int
main(int argc, char *argv[])
{
int count;
seq_t seq1, seq2;
hash_env_t he;
collec_t res, rev_res;
#if defined(DEBUG) && (DEBUG > 1)
mcheck(NULL);
mtrace();
#endif
argv0 = argv[0];
if (setlocale(LC_ALL, "POSIX") == NULL)
fprintf(stderr, "%s: Warning: could not set locale to POSIX\n", argv[0]);
signal(SIGSEGV, bug_handler);
#ifndef __MINGW32__
signal(SIGBUS, bug_handler);
#endif
/* Default options. */
options.C = DEFAULT_C;
options.cutoff = DIST_CUTOFF;
options.gapPct = DEFAULT_GAPPCT;
options.intron_window = 6;
options.K = DEFAULT_K;
options.splice_type_list = "GTAG,GCAG,GTAC,ATAC";
options.nbSplice = 4;
options.scoreSplice_window = 10;
options.mismatchScore = MISMATCH;
options.reverse = 2;
options.matchScore = MATCH;
options.W = DEFAULT_W;
options.X = DEFAULT_X;
options.filterPct = DEFAULT_FILTER;
options.minScore_cutoff = MATCH_CUTOFF;
while (1) {
int c = getopt(argc, argv, "A:C:c:E:f:g:I:K:L:M:o:q:R:r:W:X:");
if (c == -1)
break;
switch (c) {
case 'A':
options.ali_flag = atoi(optarg);
if (options.ali_flag < 0 || options.ali_flag > 4)
fatal("A must be one of 0, 1, 2, 3, or 4.\n");
break;
case 'C': {
int val = atoi(optarg);
if (val < 0)
fatal("Value for option C must be non-negative.\n");
options.C = val;
break;
}
case 'c': {
int val = atoi(optarg);
if (val < 0)
fatal("Value for option c must be non-negative.\n");
options.minScore_cutoff = val;
break;
}
case 'E':
options.cutoff = atoi(optarg);
if (options.cutoff < 3 || options.cutoff > 10)
fatal("Cutoff (E) must be within [3,10].\n");
break;
case 'f':
options.filterPct = atoi(optarg);
if (options.filterPct > 100)
fatal("Filter in percent (f) must be within [0,100].\n");
break;
case 'g':
options.gapPct = atoi(optarg);
break;
case 'I':
options.intron_window = atoi(optarg);
break;
case 'K': {
int val = atoi(optarg);
if (val < 0)
fatal("Value for option K must be non-negative.\n");
options.K = val;
break;
}
case 'L': {
size_t i;
size_t len = strlen(optarg);
options.splice_type_list = optarg;
options.nbSplice = 1;
if (len % 5 != 4)
fatal("Splice types list has illegal length (%zu)\n", len);
for (i = 0; i < len; i++)
if (i % 5 == 4) {
if (options.splice_type_list[i] != ',')
fatal("Comma expected instead of %c at position %zu"
"in splice types list.\n",
options.splice_type_list[i], i);
options.nbSplice += 1;
} else {
if (options.splice_type_list[i] != 'A'
&& options.splice_type_list[i] != 'C'
&& options.splice_type_list[i] != 'G'
&& options.splice_type_list[i] != 'T')
fatal("Expected 'A', 'C', 'G' or 'T' instead of '%c' at"
"position %zu in splice types list.\n",
options.splice_type_list[i], i);
}
break;
}
case 'M': {
int val = atoi(optarg);
if (val < 0)
fatal("Value for option M must be non-negative.\n");
options.scoreSplice_window = val;
break;
}
case 'o':
options.dnaOffset = atoi(optarg);
break;
case 'q':
options.mismatchScore = atoi(optarg);
break;
case 'R':
options.reverse = atoi(optarg);
if (options.reverse < 0 || options.reverse > 2)
fatal("R must be one of 0, 1, or 2.\n");
break;
case 'r':
options.matchScore = atoi(optarg);
break;
case 'W':
options.W = atoi(optarg);
