/* iupac - routines to help cope with IUPAC ambiguity codes in DNA sequence. */

#ifndef IUPAC_H
#define IUPAC_H

boolean iupacMatch(char iupac, char dna);
/* See if iupac ambiguity code matches dna character */

boolean iupacMatchLower(char iupac, char dna);
/* See if iupac ambiguity code matches dna character where
 * both are lower case */

boolean isIupac(char c);
/* See if iupac c is a legal iupac char */

boolean isIupacLower(char c);
/* See if iupac c is a legal (lower case) iupac char */

void iupacFilter(char *in, char *out);
/* Filter out non-DNA non-UIPAC ambiguity code characters and change to lower case. */

boolean anyIupac(char *s);
/* Return TRUE if there are any IUPAC ambiguity codes in s */

char iupacComplementBaseLower(char iupac);
/* Return IUPAC complement for a single base */

void iupacComplementLower(char *iupac, int iuSize);
/* Return IUPAC complement many bases. Assumes iupac is lower case. */

void iupacReverseComplement(char *iu, int iuSize);
/* Reverse complement a string containing DNA and IUPAC codes. Result will be always
 * lower case. */

boolean iupacMatchStart(char *iupacPrefix, char *dnaString);
/* Return TRUE if start of DNA is compatible with iupac */

char *iupacIn(char *needle, char *haystack);
/* Return first place in haystack (DNA) that matches needle that may contain IUPAC codes. */

INLINE boolean isIupacAmbiguous(char c)
/* Return TRUE if c is an IUPAC ambiguity code. */
{
switch (tolower(c))
    {
    case 'r':
    case 'y':
    case 's':
    case 'w':
    case 'k':
    case 'm':
    case 'b':
    case 'd':
    case 'h':
    case 'v':
    case 'n':
        return TRUE;
    }
return FALSE;
}

INLINE char *iupacAmbiguousToString(char c)
/* Return a static string of [acgt] bases that C would resolve to. */
{
switch (tolower(c))
    {
    case 'r':
        return "ag";
    case 'y':
        return "ct";
    case 's':
        return "cg";
    case 'w':
        return "at";
    case 'k':
        return "gt";
    case 'm':
        return "ac";
    case 'b':
        return "cgt";
    case 'd':
        return "agt";
    case 'h':
        return "act";
    case 'v':
        return "acg";
    case 'n':
        return "acgt";
    default:
        errAbort("iupacAmbiguousToString: unrecognized character '%c'", c);
    }
return NULL;
}

#endif /* IUPAC_H */