */
+         char *str)     /* character string to convert    */
+{
+  char  *ptr;
+  int    idx;
+
+  ptr = codeseq;
+  while (*str != '\0')
+    {
+      if (islower((int) (*str))) *str = (char) toupper((int) (*str));
+      for (idx = 0; *str != iupac[idx].sym && idx <= IUPACSYMNUM; idx++)
+       ;
+      if (idx > IUPACSYMNUM)
+       {
+         *ptr = (char) NTEND;
+         return 0;
+       }
+      else
+       *ptr = iupac[idx].code;
+      ptr++;
+      str++;
+    }
+  *ptr = NTEND;
+  return 1;
+}
+
+
+int
+coded_revcomp(char *comp, char *seq)
+{
+  long  bases;
+  char *bckp, *fwdp;
+  int   idx;
+  long  pos;
+
+  bases = strlen(seq);
+
+  fwdp = comp;
+  bckp = seq + bases -1;
+  for (pos = 0; pos < bases; pos++)
+    {
+      for (idx = 0; *bckp != iupac[idx].code && idx < IUPACSYMNUM; idx++);
+      if (idx > IUPACSYMNUM)
+       {
+         *fwdp = NTEND;
+         return 0;
+       }
+      else
+       *fwdp = iupac[idx].comp;
+      fwdp++;
+      bckp--;
+    }
+  *fwdp = NTEND;
+  return(1);
+}
+  
+int
+seqdecode(char *str, char *codeseq)
+{
+  int idx;
+  int pos;
+
+  pos = 0;
+  while (*codeseq != NTEND)
+    {
+      for (idx = 0; *codeseq != iupac[idx].code && idx < IUPACSYMNUM; idx++)
+       ;
+      if (idx > IUPACSYMNUM)
+       {
+         str[pos] = 'X';
+         return 0;
+       }
+      else
+       str[pos] = iupac[idx].sym;
+      codeseq++;
+      pos++;
+    }
+  str[pos] = '\0';
+  return 1;
+}
+
+int
+seqndecode(
+     char       *str,          /* pre-allocated string to write into */
+     char *codeseq,            /* sequence to decode */
+     int         n)            /* how many bases to decode */
+{
+  int idx;
+  int pos = 0;
+
+  while (--n >= 0)
+    {
+      for (idx = 0; *codeseq != iupac[idx].code && idx < IUPACSYMNUM; idx++);
+      if (idx > IUPACSYMNUM)
+       {
+         str[pos]  = 'X';
+         return 0;
+       }
+      else
+       str[pos] = iupac[idx].sym;
+      codeseq++;
+      pos++;
+    }
+  str[pos] = '\0';
+  return 1;
+}
+