if (options.W < 1 || options.W > 15)
fatal("W must be within [1,15].\n");
break;
case 'X':
options.X = atoi(optarg);
if (options.X < 1)
fatal("X must be positive.\n");
break;
case '?':
break;
default:
fprintf(stderr, "?? getopt returned character code 0%o ??\n", c);
}
}
if (optind + 2 != argc) {
fprintf(stderr, Usage, argv[0], options.ali_flag, options.C,
options.minScore_cutoff, options.cutoff,
options.filterPct, options.gapPct, options.intron_window,
options.K, options.splice_type_list, options.scoreSplice_window,
options.dnaOffset, options.mismatchScore, options.reverse,
options.matchScore, options.W, options.X);
return 1;
}
/* read seq1 */
init_seq(argv[optind], &seq1);
if (get_next_seq(&seq1, options.dnaOffset, 1) != 0)
fatal("Cannot read sequence from %s.\n", argv[optind]);
strncpy(dna_seq_head, seq1.header, 256);
/* read seq2 */
init_seq(argv[optind + 1], &seq2);
if (get_next_seq(&seq2, 0, 0) != 0)
fatal("Cannot read sequence from %s.\n", argv[optind + 1]);
init_encoding();
init_hash_env(&he, options.W, seq1.seq, seq1.len);
init_col(&res, 1);
init_col(&rev_res, 1);
bld_table(&he);
init_splice_junctions();
count = 0;
while (!count || get_next_seq(&seq2, 0, 0) == 0) {
unsigned int curRes;
strncpy(rna_seq_head, seq2.header, 256);
++count;
switch (options.reverse) {
case 0:
SIM4(&he, &seq2, &res);
break;
case 2:
SIM4(&he, &seq2, &res);
case 1:
seq_revcomp_inplace(&seq2);
SIM4(&he, &seq2, &rev_res);
break;
default:
fatal ("Unrecognized request for EST orientation.\n");
}
/* Keep only the best matches, according to filterPct. */
if (options.filterPct > 0) {
unsigned int max_nmatches = 0;
for (curRes = 0; curRes < rev_res.nb; curRes++) {
result_p_t r = rev_res.e.result[curRes];
if (r->st.nmatches > max_nmatches)
max_nmatches = r->st.nmatches;
}
for (curRes = 0; curRes < res.nb; curRes++) {
result_p_t r = res.e.result[curRes];
if (r->st.nmatches > max_nmatches)
max_nmatches = r->st.nmatches;
}
max_nmatches = (max_nmatches * options.filterPct) / 100;
for (curRes = 0; curRes < rev_res.nb; curRes++) {
result_p_t r = rev_res.e.result[curRes];
if (r->st.nmatches < max_nmatches)
r->st.nmatches = 0;
}
for (curRes = 0; curRes < res.nb; curRes++) {
result_p_t r = res.e.result[curRes];
if (r->st.nmatches < max_nmatches)
r->st.nmatches = 0;
}
}
/* Now, print results. */
for (curRes = 0; curRes < rev_res.nb; curRes++)
print_res(rev_res.e.result[curRes], 1, &seq1, &seq2);
rev_res.nb = 0;
if (options.reverse && options.ali_flag)
/* reverse-complement back seq2 for alignment */
seq_revcomp_inplace(&seq2);
for (curRes = 0; curRes < res.nb; curRes++)
print_res(res.e.result[curRes], 0, &seq1, &seq2);
res.nb = 0;
}
#ifdef DEBUG
fprintf(stderr, "DEBUG mode: freeing all memory...\n");
fflush(stdout);
fflush(stderr);
free_hash_env(&he);
free_seq(&seq1);
free_seq(&seq2);
free(options.splice);
free(res.e.elt);
free(rev_res.e.elt);
#endif
return 0;
}
int
main(int argc_orig, char **argv)
#endif
{
int i;
/* We want the current value of argc to persist across a LONGJMP from int_error().
* Without this the compiler may put it on the stack, which LONGJMP clobbers.
