void search_buffer(struct search_state *state, const char *pattern,
int pattern_size, char *buffer, int buffer_size,
const char *file_name, ullong buffer_offset) {
const char *buffer_start = buffer;
/* Where to stop matching */
const char *buffer_end = buffer + buffer_size - pattern_size;
int buffer_hash = hash_code(buffer, pattern_size);
int pattern_hash = state->pattern_hash;
int most_significant_factor = state->most_significant_factor;
/* Loop through the buffer... */
while(buffer < buffer_end) {
/* Compare hashes, and strings if necessary */
if(buffer_hash == pattern_hash &&
!strncmp(buffer, pattern, pattern_size)) {
print_match(file_name, buffer_offset + (buffer - buffer_start));
}
/* Update hash */
buffer_hash = ((buffer_hash -
((unsigned char) *buffer) * most_significant_factor) << 1) +
(unsigned char) *(buffer + pattern_size);
buffer++;
}
/* Comparison for the last position */
if(buffer_hash == pattern_hash &&
!strncmp(buffer, pattern, pattern_size)) {
print_match(file_name, buffer_offset + (buffer - buffer_start));
}
}
int main()
{
int xmatch[MAX], ymatch[MAX];
bipartite b1(4, 5);
b1.b_g[0][0] = 1; b1.b_g[0][1] = 1; b1.b_g[0][2] = 1; b1.b_g[0][3] = 1;
b1.b_g[1][0] = 1; b1.b_g[1][1] = 1; b1.b_g[1][3] = 1; b1.b_g[1][4] = 1;
b1.b_g[2][1] = 1; b1.b_g[2][2] = 1; b1.b_g[2][3] = 1; b1.b_g[2][4] = 1;
b1.b_g[3][0] = 1; b1.b_g[3][1] = 1; b1.b_g[3][2] = 1; b1.b_g[3][4] = 1;
cout << "hungarian 1 max binary match: " << hungarian1(b1, xmatch, ymatch) << endl; //1
print_match(b1, ymatch);
cout << "hungarian 2 max binary match: " << hungarian2(b1, ymatch) << endl;
print_match(b1, ymatch);
cout << "hopcroft karp max binary match: " << hopcroft_karp(b1, xmatch, ymatch) << endl; //2
print_match(b1, ymatch);
bipartite b2(5, 5);
b2.b_g[0][0] = 3; b2.b_g[0][1] = 5; b2.b_g[0][2] = 5; b2.b_g[0][3] = 4; b2.b_g[0][4] = 1;
b2.b_g[1][0] = 2; b2.b_g[1][1] = 2; b2.b_g[1][2] = 0; b2.b_g[1][3] = 2; b2.b_g[1][4] = 2;
b2.b_g[2][0] = 2; b2.b_g[2][1] = 4; b2.b_g[2][2] = 4; b2.b_g[2][3] = 1; b2.b_g[2][4] = 0;
b2.b_g[3][0] = 0; b2.b_g[3][1] = 1; b2.b_g[3][2] = 1; b2.b_g[3][3] = 0; b2.b_g[3][4] = 0;
b2.b_g[4][0] = 1; b2.b_g[4][1] = 2; b2.b_g[4][2] = 1; b2.b_g[4][3] = 3; b2.b_g[4][4] = 3;
cout << "kuhn munkres: " << kuhn_munkres(b2, ymatch) << endl; //5
print_match(b2, ymatch);
graph_matrix g(6);
g.g_m[0][0] = 0; g.g_m[0][1] = 1; g.g_m[0][2] = 1; g.g_m[0][3] = 1; g.g_m[0][4] = INF; g.g_m[0][5] = INF;
g.g_m[1][0] = INF; g.g_m[1][1] = 0; g.g_m[1][2] = INF; g.g_m[1][3] = 1; g.g_m[1][4] = 1; g.g_m[1][5] = INF;
g.g_m[2][0] = INF; g.g_m[2][1] = INF; g.g_m[2][2] = 0; g.g_m[2][3] = 1; g.g_m[2][4] = INF; g.g_m[2][5] = 1;
g.g_m[3][0] = 0; g.g_m[3][1] = INF; g.g_m[3][2] = INF; g.g_m[3][3] = 0; g.g_m[3][4] = 1; g.g_m[3][5] = 1;
g.g_m[4][0] = INF; g.g_m[4][1] = INF; g.g_m[4][2] = INF; g.g_m[4][3] = INF; g.g_m[4][4] = 0; g.g_m[4][5] = 1;
g.g_m[5][0] = INF; g.g_m[5][1] = INF; g.g_m[5][2] = INF; g.g_m[5][3] = INF; g.g_m[5][4] = INF; g.g_m[5][5] = 0;
cout << "disjoint path covering: " << minimum_disjoint_path_covering(g) << endl;//3
cout << "joint path covering: " << minimum_joint_path_covering(g) << endl; //4
return(0);
}
void
libwacom_print_device_description(int fd, const WacomDevice *device)
{
const WacomMatch **match;
WacomClass class;
const char *class_name;
class = libwacom_get_class(device);
switch(class) {
case WCLASS_UNKNOWN: class_name = "Unknown"; break;
case WCLASS_INTUOS3: class_name = "Intuos3"; break;
case WCLASS_INTUOS4: class_name = "Intuos4"; break;
case WCLASS_INTUOS5: class_name = "Intuos5"; break;
