Fix usage of gmx_eof

[gromacs.git] / src / gromacs / utility / cstringutil.c

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with GROMACS; if not, see
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 */
/* This file is completely threadsafe - keep it that way! */
#include "cstringutil.h"

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <assert.h>
#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>

#include <sys/types.h>
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
#ifdef HAVE_PWD_H
#include <pwd.h>
#endif
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif

#include "gromacs/legacyheaders/types/simple.h"
#include "gromacs/legacyheaders/gmx_fatal.h"
#include "gromacs/legacyheaders/main.h"

#include "gromacs/fileio/futil.h"
#include "gromacs/utility/smalloc.h"

int continuing(char *s)
{
    int sl;
    assert(s);

    rtrim(s);
    sl = strlen(s);
    if ((sl > 0) && (s[sl-1] == CONTINUE))
    {
        s[sl-1] = 0;
        return TRUE;
    }
    else
    {
        return FALSE;
    }
}



char *fgets2(char *line, int n, FILE *stream)
{
    char *c;
    if (fgets(line, n, stream) == NULL)
    {
        return NULL;
    }
    if ((c = strchr(line, '\n')) != NULL)
    {
        *c = '\0';
    }
    else
    {
        /* A line not ending in a newline can only occur at the end of a file,
         * or because of n being too small.
         * Since both cases occur very infrequently, we can check for EOF.
         */
        if (!feof(stream))
        {
            gmx_fatal(FARGS, "An input file contains a line longer than %d characters, while the buffer passed to fgets2 has size %d. The line starts with: '%20.20s'", n, n, line);
        }
    }
    if ((c = strchr(line, '\r')) != NULL)
    {
        *c = '\0';
    }

    return line;
}

void strip_comment (char *line)
{
    char *c;

    if (!line)
    {
        return;
    }

    /* search for a comment mark and replace it by a zero */
    if ((c = strchr(line, COMMENTSIGN)) != NULL)
    {
        (*c) = 0;
    }
}

void upstring (char *str)
{
    int i;

    for (i = 0; (i < (int)strlen(str)); i++)
    {
        str[i] = toupper(str[i]);
    }
}

void ltrim (char *str)
{
    char *tr;
    int   i, c;

    if (NULL == str)
    {
        return;
    }

    c = 0;
    while (('\0' != str[c]) && isspace(str[c]))
    {
        c++;
    }
    if (c > 0)
    {
        for (i = c; ('\0' != str[i]); i++)
        {
            str[i-c] = str[i];
        }
        str[i-c] = '\0';
    }
}

void rtrim (char *str)
{
    int nul;

    if (NULL == str)
    {
        return;
    }

    nul = strlen(str)-1;
    while ((nul > 0) && ((str[nul] == ' ') || (str[nul] == '\t')) )
    {
        str[nul] = '\0';
        nul--;
    }
}

void trim (char *str)
{
    ltrim (str);
    rtrim (str);
}

char *
gmx_ctime_r(const time_t *clock, char *buf, int n)
{
    char tmpbuf[STRLEN];

#ifdef GMX_NATIVE_WINDOWS
    /* Windows */
    ctime_s( tmpbuf, STRLEN, clock );
#elif (defined(__sun))
    /*Solaris*/
    ctime_r(clock, tmpbuf, n);
#else
    ctime_r(clock, tmpbuf);
#endif
    strncpy(buf, tmpbuf, n-1);
    buf[n-1] = '\0';

    return buf;
}

void nice_header (FILE *out, const char *fn)
{
    const char    *unk = "onbekend";
    time_t         clock;
    const char    *user = unk;
    int            gh;
#ifdef HAVE_PWD_H
    uid_t          uid;
#else
    int            uid;
#endif
    char           buf[256] = "";
    char           timebuf[STRLEN];
#ifdef HAVE_PWD_H
    struct passwd *pw;
#endif

    /* Print a nice header above the file */
    time(&clock);
    fprintf (out, "%c\n", COMMENTSIGN);
    fprintf (out, "%c\tFile '%s' was generated\n", COMMENTSIGN, fn ? fn : unk);

