#include <R_ext/Utils.h>        /* R_CheckUserInterrupt */
#include <ctype.h>              /* isspace */
#include "ShortRead.h"

unsigned char _bDecode(char);
unsigned char _dnaDecode(char);
unsigned char _rnaDecode(char);


#include <Rversion.h>

#if R_VERSION < R_Version(4, 6, 0)
# define R_getVar(x,y,z) findVar(x,y)
#endif


/*
 * Encode / decode XString wrappers
 */

char _bEncode(char c)
{
    return c;
}

#define _dnaEncode DNAencode;
#define _rnaEncode RNAencode;

unsigned char _bDecode(char c)
{
    return (unsigned char) c;
}

unsigned char _dnaDecode(char c)
{
    return (unsigned char) DNAdecode(c);
}

unsigned char _rnaDecode(char c)
{
    return (unsigned char) RNAdecode(c);
}

DECODE_FUNC decoder(const char *base)
{
    DECODE_FUNC decode = NULL;
    if (strcmp(base, "DNAString") == 0) {
        decode = _dnaDecode;
    } else if (strcmp(base, "RNAString") == 0) {
        decode = _rnaDecode;
    } else if (strcmp(base, "BString") == 0) {
        decode = _bDecode;
    } else if (strcmp(base, "AAString") == 0) {
        decode = _bDecode;
    } else {
        Rf_error("unknown class '%s'", base);
    }
    return decode;
}

ENCODE_FUNC encoder(const char *base)
{
    ENCODE_FUNC encode = NULL;
    if (strcmp(base, "DNAString") == 0) {
        encode = _dnaEncode;
    } else if (strcmp(base, "RNAString") == 0) {
        encode = _rnaEncode;
    } else if (strcmp(base, "BString") == 0) {
        encode = _bEncode;
    } else if (strcmp(base, "AAString") == 0) {
        encode = _bEncode;
    } else {
        Rf_error("unknown class '%s'", base);
    }
    return encode;
}

SEXP _get_namespace(const char *pkg)
{
    SEXP fun = PROTECT(findFun(install("getNamespace"), R_GlobalEnv));
    SEXP nmspc = PROTECT(mkString(pkg));
    SEXP lng2 = PROTECT(lang2(fun, nmspc));
    nmspc = eval(lng2, R_GlobalEnv);
    UNPROTECT(3);
    return nmspc;
}

SEXP _get_strand_levels()
{
    SEXP nmspc = PROTECT(_get_namespace("ShortRead"));
    SEXP ans = eval(R_getVar(install(".STRAND_LEVELS"), nmspc, TRUE), nmspc);
    UNPROTECT(1);
    return ans;
}

int _char_as_strand_int(const char c, const char *fname, const int lineno)
{
    int strand = 0;
    if (c == '\0')
        strand = NA_INTEGER;
    else {
        switch (c) {
        case '+':
            strand = 1;
            break;
        case '-':
            strand = 2;
            break;
        default:
            error("invalid 'strand' field '%s', %s:%d", &c, fname, lineno);
            break;
        }
    }
    return strand;
}

/*
 * apply function 'with' to object 'from' in environment 'rho', e.g.,
 * becuase 'from' is an object and 'with' an accessor.
 */

SEXP _get_SEXP(SEXP from, SEXP rho, const char *with)
{
    SEXP fun = PROTECT(findFun(install(with), rho));
    SEXP lng2 = PROTECT(lang2(fun, from));
    SEXP res = eval(lng2, rho);
    UNPROTECT(2);
    return res;
}

/* 
 * populate elt with pointers into tab-delimited strings in ptr
 */

int _mark_field_0(char *ptr, char **elt, const int n_fields)
{
    elt[0] = ptr;
    int i = 0;
    for (; *ptr != '\0'; ++ptr)
        if (*ptr == '\t') {
            if (++i == n_fields)
                break;
            elt[i] = ptr + 1;
            *ptr = '\0';
        }
    if (*(ptr - 1) == '\n')     /* trailing newline? */
        *(ptr - 1) = '\0';
    return i + 1;
}

/*
 * parse lines into fields.
 *
 * string is parsed until a character in delim is found, or end of
 * string reached.
 *
 * return value is pointer to the start of the next field, or NULL if
 * no more fields.
 */

char *_mark_field_1(char *curr, const char *delim)
{
    char *c = curr;
    while (*c != '\0' && *c != *delim)
        c++;
    if (*c != '\0')             /* i.e., delim */
        *c++ = '\0';
    return c;
}

char *_mark_field_n(char *curr, const char *delim)
{
    const char *d = NULL;
    while (*curr != '\0' && *curr != '\n') {
        d = delim;
        while (*d != '\0' && *d != *curr)
            ++d;
        if (*d != '\0')
            *curr = '\0';
        else
            ++curr;
    }
    if (*curr == '\n') {
        *curr = '\0';
        return NULL;
    }
    return ((d == NULL) || (*d == '\0')) ? NULL : curr + 1;
}

