main()
{
int b[100];
printf("%d %d\n" , a ,b[55] );
aho( b );
}
int main (){
char t[MAXS]; char texto[MAXT];
int N;
scanf("%d", &N);
for (int i = 0; i < MAX; i++) indice[i].clear();
cnt = 1;
memset (sig, 0, sizeof (sig));
for (int i = 0; i < N; i++){
scanf("%s", t);
add (t, i);
}
aho();
scanf("%s", texto);
busca (texto);
return 0;
}
void testRCInsertAcAutomaton() {
PointerACAutomaton<KmerAffect> aho(true);
aho.insert("ACAGTC", "V", true, 0, "##-##");
aho.build_failure_functions();
// Will insert AC-GT → ACAGT, ACCGT, ACGGT, ACTGT
// and CA-TC → CAATC, CACTC, CAGTC, CATTC
// plus the revcomps:
// Will insert GA-TG → GAATG, GACTG, GAGTG, GATTG
// and AC-GT → ACAGT, ACCGT, ACGGT, ACTGT
pointer_state<KmerAffect> *state = aho.goto_state("ACCGT");
TAP_TEST_EQUAL(state->informations.size(), 1, TEST_AC_GET, "");
TAP_TEST_EQUAL(state->informations.front(), AFFECT_AMBIGUOUS, TEST_AC_GET, "");
TAP_TEST(state->is_final, TEST_AC_FINAL, "");
TAP_TEST(! aho.goto_state("CAAT")->is_final, TEST_AC_FINAL, "");
TAP_TEST(aho.goto_state("CAAT")->informations.size() == 1, TEST_AC_GET, "");
TAP_TEST(aho.goto_state("CAAT")->informations.front() == AFFECT_UNKNOWN, TEST_AC_GET, "");
TAP_TEST(aho.goto_state("GAGTG")->informations.front() == AFFECT_V_BWD, TEST_AC_GET, "");
TAP_TEST(aho.goto_state("GAGTG")->is_final, TEST_AC_FINAL, "");
TAP_TEST(aho.goto_state("GAGTG")->transitions[A] == aho.goto_state("GA"), TEST_AC_TRANSITIONS, "");
vector<KmerAffect> results = aho.getResults("ACCGTgaatgCATTCA");
vector<KmerAffect> expected = {AFFECT_AMBIGUOUS,
AFFECT_UNKNOWN, AFFECT_UNKNOWN, AFFECT_UNKNOWN,
AFFECT_UNKNOWN, AFFECT_V_BWD, AFFECT_UNKNOWN,
AFFECT_UNKNOWN, AFFECT_UNKNOWN, AFFECT_UNKNOWN,
AFFECT_V, AFFECT_UNKNOWN, AFFECT_UNKNOWN, AFFECT_UNKNOWN, AFFECT_UNKNOWN,
AFFECT_UNKNOWN };
TAP_TEST(results.size() == expected.size(), TEST_AC_GET_RESULTS, "");
TAP_TEST(results == expected, TEST_AC_GET_RESULTS, "");
}
int main (int argc, char **argv) {
findPatternFlag = 0;
std::string patternFile = "", patternStr = "";
int c, color_flag = 0, help_flag = 0, edit_flag = 0, pattern_flag = 0, emax;
while (1) {
static struct option long_options[] = {
{"help", no_argument, 0, 'h'},
{"edit", required_argument, 0, 'e'},
{"pattern", required_argument, 0, 'p'},
{"color", no_argument, 0, 'c'},
{0, 0, 0, 0}
};
// getopt_long guarda o indice da opcao aqui
int option_index = 0;
c = getopt_long (argc, argv, "che:p:", long_options, &option_index);
// detecta o fim das opcoes
if (c == -1) {
break;
}
switch (c) {
case 'c':
color_flag = 1;
break;
case 'h':
help_flag = 1;
break;
case 'e':
emax = atoi(optarg);
edit_flag = 1;
break;
case 'p':
// optarg eh o argumento da option;
patternFile = std::string(optarg);
pattern_flag = 1;
break;
default:
abort();
}
}
if (pattern_flag) {
// pegando os padroes do arquivo
wildcard = glob(patternFile);
for(std::vector<std::string>::iterator itPF = wildcard.begin(); itPF != wildcard.end(); ++itPF) {
getPatterns(*itPF);
}
}
for (int i = 1; i < argc; i++) {
if(!equalsToOptions(argv[i])) {
if((pattern_flag == 0) && (patternStr.compare("") == 0)) {
// nao achou a patternFlag e pattern continua vazio
patternStr = std::string(argv[i]);
} else {
/*
um pouco mais lento que o normal,
mas ja garante o caso de wildcards
*/
wildcard = glob(std::string(argv[i]));
for(int w = 0; w < wildcard.size(); w++) {
textFiles.push_back(wildcard[w]);
}
}
} else {
// pula o proximo ja que toda opt tem argumento, exceto a color
if (!(((tracoc.compare(argv[i])) == 0) || ((color.compare(argv[i])) == 0))) {
i++;
}
}
}
// se o usuario n tiver utilizado -h, --help
if(!help_flag) {
// percorrendo pelo vector de arquivos texto
for(std::vector<std::string>::iterator it = textFiles.begin() ; it != textFiles.end(); ++it) {
// pegando o texto dentro do arquivo
std::string file_string;
char tab2[1024];
strcpy(tab2, (*it).c_str());
std::ifstream myfile (tab2);
if (myfile.is_open()) {
FsmAho fsmAho;
Boyer_Moore bm_in;
while (!myfile.eof()) {
getline (myfile,file_string);
// caso seja -e, --edit
if(edit_flag) {
bool ret = false;
if(pattern_flag) {
for (std::set<std::string>::iterator itP = patterns_set.begin(); itP != patterns_set.end(); ++itP) {
if (color_flag) {
std::vector<int> sell_ret = sellers(file_string, *itP, emax);
