int gt_grep(GT_UNUSED bool *match, GT_UNUSED const char *pattern,
GT_UNUSED const char *line, GtError *err)
{
regex_t matcher;
int rval, had_err = 0;
gt_error_check(err);
gt_assert(pattern && line);
if ((rval = tre_regcomp(&matcher, pattern, REG_EXTENDED | REG_NOSUB))) {
grep_error(rval, &matcher, err);
had_err = -1;
}
if (!had_err) {
rval = tre_regexec(&matcher, line, 0, NULL, 0);
if (rval && rval != REG_NOMATCH) {
grep_error(rval, &matcher, err);
had_err = -1;
}
}
tre_regfree(&matcher);
if (!had_err) {
if (rval)
*match = false;
else
*match = true;
}
return had_err;
}
void setupPrimarySecondary(char *primary, char *secondary, int bidirectional)
{
if (number_secondaries == 0 || secondary_compares == NULL) {
secondary_compares = malloc(sizeof(secondaries_t));
} else {
secondary_compares = realloc(secondary_compares, sizeof(secondaries_t) * (number_secondaries + 1));
}
if (tre_regcomp(&secondary_compares[number_secondaries].primary_regex, primary, REG_EXTENDED | REG_ICASE) != 0 ||
tre_regcomp(&secondary_compares[number_secondaries].secondary_regex, secondary, REG_EXTENDED | REG_ICASE) != 0) {
tre_regfree(&secondary_compares[number_secondaries].primary_regex);
tre_regfree(&secondary_compares[number_secondaries].secondary_regex);
number_secondaries--;
ci_debug_printf(1, "Invalid REGEX In Setting parameter (PRIMARY_CATEGORY_REGEX: %s SECONDARY_CATEGORY_REGEX: %s BIDIRECTIONAL: %s)\n", primary, secondary, bidirectional ? "TRUE" : "FALSE" );
exit(-1);
}
secondary_compares[number_secondaries].bidirectional = bidirectional;
number_secondaries++;
}
void input_regex_callback(Fl_Widget*, void*)
{
if(input_regex->size() == 0) {
return;
}
buf_out->text("");
regex_t regex;
if(tre_regcomp(®ex, input_regex->value(), REG_EXTENDED|REG_NEWLINE) != 0) {
buf_out->append("regex is malformed\n");
return;
}
char *text = buf_test->text();
do_test_match(®ex, text, buf_test->length());
do_test_find(®ex, text, buf_test->length());
tre_regfree(®ex);
free(text);
}
/* Run one test with tre_reguexec */
static void
test_reguexec(const char *str, const char *regex)
{
regex_t preg;
tre_str_source *source;
regmatch_t pmatch[5];
source = make_str_source(str);
if (!source)
return;
tre_regcomp(&preg, regex, REG_EXTENDED);
if (tre_reguexec(&preg, source, elementsof(pmatch), pmatch, 0) == 0)
printf("Match: %d - %d\n", (int)pmatch[0].rm_so, (int)pmatch[0].rm_eo);
free_str_source(source);
tre_regfree(&preg);
}
int main(int argc, char **argv)
{
regex_t preg;
regmatch_t *pmatch = NULL;
int i, subject_len, match_len,
sub_len, errcode, ret = 1,
match_count, done;
char errbuf[256], *subject, *regex, *match_start,
*sub;
if( argc < 3 )
{
printf("Usage: %s [subject] [regex]\n", argv[0]);
return 0;
}
subject = strdup(argv[1]);
subject_len = strlen(subject);
regex = strdup(argv[2]);
/* compile the regex */
errcode = tre_regcomp(&preg, regex, REG_EXTENDED);
if(errcode)
{
tre_regerror(errcode, &preg, errbuf, sizeof(errbuf));
fprintf(stderr, "Error: regcomp() %s\n", errbuf);
goto err;
}
/* allocate space for match and submatches */
pmatch = (regmatch_t*)calloc(sizeof(regmatch_t),
preg.re_nsub+1);
if(pmatch == NULL)
{
perror("Error calloc()");
goto err;
}
/* find all matches */
sub = subject;
sub_len = subject_len;
match_count = 0;
done = 0;
while(!done)
{
/* execute regex */
errcode = tre_regnexec(&preg, sub, sub_len,
preg.re_nsub+1,
pmatch, 0);
switch(errcode)
{
case REG_OK:
match_count++;
/* loop through subpattern matches */
for(i=0; i < preg.re_nsub+1; i++)
{
match_len = pmatch[i].rm_eo - pmatch[i].rm_so;
match_start = sub + pmatch[i].rm_so;
