// Load gene list from file.
int loadgene(vector<Case>& tlst, vector<Case>& blst, const string& n, const string& b)
{
// Genes in the cluster: label = 1.
ifstream hGen(n.data());
if(!hGen)
{
cerr << "Can't open " << n << endl;
return 1;
}
while(hGen.good())
{
string strLn;
getline(hGen, strLn);
if(strLn == "")
continue;
istringstream strmLn(strLn);
string gene;
strmLn >> gene;
str2upper(gene);
Case c;
c.name = gene;
c.label = 1;
tlst.push_back(c);
}
hGen.close();
// Genes in the background: label = 0.
ifstream hBkg(b.data());
if(!hBkg)
{
cerr << "Can't open " << b << endl;
return 1;
}
while(hBkg.good())
{
string strLn;
getline(hBkg, strLn);
if(strLn == "")
continue;
istringstream strmLn(strLn);
string gene;
strmLn >> gene;
str2upper(gene);
Case c;
c.name = gene;
c.label = 0;
blst.push_back(c);
}
hBkg.close();
return 0;
}
// Load one motif's binding.
int loadone(GBMap& onebind, const string& motif, const set<string>& genset, const string& folder)
{
string fBind = folder + "/" + motif + ".func";
ifstream hBind(fBind.data());
if(!hBind)
{
cerr << "Can't open " << fBind << endl;
return 1;
}
while(hBind.good())
{
string strLn;
getline(hBind, strLn);
if(strLn == "")
continue;
istringstream gStrm(strLn);
string gene;
int nb;
gStrm >> gene >> nb;
str2upper(gene);
if(genset.find(gene) == genset.end())
continue;
VGB vgb;
for(int j = 0; j < nb; j++)
{
string site;
gStrm >> site;
vgb.e.push_back(extrbnd(site));
}
onebind.e[gene] = vgb;
}
return 0;
}
void enter_one_name(Game* game, short color) {
char name[MAX_NAME];
char line[MAX_LINE];
/* While the user is not satisfied with the name */
do {
/* Label for asking the black player */
ask_name:
/* Asking for the name of the black player */
printf("\nEnter the name of the %s player (maximumof %d characters - letters and digits only): ", (color==BLACK?"BLACK":"WHITE"), MAX_NAME-1);
/* Retrieving the name in the name string */
fgets(name, MAX_NAME, stdin);
/* Ungetting the last character readed if the string entered is too long */
ungetc(name[strlen(name)-1], stdin);
/* Emptying the buffer (so that extra characters won't be used for the next name */
empty_buffer();
/* If the last character of the name is a new line (that fgets can put into a string), replacing it with a string terminating character */
if(name[strlen(name)-1] == NL)
name[strlen(name)-1] = '\0';
/* If the name conatins other characters than letters and numbers, asking again */
if(!contains_only_letters(name))
goto ask_name;
/* While the answer is not Yes of No, asking if the name suits the player */
do {
printf("\n%s, is that the name you want? (Y/N) : ", name);
fgets(line, MAX_LINE, stdin);
str2upper(line);
}
while(line[ZERO] != 'Y' && line[ZERO] != 'N');
}
while(line[ZERO] == 'N');
/* If the name entered for the white player is the same as the one for te black player, asking again */
if(color == WHITE && game->p1.player_type == HUMAN && strcmp(name, game->p1.player_name) == 0) {
printf("\nThis name is already taken");
goto ask_name;
}
/* Copying the string into the reserved space for it and updating the type of the player (here HUMAN) */
if(color == BLACK) {
strcpy(game->p1.player_name, name);
game->p1.player_type = HUMAN;
}
else {
strcpy(game->p2.player_name, name);
game->p2.player_type = HUMAN;
}
printf("\n");
}
/* ------------------------------------------------------------- */
void jx_sqlUpperCaseNames(PJXSQL pSQL)
{
int i;
for (i = 0; i < pSQL->nresultcols; i++) {
PJXCOL pCol = &pSQL->cols[i];
str2upper (pCol->colname , pCol->colname);
}
}
// convert to uppercase if s is a DOS-name
void name2upper (char * s)
{
int i, l;
l = strlen (s);
for (i=0; i < l; i++)
{
if (s[i] == '.')