if (sell_ret.size() > 0){
printColorResultAho(sell_ret, file_string);
break;
}
} else {
if(sellers_bool(file_string, *itP, emax)) {
printf("%s\n", file_string.c_str());
break;
}
}
}
} else {
if(color_flag){
std::vector<int> sell_ret = sellers(file_string, patternStr, emax);
if(sell_ret.size() > 0)
printColorResultAho(sell_ret, file_string);
} else {
if(sellers_bool(file_string, patternStr, emax)) {
printf("%s\n", file_string.c_str());
}
}
}
}
// caso seja -p, --patterns
else if(pattern_flag) {
if(fsmAho.g.size() == 0){
fsmAho = returnFsmAho(patterns_set);
}
if(color_flag) {
std::vector<int> aho_r = aho_c(file_string, fsmAho);
if(aho_r.size() > 0) {
printColorResultAho(aho_r, file_string);
}
} else {
if(aho(file_string, fsmAho))
printf("%s\n", file_string.c_str());
}
}
// caso nao seja --edit
else {
if(!bm_in.isInitialized()) {
bm_in.init(patternStr, patternStr.length());
}
if (color_flag) {
std::vector<int> bm_r = bm_in.search_c(file_string, patternStr);
if(bm_r.size() > 0)
printColorResult(bm_r, file_string, patternStr);
} else {
if(bm_in.search(file_string, patternStr)) {
printf("%s\n", file_string.c_str());
}
}
}
}
myfile.close();
} else {
printf("Unable to open text file\n");
}
}
} else { // opcao -h, --help foi escolhida
showHelp();
}
exit (0);
}
int main()
{
aho(65536);
return 0;
}
/*
This test check the integrity of the getMultiResults function in
AbstractACAutomaton class and its inherited classes.
*/
void testGetMultiResults(){
map<KmerAffect,int> results;
PointerACAutomaton<KmerAffect> aho(false);
const string errorOccurence = "KmerAffect doesn't have the good number of occurences.";
const string errorSize = "Map has too many Kmers.";
seqtype seq = "TTTTAATTAAGGGGCTACCCCCAATGTCCGTGGAGCTCTGGGGGGTTA";
affect_t affect[10];
seqtype seqs[10];
char c = 'a';
for(int i = 0; i < 10; ++i){
affect[i].c = c;
c++;
}
seqs[0] = "AGCTCT";
seqs[1] = "TTTT";
seqs[2] = "AATT";
seqs[3] = "CGTGG";
seqs[4] = "CAATGTC";
seqs[5] = "AGGG";
seqs[6] = "GGGG";
seqs[7] = "TTAA";
seqs[8] = "GCTAC";
seqs[9] = "CCCC";
for(int i = 0;i < 10; ++i){
aho.insert(seqs[i], KmerAffect(affect[i]));
}
aho.build_failure_functions();
results = aho.getMultiResults(seq);
/* Best situation: every sequences is found at least once in automaton. */
TAP_TEST(results.size() <= 11, TEST_AC_OCCURENCES, errorSize);
TAP_TEST_EQUAL(results.at(aho.get(seqs[0])), 1, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[1])), 1, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[2])), 1, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[3])), 1, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[4])), 1, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[5])), 1, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[6])), 4, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[7])), 2, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[8])), 1, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[9])), 2, TEST_AC_OCCURENCES, errorOccurence);
/* Situation: Only one K-mer is in the sequence, appearing once. */
seqtype seq2 = "AAAAAAAAAAAAAAAAAATTCAAAAAAAAA";
results = aho.getMultiResults(seq2);
TAP_TEST(results.size() <= 2, TEST_AC_OCCURENCES, errorSize);
TAP_TEST_EQUAL(results.at(aho.get(seqs[2])), 1, TEST_AC_OCCURENCES, errorOccurence);
/* Situation: Only one K-mer is the sequence, appearing many times. */
seqtype seq3 = "GCTACGCTACGCTACGCTACGCTA";
results = aho.getMultiResults(seq3);
TAP_TEST(results.size() <= 2, TEST_AC_OCCURENCES, errorSize);
TAP_TEST_EQUAL(results.at(aho.get(seqs[8])), 4, TEST_AC_OCCURENCES, errorOccurence);
/* Situation: No K-mer appear in the sequence. */
seqtype seq4 = "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA";
results = aho.getMultiResults(seq4);
TAP_TEST(results.size() <= 1, TEST_AC_OCCURENCES, errorSize);
/*
If there is K-mers in automaton doesn't match the sequence, the map must
return only unknown K-mers.
*/
pair<KmerAffect, int> singleResult = *(results.begin());
KmerAffect unknownKmerAffect = singleResult.first;
TAP_TEST_EQUAL(unknownKmerAffect, AFFECT_UNKNOWN, TEST_AC_OCCURENCES, "Unknown Kmer not found");
}
int main() {
int b=AA*2;
aho();
}
void B::bbho(){
aho();
}
void bho(){
aho();
}
int main() {
aho( "aho" );
}