#ifdef HAVE_PWD_H
    uid  = getuid();
    pw   = getpwuid(uid);
    gh   = gmx_gethostname(buf, 255);
    /* pw returns null on error (e.g. compute nodes lack /etc/passwd) */
    user = pw ? pw->pw_name : unk;
#else
    uid = 0;
    gh  = -1;
#endif

    gmx_ctime_r(&clock, timebuf, STRLEN);
    fprintf (out, "%c\tBy user: %s (%d)\n", COMMENTSIGN,
             user ? user : unk, (int) uid);
    fprintf(out, "%c\tOn host: %s\n", COMMENTSIGN, (gh == 0) ? buf : unk);

    fprintf (out, "%c\tAt date: %s", COMMENTSIGN, timebuf);
    fprintf (out, "%c\n", COMMENTSIGN);
}


int gmx_strcasecmp_min(const char *str1, const char *str2)
{
    char ch1, ch2;

    do
    {
        do
        {
            ch1 = toupper(*(str1++));
        }
        while ((ch1 == '-') || (ch1 == '_'));
        do
        {
            ch2 = toupper(*(str2++));
        }
        while ((ch2 == '-') || (ch2 == '_'));

        if (ch1 != ch2)
        {
            return (ch1-ch2);
        }
    }
    while (ch1);
    return 0;
}

int gmx_strncasecmp_min(const char *str1, const char *str2, int n)
{
    char  ch1, ch2;
    char *stri1, *stri2;

    stri1 = (char *)str1;
    stri2 = (char *)str2;
    do
    {
        do
        {
            ch1 = toupper(*(str1++));
        }
        while ((ch1 == '-') || (ch1 == '_'));
        do
        {
            ch2 = toupper(*(str2++));
        }
        while ((ch2 == '-') || (ch2 == '_'));

        if (ch1 != ch2)
        {
            return (ch1-ch2);
        }
    }
    while (ch1 && (str1-stri1 < n) && (str2-stri2 < n));
    return 0;
}

int gmx_strcasecmp(const char *str1, const char *str2)
{
    char ch1, ch2;

    do
    {
        ch1 = toupper(*(str1++));
        ch2 = toupper(*(str2++));
        if (ch1 != ch2)
        {
            return (ch1-ch2);
        }
    }
    while (ch1);
    return 0;
}

int gmx_strncasecmp(const char *str1, const char *str2, int n)
{
    char ch1, ch2;

    if (n == 0)
    {
        return 0;
    }

    do
    {
        ch1 = toupper(*(str1++));
        ch2 = toupper(*(str2++));
        if (ch1 != ch2)
        {
            return (ch1-ch2);
        }
        n--;
    }
    while (ch1 && n);
    return 0;
}

char *gmx_strdup(const char *src)
{
    char *dest;

    snew(dest, strlen(src)+1);
    strcpy(dest, src);

    return dest;
}

char *
gmx_strndup(const char *src, int n)
{
    int   len;
    char *dest;

    len = strlen(src);
    if (len > n)
    {
        len = n;
    }
    snew(dest, len+1);
    strncpy(dest, src, len);
    dest[len] = 0;
    return dest;
}

/* Magic hash init number for Dan J. Bernsteins algorithm.
 * Do NOT use any other value unless you really know what you are doing.
 */
const unsigned int
    gmx_string_hash_init = 5381;


unsigned int
gmx_string_fullhash_func(const char *s, unsigned int hash_init)
{
    int c;

    while ((c = (*s++)) != '\0')
    {
        hash_init = ((hash_init << 5) + hash_init) ^ c; /* (hash * 33) xor c */
    }
    return hash_init;
}

unsigned int
gmx_string_hash_func(const char *s, unsigned int hash_init)
{
    int c;

    while ((c = toupper(*s++)) != '\0')
    {
        if (isalnum(c))
        {
            hash_init = ((hash_init << 5) + hash_init) ^ c;            /* (hash * 33) xor c */
        }
    }
    return hash_init;
}

int
gmx_wcmatch(const char *pattern, const char *str)
{
    while (*pattern)
    {
        if (*pattern == '*')
        {
            /* Skip multiple wildcards in a sequence */
            while (*pattern == '*' || *pattern == '?')
            {
                ++pattern;
                /* For ?, we need to check that there are characters left
                 * in str. */
                if (*pattern == '?')
                {
                    if (*str == 0)
                    {
                        return GMX_NO_WCMATCH;
                    }
                    else
                    {
                        ++str;
                    }
                }
            }
            /* If the pattern ends after the star, we have a match */
            if (*pattern == 0)
            {
                return 0;
            }
            /* Match the rest against each possible suffix of str */
            while (*str)
            {
                /* Only do the recursive call if the first character
                 * matches. We don't have to worry about wildcards here,
                 * since we have processed them above. */
                if (*pattern == *str)
                {
                    int rc;
                    /* Match the suffix, and return if a match or an error */
                    rc = gmx_wcmatch(pattern, str);
                    if (rc != GMX_NO_WCMATCH)
                    {
                        return rc;
                    }
                }
                ++str;
            }
            /* If no suffix of str matches, we don't have a match */
            return GMX_NO_WCMATCH;
        }
        else if ((*pattern == '?' && *str != 0) || *pattern == *str)
        {
            ++str;
        }
        else
        {
            return GMX_NO_WCMATCH;
        }
        ++pattern;
    }
    /* When the pattern runs out, we have a match if the string has ended. */
    return (*str == 0) ? 0 : GMX_NO_WCMATCH;
}

