int main(int argc, char *argv[])
{
int nameLength = 3;
char name[3] = {'m', 'r', 'c'};
printf("String: %s\n", name);
printf("As ints: %d %d %d\n", name[0], name[1], name[2]);
printf("As num: %ld\n", charToNum(name, nameLength, 0) +
charToNum(name, nameLength, 1) +
charToNum(name, nameLength, 2));
return 0;
}
void Modules::subsets(string soFar, string rest, char out, ofstream &outFile) {
if (rest == "") { // convert char symbols from the sub-strings of soFar to pitches, then print out
for (int i = 0; i < static_cast<int>(soFar.length()); i++) {
cout << TABLE[charToNum(soFar[i])];
if (out == 'y')
outFile << TABLE[charToNum(soFar[i])];
}
cout << endl;
if (out == 'y')
outFile << endl;
} else {
// add to subset, remove from rest, recursion
subsets(soFar + rest[0], rest.substr(1), out, outFile);
// don't add to subset, remove from rest, recursion
subsets(soFar, rest.substr(1), out, outFile);
}
}
void Modules::permute(string soFar, string rest, int arrSize, char out, ofstream &outFile) {
if (rest == "") { // convert char symbols from the sub-strings of soFar to pitches, then print out
for (int i = 0; i < arrSize; i++) {
cout << TABLE[charToNum(soFar[i])];
if (out == 'y')
outFile << TABLE[charToNum(soFar[i])];
}
cout << endl;
if (out == 'y')
outFile << endl;
} else {
for (int i = 0; i < static_cast<int>(rest.length()); i++) {
string next = soFar + rest[i];
string remaining = rest.substr(0, i) + rest.substr(i + 1);
permute(next, remaining, arrSize, out, outFile);
}
}
}
//This method offers no error checking, so use strIsNum to check if string is a valid number before
//using this function
int strToNum(char * str){
int num = 0;
int i = 0;
while((str[i] != '\0')&&(str[i] != '\n')){
num += charToNum(str[i]) * pow(10, i);
i++;
}
return num;
}
int romanToInt(string s) {
int ans = 0, last = INT_MAX;
for (char c : s) {
int n = charToNum(c);
if (n > last) ans -= 2 * last;
ans += n;
last = n;
}
return ans;
}
inline int getNum(char *str, int base)
{
int num = 0, exp = 1, len = strlen(str);
for (int i = len - 1; i >= 0; i--)
{
num += charToNum(str[i])*exp;
exp *= base;
}
return num;
}
/**
* Returns non-zero if the account number could be valid according to the Luhn
* algorithm (used for credit card numbers).
*/
int luhn(char *number) {
int length = strlen(number);
int lastIndex = length - 1;
int sum = 0;
for (int i = 0; i < length; i++); {
int index = length - 1 - i;
int num = charToNum(number[index]);
if (i % 2 == 1) {
sum += sumOfDigits(num * 2);
} else {
sum += num;
}
}
int checksum = (sum * 9) % 10;
return checksum = 0;
}
void cmdIndexed(u08 cmdInput)
{
switch (cpState)
{
case INDEX:
//
// Validate index parameter (0-9,a-z)
//
if (-1 == (input[INDEX] = charToNum(cmdInput)))
{
cmdInit();
return;
}
cpState = PARAM1;
break;
case PARAM1:
input[PARAM1] = cmdInput;
cpState = PARAM2;
break;
case PARAM2:
if (input[INDEX] > 1)
{
uart_send_buffered(input[COMMAND]);
uart_send_buffered(numToChar(input[INDEX] - 2));
uart_send_buffered(input[PARAM1]);
uart_send_buffered(cmdInput);
}
else
{
switch (input[COMMAND])
{
case CMD_PIXEL_ON:
case CMD_PIXEL_OFF:
dm_pixel(input[INDEX],
(input[COMMAND] == CMD_PIXEL_ON ? 1 : 0),
input[PARAM1] - '0',
cmdInput - '0');
break;
}
}
cmdInit();
break;
}
}
void cmdSetBits(u08 cmdInput)
{
char length;
if (LENGTH == cpState)
{
//
// Validate length parameter (0-9,a-z)
//
if (-1 == (length = charToNum(cmdInput)))
{
cmdInit();
return;
}
//
// if length > 2 then subtract 2 and pass this command on to the
// next controller in the chain
//
input[REMAINING] = length * 5;
length -= 2;
if (length > 0)
{
uart_send_buffered(input[COMMAND]);
uart_send_buffered(numToChar(length));
}
input[INDEX] = 0;
cpState = PARAM1;
return;
}
if (input[INDEX] < 10)
{
dm_progColumn(input[INDEX] / 5, input[INDEX] % 5, cmdInput);
}
else
{
uart_send_buffered(cmdInput);
}
input[INDEX]++;
input[REMAINING]--;
if (0 == input[REMAINING])
{
cmdInit();
}
}
void getCmdLineParamsToConfig(int argc, char **argv, ConfigInfo *configinfo)
{
char c;
