struct cmdline *
cmdline_term_new(cmdline_parse_ctx_t *ctx, const char *prompt, char *ptyname)
{
int fd;
struct cmdline *cl;
fd = open(ptyname, O_RDWR);
if (fd > 0) {
cl = cmdline_new(ctx, prompt, fd, fd);
#ifdef RTE_EXEC_ENV_LINUXAPP
{
struct termios oldterm, term;
tcgetattr(fd, &oldterm);
memcpy(&term, &oldterm, sizeof(term));
// term.c_lflag &= ~(ICANON | ECHO | ISIG);
// term.c_lflag &= ~(ICANON | ECHO); /* To have GDB ctrl-c stop */
// tcsetattr(fd, TCSANOW, &term);
if (cl)
memcpy(&cl->oldterm, &oldterm, sizeof(term));
}
#endif
return cl;
}
else {
return NULL;
}
}
struct cmdline *
cmdline_file_new(cmdline_parse_ctx_t *ctx, const char *prompt, const char *path)
{
int fd;
/* everything else is checked in cmdline_new() */
if (!path)
return NULL;
fd = open(path, O_RDONLY, 0);
if (fd < 0) {
dprintf("open() failed\n");
return NULL;
}
return cmdline_new(ctx, prompt, fd, -1);
}
static cmdline_t
local_cmdlineSetup(void)
{
cmdline_t cmdline;
cmdline = cmdline_new(6, 6, "cubepm_dumpSelection");
(void)cmdline_addOpt(cmdline, "version",
"This will output a version information.",
false, CMDLINE_TYPE_NONE);
(void)cmdline_addOpt(cmdline, "help",
"This will print this help text.",
false, CMDLINE_TYPE_NONE);
(void)cmdline_addOpt(cmdline, "boxsize",
"The boxsize in Mpc/h.",
true, CMDLINE_TYPE_DOUBLE);
(void)cmdline_addOpt(cmdline, "omega0",
"Omega0",
true, CMDLINE_TYPE_DOUBLE);
(void)cmdline_addOpt(cmdline, "lambda0",
"Lambda0",
true, CMDLINE_TYPE_DOUBLE);
(void)cmdline_addOpt(cmdline, "properUnits",
"Converts from file units to Mpc/h and km/s.",
false, CMDLINE_TYPE_NONE);
(void)cmdline_addArg(cmdline,
"The prefix of the filenames.",
CMDLINE_TYPE_STRING);
(void)cmdline_addArg(cmdline,
"The stem of the filenames",
CMDLINE_TYPE_STRING);
(void)cmdline_addArg(
cmdline,
"The number of nodes (1D) used to write the files.",
CMDLINE_TYPE_INT);
(void)cmdline_addArg(cmdline,
"The size of the grid.",
CMDLINE_TYPE_INT);
(void)cmdline_addArg(cmdline,
"The number of particles to skip.",
CMDLINE_TYPE_LONG);
(void)cmdline_addArg(cmdline,
"The number of particles to read.",
CMDLINE_TYPE_LONG);
return cmdline;
} /* local_cmdlineSetup */
static cmdline_t
local_cmdlineSetup(void)
{
cmdline_t cmdline;
cmdline = cmdline_new(1, 2, localProgramName);
(void)cmdline_addOpt(cmdline, "version",
"This will output a version information.",
false, CMDLINE_TYPE_NONE);
(void)cmdline_addOpt(cmdline, "help",
"This will print this help text.",
false, CMDLINE_TYPE_NONE);
(void)cmdline_addArg(cmdline,
"The filename.",
CMDLINE_TYPE_STRING);
return cmdline;
}
static cmdline_t
local_cmdlineSetup(void)
{
cmdline_t cmdline;
cmdline = cmdline_new(1, 3, localProgramName);
(void)cmdline_addOpt(cmdline, "version",
"This will output a version information.",
false, CMDLINE_TYPE_NONE);
(void)cmdline_addOpt(cmdline, "help",
"This will print this help text.",
false, CMDLINE_TYPE_NONE);
(void)cmdline_addOpt(cmdline, "numFiles",
"Gives the number of files in the file set.",
true, CMDLINE_TYPE_INT);
(void)cmdline_addArg(cmdline,
"The name of the Gadget file.",
CMDLINE_TYPE_STRING);
return cmdline;
}
int main(int argc, char* argv[])
{
#ifdef SEQ_ALIGN_VERBOSE
printf("VERBOSE: on\n");
#endif
sw_set_default_scoring();
cmd = cmdline_new(argc, argv, &scoring, SEQ_ALIGN_SW_CMD);
// Align!