case WCLASS_CINTIQ: class_name = "Cintiq"; break;
case WCLASS_BAMBOO: class_name = "Bamboo"; break;
case WCLASS_GRAPHIRE: class_name = "Graphire";break;
case WCLASS_ISDV4: class_name = "ISDV4"; break;
case WCLASS_INTUOS: class_name = "Intuos"; break;
case WCLASS_INTUOS2: class_name = "Intuos2"; break;
case WCLASS_PEN_DISPLAYS: class_name = "PenDisplay"; break;
case WCLASS_REMOTE: class_name = "Remote"; break;
default: g_assert_not_reached(); break;
}
dprintf(fd, "[Device]\n");
dprintf(fd, "Name=%s\n", libwacom_get_name(device));
dprintf(fd, "DeviceMatch=");
for (match = libwacom_get_matches(device); *match; match++)
print_match(fd, *match);
dprintf(fd, "\n");
if (libwacom_get_paired_device(device)) {
dprintf(fd, "PairedID=");
print_match(fd, libwacom_get_paired_device(device));
dprintf(fd, "\n");
}
dprintf(fd, "Class=%s\n", class_name);
dprintf(fd, "Width=%d\n", libwacom_get_width(device));
dprintf(fd, "Height=%d\n", libwacom_get_height(device));
print_integrated_flags_for_device(fd, device);
print_layout_for_device(fd, device);
print_styli_for_device(fd, device);
dprintf(fd, "\n");
dprintf(fd, "[Features]\n");
dprintf(fd, "Reversible=%s\n", libwacom_is_reversible(device) ? "true" : "false");
dprintf(fd, "Stylus=%s\n", libwacom_has_stylus(device) ? "true" : "false");
dprintf(fd, "Ring=%s\n", libwacom_has_ring(device) ? "true" : "false");
dprintf(fd, "Ring2=%s\n", libwacom_has_ring2(device) ? "true" : "false");
dprintf(fd, "Touch=%s\n", libwacom_has_touch(device) ? "true" : "false");
dprintf(fd, "TouchSwitch=%s\n", libwacom_has_touchswitch(device)? "true" : "false");
print_supported_leds(fd, device);
dprintf(fd, "NumStrips=%d\n", libwacom_get_num_strips(device));
dprintf(fd, "Buttons=%d\n", libwacom_get_num_buttons(device));
print_buttons_for_device(fd, device);
}
/*
* Searches through a nucleic acid sequence and matchs the K-mer and the K-mer reverse complement.
* Uses a binary AND operation to limit the number of conditionals within the for loop.
*/
void search_nucleic_acid(Sequence* currentSequence, char* k_mer, char* reverseComplementKmer, int k)
{
int i;
int j;
float gcContent;
int gc = 0;
for (i = 0; i <= currentSequence->sequenceLength - k; i++)
{
if (k_mer[0] & currentSequence->data[i])
{
for (j = 1; j < k; j++)
{
if (!(k_mer[j] & currentSequence->data[ i + j ]))
{
break;
}
}
if (j == k)
{
print_match(currentSequence, i, i + k, '+');
}
}
if (reverseComplementKmer[0] & currentSequence->data[i])
{
for (j = 1; j < k; j++)
{
if (!(reverseComplementKmer[j] & currentSequence->data[ i + j ]))
{
break;
}
}
if (j == k)
{
print_match(currentSequence, i, i + k, '-');
}
}
if (currentSequence->data[i] & 6)
{
gc++;
}
}
for (; i <= currentSequence->sequenceLength; i++)
{
if (currentSequence->data[i] & 6)
{
gc++;
}
}
gcContent = 100 * ((float)gc / currentSequence->sequenceLength);
printf("GC content for sequence %s: %.2f\%\n\n", currentSequence->sequenceName, gcContent);
}
static void
set_save_v1(const void *ip, const struct xt_entry_match *match)
{
const struct xt_set_info_match_v1 *info = (const void *)match->data;
print_match("--match-set", &info->match_set);
}
/* Prints out the matchinfo. */
static void
set_print_v1(const void *ip, const struct xt_entry_match *match, int numeric)
{
const struct xt_set_info_match_v1 *info = (const void *)match->data;
print_match("match-set", &info->match_set);
}
/* Saves the matchinfo in parsable form to stdout. */
static void set_save(const void *ip, const struct xt_entry_match *match)
{
struct ipt_set_info_match *info =
(struct ipt_set_info_match *) match->data;