break;
}
if (i > 8 || l - i > 4)
return;
str2upper(s);
}
int searchpattern (char *pattern) {
char *toprocess;
int found=0;
int size;
char pline[MAX_LINE_SIZE];
char unhex[MAX_LINE_SIZE];
toprocess=pattern;
size=strlen(toprocess);
if (opt_ignorecase) {
toprocess=str2upper(toprocess,pline);
}
if (opt_unhex) {
size=hexstr2char(toprocess,unhex,MAX_LINE_SIZE);
toprocess=unhex;
}
found=bloom_check(&bloom, toprocess, size);
return (found);
}
/*
* Given an interface name (e.g., eth0), return the MAC address in human
* readable format (e.g., 00:11:52:12:D9:A0). Return NULL for no match.
*/
char *iface_mac2str(char *ifname) {
int buflen = 20;
char *buf = NULL;
struct nl_handle *handle = NULL;
struct nl_cache *cache = NULL;
struct rtnl_link *link = NULL;
struct nl_addr *addr = NULL;
if (ifname == NULL) {
return NULL;
}
if ((cache = _iface_get_link_cache(&handle)) == NULL) {
return NULL;
}
if ((link = rtnl_link_get_by_name(cache, ifname)) == NULL) {
goto mac2str_error2;
}
if ((addr = rtnl_link_get_addr(link)) == NULL) {
goto mac2str_error3;
}
if ((buf = calloc(sizeof(char *), buflen)) == NULL) {
goto mac2str_error4;
}
if ((buf = nl_addr2str(addr, buf, buflen)) != NULL) {
buf = str2upper(buf);
}
mac2str_error4:
nl_addr_destroy(addr);
mac2str_error3:
rtnl_link_put(link);
mac2str_error2:
nl_close(handle);
nl_handle_destroy(handle);
return buf;
}
int main (int argc, char *argv[]) {
int count;
unsigned long maxitems=0;
int c;
int index;
FILE *fp;
unsigned long items;
char line[MAX_LINE_SIZE];
char pline[MAX_LINE_SIZE];
char unhex[MAX_LINE_SIZE];
char *toprocess;
int size;
int found=0;
/* safe defaults */
opt_errorrate=0.01;
opt_bloomfile=NULL;
/* load config */
loadconfig();
while ((c = getopt (argc, argv, "huicp:svde:b:f:")) != -1)
switch (c)
{
case 'h':
displayhelp();
exit(0);
break;
case 'u':
opt_unhex = 1;
break;
case 'i':
opt_ignorecase = 1;
break;
case 'c':
opt_init = 1;
break;
case 'p':
opt_progressitems = atoi(optarg);
break;
case 'e':
opt_errorrate = atof(optarg);
break;
case 'b':
opt_bloomfile = optarg;
break;
case 'f':
opt_readfromfile = optarg;
break;
case 's':
opt_search = 1;
break;
case 'v':
opt_verbose++;
break;
case 'd':
opt_debug++;
break;
case '?':
if (optopt == 'b')
fprintf (stderr, "Option -%c requires an argument.\n", optopt);
else if (isprint (optopt))
fprintf (stderr, "Unknown option `-%c'.\n", optopt);
else
fprintf (stderr,
"Unknown option character `\\x%x'.\n",
optopt);
return 1;
default:
abort ();
}
if (opt_debug) {
printf ("opt_init = %d, opt_search = %d, opt_bloomfile = %s\n",
opt_init, opt_search, opt_bloomfile);
for (count = 1; count < argc; count++) {
printf("argv[%d] = %s\n", count, argv[count]);
}
for (index = optind; index < argc; index++)
printf ("Non-option argument %s\n", argv[index]);
}
if (opt_init) {
for (index = optind; index < argc; index++) {
if (opt_verbose) fprintf(stderr,"[i] Counting lines for %s\n", argv[index]);
fp=fopen(argv[index],"r");
if (fp==NULL) {