if(i == 0)
printf("Match [%d] %.*s\n", match_count,
match_len, match_start);
else
printf(":: group [%d] %.*s\n", i, match_len,
match_start);
}
/* set up for next regexec call */
sub_len -= pmatch[0].rm_eo;
assert(sub_len >= 0);
/* entire subject consumed */
if(sub_len == 0)
{
done = 1;
break;
}
/* start next match were we left off */
sub += pmatch[0].rm_eo;
break;
case REG_NOMATCH:
if(match_count == 0)
puts("No matches found.");
done = 1;
break;
case REG_ESPACE:
fprintf(stderr,"Error: Out of memory.\n");
goto err;
default:
/* should not be here, abort */
assert(0);
}
}
/* success */
ret = 0;
err:
/* cleanup */
if(regex)
free(regex);
if(subject)
free(subject);
if(&preg)
tre_regfree(&preg);
if(pmatch)
free(pmatch);
return ret;
}
/* M A I N *******************************************************************/
int main(int argc, char *argv[]) {
int opt_index;
opt_index = process_options(argc, argv);
if (opt_index >= argc) {
fprintf(stderr, "%s : %s\n",
PRG_NAME, "[err] specify a record string to process!");
exit(1);
}
if (argv[1])
strncpy (record, argv[opt_index], MAX_CHAR);
if ( strlen(record) == 0 ) {
fprintf(stdout, "Please enter a valid string to search pattern for!\n");
fprintf(stdout, "Usage: %s %s %s %s\n", PRG_NAME, "[COSTS]", "[PATTERN]", "[STRING]");
exit(1);
}
/* Testing patterns */
// char record[] = "ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG";
// char regexp[] = "GATTT";
// char regexp[] = "GTAAAGA";
// char regexp[] = "(G|T)A*GAT";
int comp_flags = REG_EXTENDED | REG_ICASE ;
static regex_t preg; /* Compiled pattern to search for. */
static regaparams_t match_params; /* regexp matching parameters */
int errcode;
regmatch_t pmatch = { 0, 0 }; /* matched pattern structure */
regamatch_t match; /* overall match structure */
memset(&match, 0, sizeof(match)); /* initialize the overall match struct */
match.pmatch = &pmatch; /* assign default pattern structure */
match.nmatch = 1; /* initialization of pmatch array */
/* setup the default match parameters */
tre_regaparams_default(&match_params);
/* Set the maximum number of errors allowed for a record to match. */
match_params.max_cost = max_cost;
match_params.cost_ins = cost_ins;
match_params.cost_del = cost_del;
match_params.cost_subst = cost_subs;
fprintf(stdout, "Default regex params set by TRE:\n");
fprintf(stdout, "\t%-12s : %4d\n", "cost_ins", match_params.cost_ins);
fprintf(stdout, "\t%-12s : %4d\n", "cost_del", match_params.cost_del);
fprintf(stdout, "\t%-12s : %4d\n", "cost_substr", match_params.cost_subst);
fprintf(stdout, "\t%-12s : %4d\n", "max_cost", match_params.max_cost);
fprintf(stdout, "\t%-12s : %4d\n", "max_ins", match_params.max_ins);
fprintf(stdout, "\t%-12s : %4d\n", "max_del", match_params.max_del);
fprintf(stdout, "\t%-12s : %4d\n", "max_subst", match_params.max_subst);
fprintf(stdout, "\t%-12s : %4d\n", "max_err", match_params.max_err);
fprintf(stdout, "\n\n");
/* Step 1: compile the regex */
errcode = tre_regcomp(&preg, regexp, comp_flags);
if (errcode)
{
char errbuf[256];
tre_regerror(errcode, &preg, errbuf, sizeof(errbuf));
fprintf(stderr, "%s: %s: %s\n",
PRG_NAME, "Error in search pattern", errbuf);
exit(1);
}
// if (tre_regexec(&delim, "", 0, NULL, 0) == REG_OK)
// {
// fprintf(stderr, "%s: %s\n", PRG_NAME,
// "Record delimiter pattern must not match an empty string");
// exit(1);
// }
/* Step 2: search for the pattern in the haystack */
errcode = tre_regaexec(&preg, record, &match, match_params, 0);
if (errcode == REG_OK) {
fprintf(stdout, "Found match!\n");
fprintf(stdout, "\t%10s : %s\n", "record", record);