print_match("--set", &info->match_set);
}
/* Prints out the matchinfo. */
static void set_print(const void *ip, const struct xt_entry_match *match,
int numeric)
{
struct ipt_set_info_match *info =
(struct ipt_set_info_match *) match->data;
print_match("set", &info->match_set);
}
static void
statistic_print(const void *ip, const struct xt_entry_match *match, int numeric)
{
struct xt_statistic_info *info = (struct xt_statistic_info *)match->data;
printf("statistic ");
print_match(info, "");
}
/* Prints the matches that takes place within the timespan of the range */
void print_range_matches(match_s *match_range, int matches_in_range) {
int match_number = 0;
printf("Weekday\tDate & Time\tHome Out\tGoals\tSpectators\n");
for(match_number = 0; match_number < matches_in_range; match_number++) {
print_match(match_range, match_number);
}
}
static void
set_save_v2(const void *ip, const struct xt_entry_match *match)
{
const struct xt_set_info_match_v1 *info = (const void *)match->data;
print_match("--match-set", &info->match_set);
if (info->match_set.flags & IPSET_RETURN_NOMATCH)
printf(" --return-nomatch");
}
/* Task one - performs all work for task one */
void task_one(match_s *match, int number_of_matches) {
int match_number = 0;
printf("The following matches have a total of 7 or more goals:\n");
printf("Weekday\tDate & Time\tHome Out\tGoals\tSpectators\n");
for(match_number = 0; match_number < number_of_matches; match_number++) {
if(match[match_number].home_goal + match[match_number].out_goal >= 7) {
print_match(match, match_number);
}
}
}
static void
set_print_v4_matchinfo(const struct xt_set_info_match_v4 *info,
const char *opt, const char *sep)
{
print_match(opt, &info->match_set);
if (info->flags & IPSET_FLAG_RETURN_NOMATCH)
printf(" %sreturn-nomatch", sep);
if ((info->flags & IPSET_FLAG_SKIP_COUNTER_UPDATE))
printf(" ! %supdate-counters", sep);
if ((info->flags & IPSET_FLAG_SKIP_SUBCOUNTER_UPDATE))
printf(" ! %supdate-subcounters", sep);
set_printv4_counter(&info->packets, "packets", sep);
set_printv4_counter(&info->bytes, "bytes", sep);
}
int main(int argc, char **argv) {
if (argc != 4) {
printUsage();
}
int number = atoi(argv[1]);
int pos_1 = atoi(argv[2]);
int pos_2 = atoi(argv[3]);
char *pointer = dec_to_bin(number);
int check = check_bits(pointer, pos_1, pos_2);
print_match(check);
free(pointer);
return 0;
}
void printer::run() {
for (;;) {
{
std::unique_lock<std::mutex> lock(contents_mtx);
contents_cv.wait(lock, [this] { return !this->contents.empty(); });
while (!contents.empty()) {
auto&& top = contents.front();
switch (top.t) {
case tag::finish:
return;
case tag::match:
print_match(os, *top.result);
break;
}
contents.pop();
}
}
}
}
void print_align_list_segments (alignel* alignList)
{
alignel* a;
unspos beg1, end1, beg2, end2;
unspos height, width, i, j, prevI, prevJ, run;
u32 opIx;
score s;
for (a=alignList ; a!=NULL ; a=a->next)
{
beg1 = a->beg1;
end1 = a->end1;
beg2 = a->beg2;
end2 = a->end2;
height = end1 - beg1 + 1;
width = end2 - beg2 + 1;
snoopGenpaf_1;
// print the alignment's segments
opIx = 0;
for (i=j=0 ; (i< height)||(j<width) ; )
{
prevI = i; prevJ = j;
run = edit_script_run_of_subs (a->script, &opIx);
i += run; j += run;
if ((i < height) || (j < width))
edit_script_indel_len (a->script, &opIx, &i, &j);
s = score_match (currParams->scoring,
currParams->seq1, beg1-1+prevI,
currParams->seq2, beg2-1+prevJ,
run);
print_match (beg1-1+prevI, beg2-1+prevJ, run, s);
}
}
}
/*
* Searches through an amino acid sequence to match a given K-mer.
* Uses exact matching to locate a match.