fprintf(stderr,"Error opening %s\n",argv[index]);
break;
}
items=getlinecount(fp);
if (opt_verbose) fprintf(stderr,"[i] %s have %lu lines/items\n",argv[index],items);
maxitems=maxitems+items;
fclose(fp);
}
if (opt_verbose) fprintf(stderr,"[i] Maximum number of items: %lu\n",maxitems);
bloom_init(&bloom, maxitems, opt_errorrate);
items=0;
for (index = optind; index < argc; index++) {
if (opt_verbose) fprintf(stderr,"[i] Processing %s\n", argv[index]);
fp=fopen(argv[index],"r");
if (fp==NULL) {
fprintf(stderr,"Error opening %s\n",argv[index]);
break;
}
/* read line by line */
while (fgets (line, sizeof(line), fp)) {
toprocess=line;
size=strlen(line);
if (line[size-1]=='\n') line[--size]='\0';
if (line[size-1]=='\r') line[--size]='\0';
if (opt_debug) fprintf(stderr,"Line (%d): %s \n",size,line);
if (opt_verbose && (items++ % opt_progressitems==0)) fprintf(stderr,"\r[i] Line %lu of %lu", items, maxitems);
if (opt_ignorecase) {
toprocess=str2upper(toprocess,pline);
}
if (opt_unhex) {
size=hexstr2char(toprocess,unhex,MAX_LINE_SIZE);
toprocess=unhex;
}
bloom_add(&bloom, toprocess, size);
}
if (opt_verbose) fprintf(stderr,"\n[i] Done for %s!\n",argv[index]);
fclose(fp);
}
if (opt_bloomfile==NULL) {
fprintf(stderr,"No bloom file specified for init. Not saving.\n");
} else {
if (opt_verbose) fprintf(stderr,"[i] Saving to %s\n",opt_bloomfile);
bloom_save(&bloom,opt_bloomfile);
/* if (opt_verbose) bloom_print(&bloom); */
}
}
if (opt_search || (!opt_init)) {
if (opt_bloomfile==NULL) {
fprintf(stderr,"No bloom file specified.\n");
} else {
if (opt_verbose) fprintf(stderr,"[i] Opening bloom file: %s\n", opt_bloomfile);
if (bloom_load(&bloom, opt_bloomfile)) {
fprintf(stderr,"[i] Error loading bloom file: %s\n", opt_bloomfile);
return (1);
}
}
if (opt_verbose) fprintf(stderr,"[i] Searching patterns\n");
for (index = optind; index < argc; index++) {
toprocess=argv[index];
if (opt_verbose) fprintf(stderr,"[i] Processing %s\n", toprocess);
if (searchpattern(toprocess)) {
fprintf(stdout,"%s found\n", argv[index]);
} else {
fprintf(stdout,"%s not found\n", argv[index]);
}
}
if (opt_readfromfile!=NULL) {
if (opt_verbose) fprintf(stderr,"[v] Reading from file %s\n",opt_readfromfile);
if (strcmp(opt_readfromfile,"-")==0) {
fprintf (stderr,"[i] Reading from standard input. Specify pattern separated by new line.\n");
fp=stdin;
} else {
fp=fopen(opt_readfromfile,"r");
}
if (fp==NULL) {
fprintf(stderr,"[!] Error opening file: %s\n",opt_readfromfile);
exit(1);
}
while (fgets (line, sizeof(line), fp)) {
toprocess=line;
size=strlen(line);
if (line[size-1]=='\n') line[--size]='\0';
if (line[size-1]=='\r') line[--size]='\0';
if (opt_debug) fprintf(stderr,"[d] Line in pattern (%d): %s \n",size,line);
if (opt_verbose) fprintf(stderr,"[v] Processing from file %s\n", toprocess);
if (searchpattern(toprocess)) {
fprintf(stdout,"%s found\n", toprocess);
} else {
fprintf(stdout,"%s not found\n", toprocess);
}
}
if (fp!=stdin) fclose (fp);
}
}
}