* Here we try make it a volatile variable that optimization will not affect.
* Why do we not have to do the same for argv? I don't know.
* But the test cases that broke with generic argc seem fine with generic argv.
*/
static volatile int argc;
argc = argc_orig;
#ifdef LINUXVGA
LINUX_setup(); /* setup VGA before dropping privilege DBT 4/5/99 */
drop_privilege();
#endif
/* make sure that we really have revoked root access, this might happen if
gnuplot is compiled without vga support but is installed suid by mistake */
#ifdef __linux__
if (setuid(getuid()) != 0) {
fprintf(stderr,"gnuplot: refusing to run at elevated privilege\n");
exit(EXIT_FAILURE);
}
#endif
/* HBB: Seems this isn't needed any more for DJGPP V2? */
/* HBB: disable all floating point exceptions, just keep running... */
#if defined(DJGPP) && (DJGPP!=2)
_control87(MCW_EM, MCW_EM);
#endif
#if defined(OS2)
{
int rc;
#ifdef OS2_IPC
char semInputReadyName[40];
sprintf(semInputReadyName, "\\SEM32\\GP%i_Input_Ready", getpid());
rc = DosCreateEventSem(semInputReadyName, &semInputReady, 0, 0);
if (rc != 0)
fputs("DosCreateEventSem error\n", stderr);
#endif
rc = RexxRegisterSubcomExe("GNUPLOT", (PFN) RexxInterface, NULL);
}
#endif
/* malloc large blocks, otherwise problems with fragmented mem */
#ifdef MALLOCDEBUG
malloc_debug(7);
#endif
/* init progpath and get helpfile from executable directory */
#if defined(MSDOS) || defined(OS2)
{
char *s;
#ifdef __EMX__
_execname(progpath, sizeof(progpath));
#else
safe_strncpy(progpath, argv[0], sizeof(progpath));
#endif
/* convert '/' to '\\' */
for (s = progpath; *s != NUL; s++)
if (*s == DIRSEP2)
*s = DIRSEP1;
/* cut program name */
s = strrchr(progpath, DIRSEP1);
if (s != NULL)
s++;
else
s = progpath;
*s = NUL;
/* init HelpFile */
strcpy(HelpFile, progpath);
strcat(HelpFile, "gnuplot.gih");
/* remove trailing "bin/" from progpath */
if ((s != NULL) && (s - progpath >= 4)) {
s -= 4;
if (strncasecmp(s, "bin", 3) == 0)
*s = NUL;
}
}
#endif /* DJGPP */
#if (defined(PIPE_IPC) || defined(_WIN32)) && (defined(HAVE_LIBREADLINE) || (defined(HAVE_LIBEDITLINE) && defined(X11)))
/* Editline needs this to be set before the very first call to readline(). */
/* Support for rl_getc_function is broken for utf-8 in editline. Since it is only
really required for X11, disable this section when building without X11. */
rl_getc_function = getc_wrapper;
#endif
#if defined(HAVE_LIBREADLINE) || defined(HAVE_LIBEDITLINE)
/* T.Walter 1999-06-24: 'rl_readline_name' must be this fix name.