*/
void search_amino_acid(Sequence* currentSequence, char* k_mer, int k)
{
int i;
int j;
for (i = 0; i < currentSequence->sequenceLength - k; i++)
{
if (k_mer[0] == currentSequence->data[i])
{
for (j = 1; j < k; j++)
{
if (k_mer[j] != currentSequence->data[i+j])
{
break;
}
}
if (j == k)
{
print_match(currentSequence, i, i + k, '.');
}
}
}
}
static void save(const struct ipt_ip *ip, const struct ipt_entry_match *match)
{
#ifdef IPTABLES_SAVE
print_match((const struct ipt_web_info *)match->data);
#endif
}
int main(int argc, char *const argv[])
{
size_t before = 16;
size_t after = 16;
int color = 0;
bool hexlify = true;
int ch;
long ia, ib;
while ((ch = getopt(argc, argv, "a:b:chH")) != -1)
{
switch(ch)
{
case 'a':
ia = strtol(optarg, NULL, 10);
if ((ia > 0) && (ia < 1024))
{
after = (size_t)ia;
}
break;
case 'b':
ib = strtol(optarg, NULL, 10);
if ((ib > 0) && (ib < 1024))
{
before = (size_t)ib;
}
break;
case 'c':
color++;
break;
case 'H':
hexlify = !hexlify;
break;
case 'h':
default:
usage();
break;
}
}
if (!isatty(STDOUT_FILENO) && color)
{
color--;
}
argc -= optind;
argv += optind;
if (argc < 2)
{
usage();
}
size_t pattern_size = 0;
uint8_t *pattern;
if (hexlify)
{
pattern = hex_decode(argv[0], &pattern_size);
}
else
{
pattern_size = strlen(argv[0]);
pattern = (uint8_t*)strndup(argv[0], pattern_size);
}
if (!pattern)
{
fprintf(stderr, "Invalid pattern\n");
}
// initialize boyer-moore patterns
int *delta1 = (int*)malloc(ALPHABET_LEN * sizeof(int));
int *delta2 = (int*)malloc(pattern_size * sizeof(int));
make_delta1(delta1, pattern, pattern_size);
make_delta2(delta2, pattern, pattern_size);
size_t count = 0;
size_t errors = 0;
for (int f=1; f<argc; f++)
{
int first = 1;
const char *file_name = argv[f];
int fd = open(file_name, O_RDONLY);
if (fd < 0)
{
fprintf(stderr, "Open error ");
perror(file_name);
errors++;
continue;
}
// Get the file size, to make mmap search the whole thing
struct stat file_stat;
if (fstat(fd, &file_stat) != 0)
{
fprintf(stderr, "Stat error ");
perror(file_name);
errors++;
close(fd); // ignore error
continue;
}
size_t file_size = (size_t)file_stat.st_size;
if ((file_size == 0) || !S_ISREG(file_stat.st_mode))
{
close(fd); // ignore error
continue;
}
const uint8_t *file = mmap(0, file_size, PROT_READ, MAP_SHARED, fd, 0);
if (file == MAP_FAILED)
{
fprintf(stderr, "Mmap error ");
perror(file_name);
errors++;
close(fd); // ignore error
continue;
}
// Find all matches, don't worry about overlaps
size_t last = 0;
size_t next = 0;
while ((next = bm_search(file + last,
file_size - last,
pattern, pattern_size,
delta1, delta2)) != NOT_FOUND)
{
if (first)
{
first = 0;
printf("---- %s ----\n", file_name);
}
print_match(file, last + next, pattern_size, before, after, color);
last += next + pattern_size;
count++;
}
if (munmap((void*)file, file_size) != 0)
{
fprintf(stderr, "Unmap error ");
perror(file_name);
errors++;
}
if (close(fd) != 0)
{
fprintf(stderr, "Close error ");
perror(file_name);
errors++;
}
}
free(delta2);
free(delta1);
free(pattern);
if (count > 0)
{
return 0;
}
if (errors > 0)
{
return 2;
}
return 1;
}
int main(int argc, char *argv[]) {
kseq_t *seq;
int l, index, shift, min=5, min_keep=35;
int debug=0, verbose=1;
int contaminated=0, total=0;
quality_type qual_type=SANGER;
match *best_match;
float *qprobs, prior=default_prior;
adapter_array *aa;
gzFile adapter_fp=NULL, fp;
FILE *output_fp=stdout, *matches_fp=NULL;
int optc;
int add_tag = 0;
extern char *optarg;
while (1) {
int option_index = 0;