while ((c = getopt (argc, argv, "i:e:m:o:p:l:t:ch")) != -1)
{
switch (c)
{
case 'i':
configinfo->cover_file = optarg;
break;
case 'e':
configinfo->stego_file = optarg;
break;
case 'm':
configinfo->message_file = optarg;
break;
case 'o':
configinfo->output_file = optarg;
break;
case 'p':
configinfo->password = optarg;
break;
case 'l':
if( 0 == strcmp(optarg, "1") ) { configinfo->lsb_usage = LSB_USAGE_1; }
else if( 0 == strcmp(optarg, "2") ) { configinfo->lsb_usage = LSB_USAGE_2; }
else { configinfo->lsb_usage = LSB_USAGE_1; }
break;
case 't':
configinfo->treshold = DEFAULT_TRESHOLD;
if( 2 == strlen(optarg) )
{
if( 2 == charToNum(optarg[0]) )
{
configinfo->treshold = 20;
}
else if ( 1 == charToNum(optarg[0]) )
{
if( (0<=charToNum(optarg[1])) && (10>charToNum(optarg[1])) )
{
configinfo->treshold += charToNum(optarg[1]);
}
}
}
else if (1 == strlen(optarg))
{
if( (0<=charToNum(optarg[0])) && (10>charToNum(optarg[0])) )
{
configinfo->treshold = charToNum(optarg[0]);
}
}
break;
case 'c':
configinfo->only_calc = TRUE;
break;
case 'h':
printHelp();
exit(0);
break;
case '?':
printHelp();
exit(1);
break;
default:
printHelp();
exit(1);
break;
}
}
if( (configinfo->cover_file != NULL) && (configinfo->stego_file != NULL) && (configinfo->message_file == NULL) && (configinfo->output_file == NULL) )
{
if(configinfo->only_calc == TRUE) return;
printHelp();
exit(1);
}
if( (configinfo->stego_file != NULL) && (configinfo->cover_file != NULL) && (configinfo->message_file == NULL) )
{
if(configinfo->only_calc == TRUE) return;
printHelp();
exit(1);
}
if( (configinfo->cover_file == NULL) && (configinfo->stego_file == NULL) )
{
printHelp();
exit(1);
}
}
aMap readhap( char *fname,int minDist,double minMaf,int startPos,int stopPos,int skiptrans){
// fprintf(stderr,"[%s] fname:%s\tminDist:%d LENS:%d\n",__FUNCTION__,fname,minDist,LENS);
gzFile gz=getgz(fname,"rb");
char *buf = new char[LENS];
int viggo=3;
aMap myMap;//<- this will be our return object
gzgets(gz,buf,LENS);
while(gzgets(gz,buf,LENS)){//loop over sites
hapSite hs;
int p = atoi(strtok(buf,"\t\n "));// pos
if(p<startPos)
continue;
if(p>stopPos)
continue;
hs.allele1 = charToNum(strtok(NULL,"\t\n ")[0]);
hs.freq = atof(strtok(NULL,"\t\n "));
if(hs.freq<minMaf||(1-hs.freq)<minMaf)
continue;
char strand= strtok(NULL,"\t\n ")[0];
hs.allele2 = charToNum(strtok(NULL,"\t\n ")[0]);
if(hs.allele1==-1||hs.allele2==-1)
continue;
if(strand=='-'){
hs.allele1 = flip(hs.allele1);
hs.allele2 = flip(hs.allele2);
}
if(hs.allele1==hs.allele2)
continue;
if(skiptrans){
if(hs.allele1 == 0 && hs.allele2 == 2)
continue;
if(hs.allele1 == 2 && hs.allele2 == 0)
continue;
if(hs.allele1 == 1 && hs.allele2 == 3)
continue;
if(hs.allele1 == 3 && hs.allele2 == 1)
continue;
}
if(myMap.count(p)>0){
if(viggo>0){
// fprintf(stderr,"[%s] Duplicate positions found in file: %s, pos:%d\n",__FUNCTION__,fname,p);
//fprintf(stderr,"[%s] Will only use first entry\n",__FUNCTION__);
//fprintf(stderr,"[%s] This message is only printed 3 times\n",__FUNCTION__);
viggo--;
}
}else{
myMap[p]=hs;
}
}
// fprintf(stderr,"[%s] We have read: %zu sites from hapfile (after filtering for start/stop pos):%s\n",__FUNCTION__,myMap.size(),fname);
//fprintf(stderr,"[%s] will remove snp sites to close:\n",__FUNCTION__);
assert(myMap.size()>0);
int *vec = new int[myMap.size() -1];
aMap::iterator it = myMap.begin();
for(int i=0;i<myMap.size()-1;i++){
aMap::iterator it2 = it;
it2++;
vec[i]=it2->first - it->first;
it=it2;
}
it = myMap.begin();
aMap newMap;
for(int i=0;i<myMap.size()-1;i++){
if(std::abs(vec[i])>=minDist){
newMap[it->first] = it->second;
// fprintf(stdout,"test\t%d\n",it->first);
}
it++;
}
newMap[it->first] = it->second;
//.. exit(0);
delete [] vec;
fprintf(stderr,"[%s] We now have: %lu snpSites after filtering based on hapMapfile\n",__FUNCTION__,newMap.size());
#if 0
for(aMap::iterator it=newMap.begin();it!=newMap.end();++it)
print(stdout,it->first,it->second);
exit(0);
#endif
delete [] buf;
gzclose(gz);
return newMap;
}