* It is used to parse a 'gnuplot' specific section in '~/.inputrc'
* or gnuplot specific commands in '.editrc' (when using editline
* instead of readline) */
rl_readline_name = "Gnuplot";
rl_terminal_name = getenv("TERM");
#if defined(HAVE_LIBREADLINE)
using_history();
#else
history_init();
#endif
#endif
#if defined(HAVE_LIBREADLINE) && !defined(MISSING_RL_TILDE_EXPANSION)
rl_complete_with_tilde_expansion = 1;
#endif
for (i = 1; i < argc; i++) {
if (!argv[i])
continue;
if (!strcmp(argv[i], "-V") || !strcmp(argv[i], "--version")) {
printf("gnuplot %s patchlevel %s\n",
gnuplot_version, gnuplot_patchlevel);
return 0;
} else if (!strcmp(argv[i], "-h") || !strcmp(argv[i], "--help")) {
printf( "Usage: gnuplot [OPTION] ... [FILE]\n"
#ifdef X11
"for X11 options see 'help X11->command-line-options'\n"
#endif
" -V, --version\n"
" -h, --help\n"
" -p --persist\n"
" -s --slow\n"
" -d --default-settings\n"
" -c scriptfile ARG1 ARG2 ... \n"
" -e \"command1; command2; ...\"\n"
"gnuplot %s patchlevel %s\n",
gnuplot_version, gnuplot_patchlevel);
#ifdef DEVELOPMENT_VERSION
printf(
#ifdef DIST_CONTACT
"Report bugs to "DIST_CONTACT"\n"
" or %s\n",
#else
"Report bugs to %s\n",
#endif
bug_email);
#endif
return 0;
} else if (!strncmp(argv[i], "-persist", 2) || !strcmp(argv[i], "--persist")
#ifdef _WIN32
|| !stricmp(argv[i], "-noend") || !stricmp(argv[i], "/noend")
#endif
) {
persist_cl = TRUE;
} else if (!strncmp(argv[i], "-slow", 2) || !strcmp(argv[i], "--slow")) {
slow_font_startup = TRUE;
} else if (!strncmp(argv[i], "-d", 2) || !strcmp(argv[i], "--default-settings")) {
/* Skip local customization read from ~/.gnuplot */
skip_gnuplotrc = TRUE;
}
}
#ifdef X11
/* the X11 terminal removes tokens that it recognizes from argv. */
{
int n = X11_args(argc, argv);
argv += n;
argc -= n;
}
#endif
setbuf(stderr, (char *) NULL);
#ifdef HAVE_SETVBUF
/* This was once setlinebuf(). Docs say this is
* identical to setvbuf(,NULL,_IOLBF,0), but MS C
* faults this (size out of range), so we try with
* size of 1024 instead. [SAS/C does that, too. -lh]
*/
if (setvbuf(stdout, (char *) NULL, _IOLBF, (size_t) 1024) != 0)
(void) fputs("Could not linebuffer stdout\n", stderr);
/* Switching to unbuffered mode causes all characters in the input
* buffer to be lost. So the only safe time to do it is on program entry.
* Do any non-X platforms suffer from this problem?
* EAM - Jan 2013 YES.
*/
setvbuf(stdin, (char *) NULL, _IONBF, 0);
#endif
gpoutfile = stdout;
/* Initialize pre-loaded user variables */
/* "pi" is hard-wired as the first variable */
(void) add_udv_by_name("GNUTERM");
(void) add_udv_by_name("NaN");
init_constants();
udv_user_head = &(udv_NaN->next_udv);
init_memory();
interactive = FALSE;
/* April 2017: We used to call init_terminal() here, but now */
/* We defer initialization until error handling has been set up. */
# if defined(_WIN32) && !defined(WGP_CONSOLE)
interactive = TRUE;
# else
interactive = isatty(fileno(stdin));
# endif
/* Note: we want to know whether this is an interactive session so that we can
* decide whether or not to write status information to stderr. The old test
* for this was to see if (argc > 1) but the addition of optional command line
* switches broke this. What we really wanted to know was whether any of the
* command line arguments are file names or an explicit in-line "-e command".
*/
for (i = 1; i < argc; i++) {
# ifdef _WIN32
if (!stricmp(argv[i], "/noend"))
continue;
# endif
if ((argv[i][0] != '-') || (argv[i][1] == 'e') || (argv[i][1] == 'c') ) {
interactive = FALSE;
break;
}
}
/* Need this before show_version is called for the first time */
if (interactive)
show_version(stderr);
else
show_version(NULL); /* Only load GPVAL_COMPILE_OPTIONS */
update_gpval_variables(3); /* update GPVAL_ variables available to user */
#ifdef VMS
/* initialise screen management routines for command recall */
{
unsigned int ierror;
if (ierror = smg$create_virtual_keyboard(&vms_vkid) != SS$_NORMAL)
done(ierror);
if (ierror = smg$create_key_table(&vms_ktid) != SS$_NORMAL)
done(ierror);
}
#endif /* VMS */
if (!SETJMP(command_line_env, 1)) {
/* first time */
interrupt_setup();
get_user_env();
init_loadpath();
init_locale();
memset(&sm_palette, 0, sizeof(sm_palette));
init_fit(); /* Initialization of fitting module */
#ifdef READLINE
/* When using the built-in readline, we set the initial
encoding according to the locale as this is required
to properly handle keyboard input. */
init_encoding();
#endif
init_gadgets();
/* April 2017: Now that error handling is in place, it is safe parse
* GNUTERM during terminal initialization.