optc = getopt_long(argc, argv, "dtfp:a:o:q:m:o:n:M:", long_options, &option_index);
if (optc == -1)
break;
switch (optc) {
if (long_options[option_index].flag != 0)
break;
case 'a':
adapter_fp = gzopen(optarg, "r");
if (!adapter_fp) {
fprintf(stderr, "Could not open adapter file '%s'.\n", optarg);
return EXIT_FAILURE;
}
break;
case 'd':
debug = 1;
break;
case 't':
add_tag = 1;
break;
case 'Q':
verbose = 0;
break;
case 'o':
output_fp = fopen(optarg, "w");
if (!output_fp) {
fprintf(stderr, "Could not open output file '%s'.\n", optarg);
return EXIT_FAILURE;
}
break;
case 'm':
matches_fp = fopen(optarg, "w");
if (!matches_fp) {
fprintf(stderr, "Could not open matches file '%s'.\n", optarg);
return EXIT_FAILURE;
}
break;
case 'n':
min = atoi(optarg);
break;
case 'M':
min_keep = atoi(optarg);
break;
case 'q':
if (strcmp(optarg, "illumina") == 0)
qual_type = ILLUMINA;
else if (strcmp(optarg, "solexa") == 0)
qual_type = SOLEXA;
else if (strcmp(optarg, "sanger") == 0)
qual_type = SANGER;
else {
fprintf(stderr, "Unknown quality type '%s'.\n", optarg);
usage(EXIT_FAILURE);
}
break;
case 'p':
/* This truncation is acceptable... priors need not be doubles */
prior = (float) atof(optarg);
if (prior > 1 || prior < 0) {
fprintf(stderr, "Prior must be between 0 and 1\n");
usage(EXIT_FAILURE);
}
break;
case_GETOPT_HELP_CHAR;
case_GETOPT_VERSION_CHAR(PROGRAM_NAME, VERSION, AUTHORS);
case '?':
break;
default:
usage(EXIT_FAILURE);
}
}
if (debug) {
matches_fp = stdout;
output_fp = stdout;
}
if ((index = optind) == argc) {
fprintf(stderr, "No FASTQ file specified.\n");
usage(EXIT_FAILURE);
}
/* load all adapter sequences into memory */
if (!adapter_fp) {
fprintf(stderr, "No adapter file specified.\n");
usage(EXIT_FAILURE);
}
aa = load_adapters(adapter_fp);
gzclose(adapter_fp);
fp = strcmp(argv[index], "-") ? gzopen(argv[index], "r") : gzdopen(fileno(stdin), "r");
if (!fp) {
fprintf(stderr, "FASTQ file '%s' not found.\n", argv[index]);
return EXIT_FAILURE;
}
seq = kseq_init(fp);
/* Loop through entire sequence file. Write trimmed sequences to
file (or stdout), and record matches in a match file if specifed.
*/
while ((l = kseq_read(seq)) >= 0) {
shift = -1;
if (!seq->qual.s) {
fputs("Sequence file missing or has malformed quality line.\n", stderr);
usage(EXIT_FAILURE);
}
qprobs = qual_to_probs(seq->qual.s, qual_type);
best_match = find_best_match(aa, seq->seq.s, qprobs, prior, 0.25, min);
if (best_match && best_match->ps->is_contam) {
contaminated++;
shift = best_match->shift;
if (matches_fp) print_match(seq, best_match, matches_fp, aa, qual_type);
/* TODO */
/* aa->adapters[best_match->adapter_index].occurrences[best_match->n-1]++; */
}
write_fastq(output_fp, seq, add_tag, shift, min_keep);
if (best_match) destroy_match(best_match);
free(qprobs);
total++;
}
if (verbose)
print_summary(aa, prior, total-contaminated, contaminated, total);
kseq_destroy(seq);
destroy_adapters(aa, MAX_ADAPTERS);
gzclose(fp);
return 0;
}
void _match_pattern_indels(const cachedCharSeq *P, const cachedCharSeq *S,
int max_nmis, int fixedP, int fixedS)
{
int i0, j0, max_nmis1, nedit1, width1;
char c0;
cachedCharSeq P1;
if (P->length <= 0)
error("empty pattern");
_select_nmismatch_at_Pshift_fun(fixedP, fixedS);
if (!fixedP || !fixedS)
error("'fixed' must be TRUE when 'algorithm=\"indels\"' (for now)");
// Before we can support fixedP=FALSE or fixedS=FALSE in
// _match_pattern_indels(), we need to support them in
// _init_byte2offset_with_cachedCharSeq() and _nedit_for_Ploffset().