fprintf(stdout, "\t%10s : %s\n", "pattern", regexp);
fprintf(stdout, "\t%10s : %4d\n", "cost", match.cost);
fprintf(stdout, "\t%10s : %4d\n", "num_ins", match.num_ins);
fprintf(stdout, "\t%10s : %4d\n", "num_del", match.num_del);
fprintf(stdout, "\t%10s : %4d\n", "num_subst", match.num_subst);
fprintf(stdout, "\t%10s : %2d - %2d\n", "char pos",
pmatch.rm_so, pmatch.rm_eo);
}
else {
fprintf(stdout, "Found no matches!\n");
fprintf(stdout, "%6s : %s\n", "regexp", regexp);
fprintf(stdout, "%6s : %s\n", "record", record);
}
return 0;
}
SEXP attribute_hidden do_readDCF(SEXP call, SEXP op, SEXP args, SEXP env)
{
int nwhat, nret, nc, nr, m, k, lastm, need;
Rboolean blank_skip, field_skip = FALSE;
int whatlen, dynwhat, buflen = 8096; // was 100, but that re-alloced often
char *line, *buf;
regex_t blankline, contline, trailblank, regline, eblankline;
regmatch_t regmatch[1];
SEXP file, what, what2, retval, retval2, dims, dimnames;
Rconnection con = NULL;
Rboolean wasopen, is_eblankline;
RCNTXT cntxt;
SEXP fold_excludes;
Rboolean field_fold = TRUE, has_fold_excludes;
const char *field_name;
int offset = 0; /* -Wall */
checkArity(op, args);
file = CAR(args);
con = getConnection(asInteger(file));
wasopen = con->isopen;
if(!wasopen) {
if(!con->open(con)) error(_("cannot open the connection"));
/* Set up a context which will close the connection on error */
begincontext(&cntxt, CTXT_CCODE, R_NilValue, R_BaseEnv, R_BaseEnv,
R_NilValue, R_NilValue);
cntxt.cend = &con_cleanup;
cntxt.cenddata = con;
}
if(!con->canread) error(_("cannot read from this connection"));
args = CDR(args);
PROTECT(what = coerceVector(CAR(args), STRSXP)); /* argument fields */
nwhat = LENGTH(what);
dynwhat = (nwhat == 0);
args = CDR(args);
PROTECT(fold_excludes = coerceVector(CAR(args), STRSXP));
has_fold_excludes = (LENGTH(fold_excludes) > 0);
buf = (char *) malloc(buflen);
if(!buf) error(_("could not allocate memory for 'read.dcf'"));
nret = 20;
/* it is easier if we first have a record per column */
PROTECT(retval = allocMatrixNA(STRSXP, LENGTH(what), nret));
/* These used to use [:blank:] but that can match \xa0 as part of
a UTF-8 character (and is nbspace on Windows). */
tre_regcomp(&blankline, "^[[:blank:]]*$", REG_NOSUB & REG_EXTENDED);
tre_regcomp(&trailblank, "[ \t]+$", REG_EXTENDED);
tre_regcomp(&contline, "^[[:blank:]]+", REG_EXTENDED);
tre_regcomp(®line, "^[^:]+:[[:blank:]]*", REG_EXTENDED);
tre_regcomp(&eblankline, "^[[:space:]]+\\.[[:space:]]*$", REG_EXTENDED);
k = 0;
lastm = -1; /* index of the field currently being recorded */
blank_skip = TRUE;
void *vmax = vmaxget();
while((line = Rconn_getline2(con))) {
if(strlen(line) == 0 ||
tre_regexecb(&blankline, line, 0, 0, 0) == 0) {
/* A blank line. The first one after a record ends a new
* record, subsequent ones are skipped */
if(!blank_skip) {
k++;
if(k > nret - 1){
nret *= 2;
PROTECT(retval2 = allocMatrixNA(STRSXP, LENGTH(what), nret));
transferVector(retval2, retval);
UNPROTECT_PTR(retval);
retval = retval2;
}
blank_skip = TRUE;
lastm = -1;
field_skip = FALSE;
field_fold = TRUE;
}
} else {
blank_skip = FALSE;
if(tre_regexecb(&contline, line, 1, regmatch, 0) == 0) {
/* A continuation line: wrong if at the beginning of a
record. */
if((lastm == -1) && !field_skip) {
line[20] = '\0';
error(_("Found continuation line starting '%s ...' at begin of record."),
line);
}
if(lastm >= 0) {
need = (int) strlen(CHAR(STRING_ELT(retval,
lastm + nwhat * k))) + 2;
if(tre_regexecb(&eblankline, line, 0, NULL, 0) == 0) {
is_eblankline = TRUE;
} else {
is_eblankline = FALSE;