sw = smith_waterman_new();
result = alignment_create(256);
if(cmd->seq1 != NULL)
{
// Align seq1 and seq2
align(cmd->seq1, cmd->seq2, NULL, NULL);
}
// Align from files
size_t i, num_of_file_pairs = cmdline_get_num_of_file_pairs(cmd);
for(i = 0; i < num_of_file_pairs; i++)
{
const char *file1 = cmdline_get_file1(cmd, i);
const char *file2 = cmdline_get_file2(cmd, i);
if(file1 != NULL && *file1 == '\0' && file2 == NULL) {
wait_on_keystroke = 1;
file1 = "-";
}
align_from_file(file1, file2, &align_pair_from_file, !cmd->interactive);
}
// Free memory for storing alignment results
smith_waterman_free(sw);
alignment_free(result);
cmdline_free(cmd);
return EXIT_SUCCESS;
}
struct cmdline *
cmdline_stdin_new(cmdline_parse_ctx_t *ctx, const char *prompt)
{
struct cmdline *cl;
#ifdef RTE_EXEC_ENV_LINUXAPP
struct termios oldterm, term;
tcgetattr(0, &oldterm);
memcpy(&term, &oldterm, sizeof(term));
term.c_lflag &= ~(ICANON | ECHO | ISIG);
tcsetattr(0, TCSANOW, &term);
setbuf(stdin, NULL);
#endif
cl = cmdline_new(ctx, prompt, 0, 1);
#ifdef RTE_EXEC_ENV_LINUXAPP
if (cl)
memcpy(&cl->oldterm, &oldterm, sizeof(term));
#endif
return cl;
}
struct cmdline *
cmdline_stdin_new(cmdline_parse_ctx_t *ctx, const char *prompt)
{
struct cmdline *cl;
struct termios oldterm, term;
tcgetattr(0, &oldterm);
memcpy(&term, &oldterm, sizeof(term));
#ifdef RTE_LIBRW_PIOT
term.c_lflag &= ~(ICANON | ECHO); /* To have GDB ctrl-c stop */
#else
term.c_lflag &= ~(ICANON | ECHO | ISIG);
#endif
tcsetattr(0, TCSANOW, &term);
setbuf(stdin, NULL);
cl = cmdline_new(ctx, prompt, 0, 1);
if (cl)
memcpy(&cl->oldterm, &oldterm, sizeof(term));
return cl;
}
static cmdline_t
local_cmdlineSetup(void)
{
cmdline_t cmdline;
cmdline = cmdline_new(1, 3, THIS_PROGNAME);
(void)cmdline_addOpt(cmdline, "version",
"This will output a version information.",
false, CMDLINE_TYPE_NONE);
(void)cmdline_addOpt(cmdline, "help",
"This will print this help text.",
false, CMDLINE_TYPE_NONE);
(void)cmdline_addOpt(
cmdline,
"sectionName",
"The name of the section in the configuration file.",
true,
CMDLINE_TYPE_STRING);
(void)cmdline_addArg(cmdline,
"Gives the name of the configuration file.",
CMDLINE_TYPE_STRING);
return cmdline;
}
static int
pipeline_run(void *pipeline)
{
struct pipeline_master *p = (struct pipeline_master *) pipeline;
int status;
if (p->script_file_done == 0) {
struct app_params *app = p->app;
int fd = open(app->script_file, O_RDONLY);
if (fd < 0)
printf("Cannot open CLI script file \"%s\"\n",
app->script_file);
else {
struct cmdline *file_cl;
printf("Running CLI script file \"%s\" ...\n",
app->script_file);
file_cl = cmdline_new(p->cl->ctx, "", fd, 1);
cmdline_interact(file_cl);
close(fd);
}
p->script_file_done = 1;
}
status = cmdline_poll(p->cl);
if (status < 0)
rte_panic("CLI poll error (%" PRId32 ")\n", status);
else if (status == RDLINE_EXITED) {
cmdline_stdin_exit(p->cl);
rte_exit(0, "Bye!\n");
}
return 0;
}