_init_byte2offset_with_cachedCharSeq(byte2offset, P, 0);
provisory_match_nedit = -1; // means no provisory match yet
j0 = 0;
while (j0 < S->length) {
while (1) {
c0 = S->seq[j0];
i0 = byte2offset[(unsigned char) c0];
if (i0 != NA_INTEGER) break;
j0++;
if (j0 >= S->length) goto done;
}
P1.seq = P->seq + i0 + 1;
P1.length = P->length - i0 - 1;
max_nmis1 = max_nmis - i0;
/*
#ifdef DEBUG_BIOSTRINGS
if (debug) {
Rprintf("[DEBUG] _match_pattern_indels(): "
"j0=%d c0=%c i0=%d max_nmis1=%d\n", j0, c0, i0, max_nmis1);
}
#endif
*/
if (max_nmis1 >= 0) {
if (max_nmis1 == 0) {
nedit1 = _selected_nmismatch_at_Pshift_fun(&P1, S, j0 + 1, max_nmis1);
width1 = P1.length;
} else {
nedit1 = _nedit_for_Ploffset(&P1, S, j0 + 1, max_nmis1, 1, &width1);
}
if (nedit1 <= max_nmis1) {
#ifdef DEBUG_BIOSTRINGS
if (debug) {
Rprintf("[DEBUG] _match_pattern_indels(): "
"provisory match found at ");
print_match(j0 + 1, width1 + 1, P, S);
}
#endif
report_provisory_match(j0 + 1, width1 + 1, nedit1 + i0);
}
}
j0++;
}
done:
if (provisory_match_nedit != -1)
_report_match(provisory_match_start, provisory_match_width);
return;
}
static void print(const struct ipt_ip *ip, const struct ipt_entry_match *match, int numeric)
{
printf("web ");
print_match((const struct ipt_web_info *)match->data);
}
void _match_pattern_indels(const Chars_holder *P, const Chars_holder *S,
int max_nmis, int fixedP, int fixedS)
{
int i0, j0, max_nmis1, nedit1, width1;
char c0;
const BytewiseOpTable *bytewise_match_table;
Chars_holder P1;
if (P->length <= 0)
error("empty pattern");
bytewise_match_table = _select_bytewise_match_table(fixedP, fixedS);
_init_byte2offset_with_Chars_holder(&byte2offset, P,
bytewise_match_table);
provisory_match_nedit = -1; // means no provisory match yet
j0 = 0;
while (j0 < S->length) {
while (1) {
c0 = S->ptr[j0];
i0 = byte2offset.byte2code[(unsigned char) c0];
if (i0 != NA_INTEGER) break;
j0++;
if (j0 >= S->length) goto done;
}
P1.ptr = P->ptr + i0 + 1;
P1.length = P->length - i0 - 1;
max_nmis1 = max_nmis - i0;
/*
#ifdef DEBUG_BIOSTRINGS
if (debug) {
Rprintf("[DEBUG] _match_pattern_indels(): "
"j0=%d c0=%c i0=%d max_nmis1=%d\n", j0, c0, i0, max_nmis1);
}
#endif
*/
if (max_nmis1 >= 0) {
if (max_nmis1 == 0) {
nedit1 = _nmismatch_at_Pshift(&P1, S, j0 + 1,
max_nmis1,
bytewise_match_table);
width1 = P1.length;
} else {
nedit1 = _nedit_for_Ploffset(&P1, S, j0 + 1,
max_nmis1, 1, &width1,
bytewise_match_table);
}
if (nedit1 <= max_nmis1) {
#ifdef DEBUG_BIOSTRINGS
if (debug) {
Rprintf("[DEBUG] _match_pattern_indels(): "
"provisory match found at ");
print_match(j0 + 1, width1 + 1, P, S,
bytewise_match_table);
}
#endif
report_provisory_match(j0 + 1, width1 + 1, nedit1 + i0);
}
}
j0++;
}
done:
if (provisory_match_nedit != -1)
_report_match(provisory_match_start, provisory_match_width);
return;
}
static void statistic_save(const void *ip, const struct xt_entry_match *match)
{
struct xt_statistic_info *info = (struct xt_statistic_info *)match->data;
print_match(info, "--");
}
int main (int argc, char *argv[]) {
int i, j, n, res;
regex_t regex;
char buffer[1024];
regmatch_t matches[MAX_MATCHES];
/* At least one argument, -h | --help | <regex> */
if (argc < 2) {
usage (argv[0]);
exit (1);
}
/* Help */
if ( (strcmp (argv[1], "-h") == 0) || (strcmp (argv[1], "--help") == 0) ) {
usage (argv[0]);
exit (0);
}
/* Show version */
if ( (strcmp (argv[1], "-v") == 0) || (strcmp (argv[1], "--version") == 0) ) {
printf ("Pcre version is %s\n", pcre_version());
exit (0);
}
/* Compile regex */