* atexit processing is done in reverse order. We want
* the generic terminal shutdown in term_reset to be executed before
* any terminal specific cleanup requested by individual terminals.
*/
init_terminal();
push_terminal(0); /* remember the initial terminal */
gp_atexit(term_reset);
/* Execute commands in ~/.gnuplot */
init_session();
if (interactive && term != 0) { /* not unknown */
#ifdef GNUPLOT_HISTORY
#if (defined(HAVE_LIBREADLINE) || defined(HAVE_LIBEDITLINE)) && !defined(_WIN32)
expanded_history_filename = tilde_expand(GNUPLOT_HISTORY_FILE);
#else
expanded_history_filename = gp_strdup(GNUPLOT_HISTORY_FILE);
gp_expand_tilde(&expanded_history_filename);
#endif
read_history(expanded_history_filename);
/*
* It is safe to ignore the return values of 'atexit()' and
* 'on_exit()'. In the worst case, there is no history of your
* currrent session and you have to type all again in your next
* session.
*/
gp_atexit(wrapper_for_write_history);
#endif /* GNUPLOT_HISTORY */
#if defined(READLINE) && defined(WGP_CONSOLE)
fprintf(stderr, "Encoding set to '%s'.\n", encoding_names[encoding]);
#endif
} /* if (interactive && term != 0) */
} else {
/* come back here from int_error() */
if (!successful_initialization) {
/* Only print the warning once */
successful_initialization = TRUE;
fprintf(stderr,"WARNING: Error during initialization\n\n");
}
if (interactive == FALSE)
exit_status = EXIT_FAILURE;
#ifdef HAVE_READLINE_RESET
else {
/* reset properly readline after a SIGINT+longjmp */
rl_reset_after_signal ();
}
#endif
load_file_error(); /* if we were in load_file(), cleanup */
SET_CURSOR_ARROW;
#ifdef VMS
/* after catching interrupt */
/* VAX stuffs up stdout on SIGINT while writing to stdout,
so reopen stdout. */
if (gpoutfile == stdout) {
if ((stdout = freopen("SYS$OUTPUT", "w", stdout)) == NULL) {
/* couldn't reopen it so try opening it instead */
if ((stdout = fopen("SYS$OUTPUT", "w")) == NULL) {
/* don't use int_error here - causes infinite loop! */
fputs("Error opening SYS$OUTPUT as stdout\n", stderr);
}
}
gpoutfile = stdout;
}
#endif /* VMS */
/* Why a goto? Because we exited the loop below via int_error */
/* using LONGJMP. The compiler was not expecting this, and */
/* "optimized" the handling of argc and argv such that simply */
/* entering the loop again from the top finds them messed up. */
/* If we reenter the loop via a goto then there is some hope */
/* that code reordering does not hurt us. */
if (reading_from_dash && interactive)
goto RECOVER_FROM_ERROR_IN_DASH;
reading_from_dash = FALSE;
if (!interactive && !noinputfiles) {
term_reset();
gp_exit(EXIT_FAILURE); /* exit on non-interactive error */
}
}
/* load filenames given as arguments */
while (--argc > 0) {
++argv;
c_token = 0;
if (!strncmp(*argv, "-persist", 2) || !strcmp(*argv, "--persist")
#ifdef _WIN32
|| !stricmp(*argv, "-noend") || !stricmp(*argv, "/noend")
#endif
) {