SEXP _mark_field_test(SEXP filename, SEXP delimiters, SEXP dim)
{
    if (!IS_CHARACTER(filename) || LENGTH(filename) != 1)
        error("'%s' must be '%s'", "filename", "character(1)");
    if (!IS_CHARACTER(delimiters) || LENGTH(delimiters) != 1)
        error("'%s' must be '%s'", "delimiters", "character(1)");
    if (!IS_INTEGER(dim) || LENGTH(dim) != 2)
        error("'%s' must be '%s'", "dim", "integer(2)");

    SEXP ans = PROTECT(NEW_LIST(INTEGER(dim)[0]));
    int i, j;
    for (i = 0; i < INTEGER(dim)[0]; ++i)
        SET_VECTOR_ELT(ans, i, NEW_CHARACTER(INTEGER(dim)[1]));

#define LINEBUF_SIZE 1024
    FILE *file;
    char linebuf[LINEBUF_SIZE];
    if ((file = fopen(CHAR(STRING_ELT(filename, 0)), "rb")) == NULL)
        error("cannot open file '%s'", CHAR(STRING_ELT(filename, 0)));
    const char *delim = CHAR(STRING_ELT(delimiters, 0));

    for (i = 0; i < INTEGER(dim)[0]; ++i) {
        if (fgets(linebuf, LINEBUF_SIZE, file) == NULL)
            error("unexpected end-of-file");
        j = 0;
        char *curr = linebuf, *next;
        while (curr != NULL) {
            if (j >= INTEGER(dim)[1])
                error("too many fields");
            next = _mark_field_n(curr, delim);
            SET_STRING_ELT(VECTOR_ELT(ans, i), j, mkChar(curr));
            j++;
            curr = next;
        }
    }
    fclose(file);
#undef LINEBUF_SIZE

    UNPROTECT(1);
    return ans;
}

const int LINEBUF_SIZE = 2000001;

/*
 * open and check file; signal error
 */
gzFile _fopen(const char *fname, const char *mode)
{
    gzFile file = gzopen(fname, mode);
    if (file == NULL)
        error("cannot open file %s", fname);
    return file;
}

/*
 * trim & check linebuf, return 0 if processing should continue
 */
int _linebuf_skip_p(char *linebuf, gzFile file, const char *fname, int lineno,
                    const char *commentChar)
{
    int nchar_in_buf;
    nchar_in_buf = _rtrim(linebuf);
    if (nchar_in_buf >= LINEBUF_SIZE - 1) {	// should never be >
        gzclose(file);
        error("line too long %s:%d", fname, lineno);
    } else if (nchar_in_buf == 0) {
        gzclose(file);
        error("unexpected empty line %s:%d", fname, lineno);
    }
    return *linebuf == *commentChar;
}

/*
 * Return the number of chars that remain in the buffer after we've removed
 * the right spaces ('\n', '\r', '\t', ' ', etc...)
 */
int _rtrim(char *linebuf)
{
    int i;

    i = strlen(linebuf) - 1;
    while (i >= 0 && isspace(linebuf[i]))
        i--;
    linebuf[++i] = 0;
    return i;
}

/*
 * Solexa sometimes encodes an uncalled base as '.', but the
 * Biostrings standard is '-'. Convert a null-terminated character
 * string in-place.
 */
void _solexa_to_IUPAC(char *p)
{
    while ((p = strchr(p, '.')) != NULL)
        *p = '-';
}

void _reverse(char *linebuf)
{
    size_t len = strlen(linebuf);
    int i;
    char tmp;
    for (i = 0; i < floor(len / 2); ++i) {
        tmp = linebuf[len - i - 1];
        linebuf[len - i - 1] = linebuf[i];
        linebuf[i] = tmp;
    }
}

void _reverseComplement(char *linebuf)
{
    static const int MAX_MAP = 256;
    static char map[256];
    static int init = 0;
    if (init == 0) {
        init = 1;
        for (int i = 0; i < MAX_MAP; ++i)
            map[i] = (char) i;
        map['A'] = 'T';
        map['C'] = 'G';
        map['G'] = 'C';
        map['T'] = 'A';
        map['a'] = 't';
        map['c'] = 'g';
        map['g'] = 'c';
        map['t'] = 'a';
    }
    _reverse(linebuf);
    for (unsigned int i = 0; i < strlen(linebuf); ++i)
        linebuf[i] = map[(int) linebuf[i]];
}

/*
 * Chenge vector class and attribute to represent factor
 */
void _as_factor_SEXP(SEXP vec, SEXP lvls)
{
    SEXP cls = PROTECT(NEW_CHARACTER(1));
    SET_STRING_ELT(cls, 0, mkChar("factor"));
    SET_CLASS(vec, cls);
    SET_ATTR(vec, install("levels"), lvls);
    UNPROTECT(1);
}

void _as_factor(SEXP vec, const char **levels, const int n_lvls)
{
    SEXP lvls = PROTECT(NEW_CHARACTER(n_lvls));
    int i;
    for (i = 0; i < n_lvls; ++i)
        SET_STRING_ELT(lvls, i, mkChar(levels[i]));
    _as_factor_SEXP(vec, lvls);
    UNPROTECT(1);
}