if(field_fold) {
offset = regmatch[0].rm_eo;
/* Also remove trailing whitespace. */
if((tre_regexecb(&trailblank, line, 1,
regmatch, 0) == 0))
line[regmatch[0].rm_so] = '\0';
} else {
offset = 0;
}
need += (int) strlen(line + offset);
}
if(buflen < need) {
char *tmp = (char *) realloc(buf, need);
if(!tmp) {
free(buf);
error(_("could not allocate memory for 'read.dcf'"));
} else buf = tmp;
buflen = need;
}
strcpy(buf,CHAR(STRING_ELT(retval, lastm + nwhat * k)));
strcat(buf, "\n");
if(!is_eblankline) strcat(buf, line + offset);
SET_STRING_ELT(retval, lastm + nwhat * k, mkChar(buf));
}
} else {
if(tre_regexecb(®line, line, 1, regmatch, 0) == 0) {
for(m = 0; m < nwhat; m++){
whatlen = (int) strlen(CHAR(STRING_ELT(what, m)));
if(strlen(line) > whatlen &&
line[whatlen] == ':' &&
strncmp(CHAR(STRING_ELT(what, m)),
line, whatlen) == 0) {
/* An already known field we are recording. */
lastm = m;
field_skip = FALSE;
field_name = CHAR(STRING_ELT(what, lastm));
if(has_fold_excludes) {
field_fold =
field_is_foldable_p(field_name,
fold_excludes);
}
if(field_fold) {
offset = regmatch[0].rm_eo;
/* Also remove trailing whitespace. */
if((tre_regexecb(&trailblank, line, 1,
regmatch, 0) == 0))
line[regmatch[0].rm_so] = '\0';
} else {
offset = 0;
}
SET_STRING_ELT(retval, m + nwhat * k,
mkChar(line + offset));
break;
} else {
/* This is a field, but not one prespecified */
lastm = -1;
field_skip = TRUE;
}
}
if(dynwhat && (lastm == -1)) {
/* A previously unseen field and we are
* recording all fields */
field_skip = FALSE;
PROTECT(what2 = allocVector(STRSXP, nwhat+1));
PROTECT(retval2 = allocMatrixNA(STRSXP,
nrows(retval)+1,
ncols(retval)));
if(nwhat > 0) {
copyVector(what2, what);
for(nr = 0; nr < nrows(retval); nr++){
for(nc = 0; nc < ncols(retval); nc++){
SET_STRING_ELT(retval2, nr+nc*nrows(retval2),
STRING_ELT(retval,
nr+nc*nrows(retval)));
}
}
}
UNPROTECT_PTR(retval);
UNPROTECT_PTR(what);
retval = retval2;
what = what2;
/* Make sure enough space was used */
need = (int) (Rf_strchr(line, ':') - line + 1);
if(buflen < need){
char *tmp = (char *) realloc(buf, need);
if(!tmp) {
free(buf);
error(_("could not allocate memory for 'read.dcf'"));
} else buf = tmp;
buflen = need;
}
strncpy(buf, line, Rf_strchr(line, ':') - line);
buf[Rf_strchr(line, ':') - line] = '\0';
SET_STRING_ELT(what, nwhat, mkChar(buf));
nwhat++;
/* lastm uses C indexing, hence nwhat - 1 */
lastm = nwhat - 1;
field_name = CHAR(STRING_ELT(what, lastm));
if(has_fold_excludes) {
field_fold =
field_is_foldable_p(field_name,
fold_excludes);
}
offset = regmatch[0].rm_eo;
if(field_fold) {
/* Also remove trailing whitespace. */
if((tre_regexecb(&trailblank, line, 1,
regmatch, 0) == 0))
line[regmatch[0].rm_so] = '\0';
}
SET_STRING_ELT(retval, lastm + nwhat * k,
mkChar(line + offset));
}
} else {
/* Must be a regular line with no tag ... */
line[20] = '\0';
error(_("Line starting '%s ...' is malformed!"), line);
}
}
}
}
vmaxset(vmax);
if(!wasopen) {endcontext(&cntxt); con->close(con);}
free(buf);
tre_regfree(&blankline);
tre_regfree(&contline);
tre_regfree(&trailblank);
tre_regfree(®line);
tre_regfree(&eblankline);
if(!blank_skip) k++;
/* and now transpose the whole matrix */
PROTECT(retval2 = allocMatrixNA(STRSXP, k, LENGTH(what)));
copyMatrix(retval2, retval, 1);
PROTECT(dimnames = allocVector(VECSXP, 2));
PROTECT(dims = allocVector(INTSXP, 2));
INTEGER(dims)[0] = k;
INTEGER(dims)[1] = LENGTH(what);
SET_VECTOR_ELT(dimnames, 1, what);
setAttrib(retval2, R_DimSymbol, dims);
setAttrib(retval2, R_DimNamesSymbol, dimnames);
UNPROTECT(6);
return(retval2);
}