res = regcomp (®ex, argv[1], 0);
if (res != 0) {
(void) regerror (res, ®ex, buffer, sizeof(buffer));
fprintf (stderr, "ERROR: Compilation has failed with error: %s\n",
buffer);
exit (1);
}
/* Check strings */
for (i = 3; i <= argc; i++) {
/* Compile */
res = regexec (®ex, argv[i-1], MAX_MATCHES, matches, 0);
if (res == REG_NOMATCH) {
printf ("No match\n");
continue;
}
if (res != 0) {
(void) regerror (res, ®ex, buffer, sizeof(buffer));
fprintf (stderr, "ERROR: Execution has failed with error: %s\n",
buffer);
exit (1);
}
/* Print result */
print_match (matches[0]);
/* Count matching substrings */
n = 0;
for (j = MAX_MATCHES - 1; j >= 0; j--) {
if (matches[j].rm_so != -1) {
n = j;
break;
}
}
/* Print matching substrings */
for (j = 1; j <= n; j++) {
print_match (matches[j]);
}
}
/* Cleanup */
regfree (®ex);
/* Done */
exit (0);
}
//TODO: append matches to some data structure instead of just printing them out
// then there can be sweet summaries of matches/files scanned/time/etc
int search_dir(pcre *re, const char* path, const int depth) {
//TODO: don't just die. also make max depth configurable
if(depth > MAX_SEARCH_DEPTH) {
log_err("Search depth greater than %i, giving up.", depth);
exit(1);
}
struct dirent **dir_list = NULL;
struct dirent *dir = NULL;
int results = 0;
FILE *fp = NULL;
int f_len;
size_t r_len;
char *buf = NULL;
int rv = 0;
char *dir_full_path = NULL;
size_t path_length = 0;
results = scandir(path, &dir_list, &ignorefile_filter, &alphasort);
if (results > 0) {
for (int i = 0; i < results; i++) {
dir = dir_list[i];
path_length = (size_t)(strlen(path) + strlen(dir->d_name) + 2); // 2 for slash and null char
dir_full_path = malloc(path_length);
dir_full_path = strncpy(dir_full_path, path, path_length);
dir_full_path = strncat(dir_full_path, "/", path_length);
dir_full_path = strncat(dir_full_path, dir->d_name, path_length);
load_ignore_patterns(dir_full_path);
free(dir);
free(dir_full_path);
}
}
free(dir_list);
results = scandir(path, &dir_list, &filename_filter, &alphasort);
if (results == 0)
{
log_debug("No results found");
free(dir_list);
return(0);
}
else if (results == -1) {
log_err("Error opening directory %s", path);
return(0);
}
for (int i=0; i<results; i++) {
dir = dir_list[i];
// XXX: this is copy-pasted from about 30 lines above
path_length = (size_t)(strlen(path) + strlen(dir->d_name) + 2); // 2 for slash and null char
dir_full_path = malloc(path_length);
dir_full_path = strncpy(dir_full_path, path, path_length);
dir_full_path = strncat(dir_full_path, "/", path_length);
dir_full_path = strncat(dir_full_path, dir->d_name, path_length);
log_debug("dir %s type %i", dir_full_path, dir->d_type);
//TODO: scan files in current dir before going deeper
if (dir->d_type == DT_DIR && opts.recurse_dirs) {
log_debug("searching dir %s", dir_full_path);
rv = search_dir(re, dir_full_path, depth + 1);
goto cleanup;
continue;
}
fp = fopen(dir_full_path, "r");
if (fp == NULL) {
log_err("Error opening file %s. Skipping...", dir_full_path);
goto cleanup;
continue;
}
rv = fseek(fp, 0, SEEK_END);
if (rv != 0) {
log_err("Error fseek()ing file %s. Skipping...", dir_full_path);
goto cleanup;
}
f_len = ftell(fp); //TODO: behave differently if file is HUGE. on 32 bit, anything > 2GB will screw up this program
if (f_len == 0) {
log_debug("file is empty. skipping");
goto cleanup;
}
rewind(fp);
buf = (char*) malloc(sizeof(char) * f_len + 1);
r_len = fread(buf, 1, f_len, fp);
buf[r_len] = '\0';
int buf_len = (int)r_len;