FPRINTF((stderr,"'persist' command line option recognized\n"));
} else if (strcmp(*argv, "-") == 0) {
#if defined(_WIN32) && !defined(WGP_CONSOLE)
TextShow(&textwin);
interactive = TRUE;
#else
interactive = isatty(fileno(stdin));
#endif
RECOVER_FROM_ERROR_IN_DASH:
reading_from_dash = TRUE;
while (!com_line());
reading_from_dash = FALSE;
interactive = FALSE;
noinputfiles = FALSE;
} else if (strcmp(*argv, "-e") == 0) {
int save_state = interactive;
--argc; ++argv;
if (argc <= 0) {
fprintf(stderr, "syntax: gnuplot -e \"commands\"\n");
return 0;
}
interactive = FALSE;
noinputfiles = FALSE;
do_string(*argv);
interactive = save_state;
} else if (!strncmp(*argv, "-slow", 2) || !strcmp(*argv, "--slow")) {
slow_font_startup = TRUE;
} else if (!strncmp(*argv, "-d", 2) || !strcmp(*argv, "--default-settings")) {
/* Ignore this; it already had its effect */
FPRINTF((stderr, "ignoring -d\n"));
} else if (strcmp(*argv, "-c") == 0) {
/* Pass command line arguments to the gnuplot script in the next
* argument. This consumes the remainder of the command line
*/
interactive = FALSE;
noinputfiles = FALSE;
--argc; ++argv;
if (argc <= 0) {
fprintf(stderr, "syntax: gnuplot -c scriptname args\n");
gp_exit(EXIT_FAILURE);
}
call_argc = GPMIN(9, argc - 1);
for (i=0; i<=call_argc; i++) {
/* Need to stash argv[i] somewhere visible to load_file() */
call_args[i] = gp_strdup(argv[i+1]);
}
load_file(loadpath_fopen(*argv, "r"), gp_strdup(*argv), 5);
gp_exit(EXIT_SUCCESS);
} else if (*argv[0] == '-') {
fprintf(stderr, "unrecognized option %s\n", *argv);
} else {
interactive = FALSE;
noinputfiles = FALSE;
load_file(loadpath_fopen(*argv, "r"), gp_strdup(*argv), 4);
}
}
/* take commands from stdin */
if (noinputfiles) {
while (!com_line())
ctrlc_flag = FALSE; /* reset asynchronous Ctrl-C flag */
}
#ifdef _WIN32
/* On Windows, handle 'persist' by keeping the main input loop running (windows/wxt), */
/* but only if there are any windows open. Note that qt handles this properly. */
if (persist_cl) {
if (WinAnyWindowOpen()) {
#ifdef WGP_CONSOLE
if (!interactive) {
/* no further input from pipe */
while (WinAnyWindowOpen())
win_sleep(100);
} else
#endif
{
interactive = TRUE;
while (!com_line())
ctrlc_flag = FALSE; /* reset asynchronous Ctrl-C flag */
interactive = FALSE;
}
}
}
#endif
#if (defined(HAVE_LIBREADLINE) || defined(HAVE_LIBEDITLINE)) && defined(GNUPLOT_HISTORY)
#if !defined(HAVE_ATEXIT) && !defined(HAVE_ON_EXIT)
/* You should be here if you neither have 'atexit()' nor 'on_exit()' */
wrapper_for_write_history();
#endif /* !HAVE_ATEXIT && !HAVE_ON_EXIT */
#endif /* (HAVE_LIBREADLINE || HAVE_LIBEDITLINE) && GNUPLOT_HISTORY */
#ifdef OS2
RexxDeregisterSubcom("GNUPLOT", NULL);
#endif
/* HBB 20040223: Not all compilers like exit() to end main() */
/* exit(exit_status); */
#if ! defined(_WIN32)
/* Windows does the cleanup later */
gp_exit_cleanup();
#endif
return exit_status;
}