char *wrap_lines(const char *buf, int line_width, int indent, gmx_bool bIndentFirst)
{
    char    *b2;
    int      i, i0, i2, j, b2len, lspace = 0, l2space = 0;
    gmx_bool bFirst, bFitsOnLine;

    /* characters are copied from buf to b2 with possible spaces changed
     * into newlines and extra space added for indentation.
     * i indexes buf (source buffer) and i2 indexes b2 (destination buffer)
     * i0 points to the beginning of the current line (in buf, source)
     * lspace and l2space point to the last space on the current line
     * bFirst is set to prevent indentation of first line
     * bFitsOnLine says if the first space occurred before line_width, if
     * that is not the case, we have a word longer than line_width which
     * will also not fit on the next line, so we might as well keep it on
     * the current line (where it also won't fit, but looks better)
     */

    b2    = NULL;
    b2len = strlen(buf)+1+indent;
    snew(b2, b2len);
    i0 = i2 = 0;
    if (bIndentFirst)
    {
        for (i2 = 0; (i2 < indent); i2++)
        {
            b2[i2] = ' ';
        }
    }
    bFirst = TRUE;
    do
    {
        l2space = -1;
        /* find the last space before end of line */
        for (i = i0; ((i-i0 < line_width) || (l2space == -1)) && (buf[i]); i++)
        {
            b2[i2++] = buf[i];
            /* remember the position of a space */
            if (buf[i] == ' ')
            {
                lspace  = i;
                l2space = i2-1;
            }
            /* if we have a newline before the line is full, reset counters */
            if (buf[i] == '\n' && buf[i+1])
            {
                i0     = i+1;
                b2len += indent;
                srenew(b2, b2len);
                /* add indentation after the newline */
                for (j = 0; (j < indent); j++)
                {
                    b2[i2++] = ' ';
                }
            }
        }
        /* If we are at the last newline, copy it */
        if (buf[i] == '\n' && !buf[i+1])
        {
            b2[i2++] = buf[i++];
        }
        /* if we're not at the end of the string */
        if (buf[i])
        {
            /* check if one word does not fit on the line */
            bFitsOnLine = (i-i0 <= line_width);
            /* reset line counters to just after the space */
            i0 = lspace+1;
            i2 = l2space+1;
            /* if the words fit on the line, and we're beyond the indentation part */
            if ( (bFitsOnLine) && (l2space >= indent) )
            {
                /* start a new line */
                b2[l2space] = '\n';
                /* and add indentation */
                if (indent)
                {
                    if (bFirst)
                    {
                        line_width -= indent;
                        bFirst      = FALSE;
                    }
                    b2len += indent;
                    srenew(b2, b2len);
                    for (j = 0; (j < indent); j++)
                    {
                        b2[i2++] = ' ';
                    }
                    /* no extra spaces after indent; */
                    while (buf[i0] == ' ')
                    {
                        i0++;
                    }
                }
            }
        }
    }
    while (buf[i]);
    b2[i2] = '\0';

    return b2;
}

gmx_int64_t
str_to_int64_t(const char *str, char **endptr)
{
#ifndef _MSC_VER
    return strtoll(str, endptr, 10);
#else
    return _strtoi64(str, endptr, 10);
#endif
}

void parse_digits_from_plain_string(const char *digitstring, int *ndigits, int **digitlist)
{
    int i;

    if (NULL == digitstring)
    {
        *ndigits   = 0;
        *digitlist = NULL;
        return;
    }

    *ndigits = strlen(digitstring);

    snew(*digitlist, *ndigits);

    for (i = 0; i < *ndigits; i++)
    {
        if (digitstring[i] < '0' || digitstring[i] > '9')
        {
            gmx_fatal(FARGS, "Invalid character in digit-only string: '%c'\n",
                      digitstring[i]);
        }
        (*digitlist)[i] = digitstring[i] - '0';
    }
}

static void parse_digits_from_csv_string(const char gmx_unused *digitstring, int gmx_unused *ndigits, int gmx_unused *digitlist)
{
    /* TODO Implement csv format to support (e.g.) more than 10
       different GPUs in a node. */
    gmx_incons("Not implemented yet");
}