int buf_offset = 0;
int offset_vector[MAX_MATCHES_PER_FILE * 2]; //XXXX
int rc = 0;
char *match_start = NULL;
char *match_end = NULL;
int first_match = 1;
// In my profiling, most of the execution time is spent in this pcre_exec
while(buf_offset < buf_len && (rc = pcre_exec(re, NULL, buf, r_len, buf_offset, 0, offset_vector, sizeof(offset_vector))) >= 0 ) {
log_debug("Match found. File %s, offset %i bytes.", dir_full_path, offset_vector[0]);
match_start = buf + offset_vector[0];
match_end = buf + offset_vector[1];
buf_offset = offset_vector[1];
print_match(dir_full_path, buf, match_start, match_end, first_match);
first_match = 0;
}
free(buf);
cleanup:
if (fp != NULL) {
fclose(fp);
}
free(dir);
free(dir_full_path);
}
free(dir_list);
return(0);
}
void fix_adrb(struct tree **root)
{
FILE *fp;
char chose[MAXLEN];
char items[2][MAXLEN];
struct adrb *data[MAXLEN];
struct tree **view;
struct tree *temp;
int loop_main, loop_sub, flag_x;
int i, j, num;
data[0] = NULL;
loop_main = 0;
while( loop_main != 1 ) {
loop_sub = 0;
while(loop_sub != 1) {
loop_sub = 1;
printf("修正する住所録を検索します…\n");
printf("修正したい住所録の「氏名」を入力してください。終了するには「Ctrlキーを押しながらDを押してください」。\n");
printf("> ");
if( scanf("%s", items[0] ) == EOF ) {
printf("住所録の修正を終了します…\n\n");
return;
}
}
i = 0;
print_match(*root, data, items[0], 0, &i);
if( data[0] == NULL ) {
printf("一致する住所録はありませんでした…\n\n");
continue;
} else {
printf("一致する住所録があります…\n");
for(j = 0; j < i; j++)
printf("・%2d: %s\t%s\t%s\t%s\t%s\n", j+1, data[j]->name, data[j]->posc, data[j]->adre, data[j]->tell, data[j]->mail);
}
loop_sub = 0;
while( loop_sub != 1 ) {
printf("\nどの住所録を修正しますか?左の番号を入力してください。修正せずに終了するには「Ctrlキーを押しながらDを押してください」。\n");
printf("> ");
if( scanf("%s", chose) == EOF ) {
printf("住所録の修正を終了します…\n\n");
return;
};
if(strlen(chose) != 1) {
printf("入力エラーです!\n");
continue;
}
if( atoi(chose) < 1 || i < atoi(chose) ) {
printf("入力エラーです!\n");
continue;
}
printf("次の住所録が選択されました。\n");
printf("・%2d: %s\t%s\t%s\t%s\t%s\n", atoi(chose), data[atoi(chose)-1]->name, data[atoi(chose)-1]->posc, data[atoi(chose)-1]->adre, data[atoi(chose)-1]->tell, data[atoi(chose)-1]->mail);
num = atoi(chose) - 1;
loop_sub = 1;
}
loop_sub = 0;
while( loop_sub != 1 ) {
printf("\nどの項目を修正しますか?番号を入力してください。修正せずに終了するには5を入力してください。\n");
printf("0: 氏名\n1: 郵便番号\n2: 住所\n3: 電話番号\n4: メールアドレス\n");
printf("> ");
if( scanf("%s", chose) == EOF ) {
printf("入力エラーです!\n");
continue;
};
if(strlen(chose) != 1) {
printf("入力エラーです!\n");
continue;
}
switch(chose[0]) {
case '0':
loop_sub = 1;
break;
case '1':
loop_sub = 1;
break;
case '2':
loop_sub = 1;
break;
case '3':
loop_sub = 1;
break;
case '4':
loop_sub = 1;
break;
case '5':
printf("住所録の修正を終了します…\n\n");
return;
default:
printf("入力エラーです!\n");
break;
}
}
loop_sub = 0;
while(loop_sub != 1) {
loop_sub = 1;
printf("修正してください。\n");
printf("> ");
if( scanf("%s", items[1]) == EOF ) {
printf("入力エラーです!\n\n");
loop_sub = 0;
continue;
}
}
fix_item( data[num], items[1], atoi(chose) );
printf("修正完了\n");
print_adrb(*root);
printf("\n");
fp = fopen( "adrb.dat", "w");
if( fp == NULL ) {
return;
}
save_file( fp, root );
fclose(fp);
loop_sub = 0;
while( loop_sub != 1 ) {
printf("住所録の修正を続けますか？番号を入力してください！\n");
printf("0: Yes\n1: No\n");
printf("> ");
if( scanf("%s", chose) == EOF ) {
printf("入力エラーです!\n");
continue;
};
if( strlen(chose) != 1) {
printf("入力エラーです。\n");
continue;
}
switch(chose[0]) {
case '0':
loop_sub = 1;
break;
case '1':
loop_sub = loop_main = 1;
break;
default:
printf("入力エラーです!\n");
break;
}
}
}
printf("住所録の修正を終了します…\n\n");
}
