iMatrix *readmatrix(std::string filename,const std::string delim=",;: \t"){
///@param filename A filename to read.@param delim A string of delimiters.
std::vector<std::string> tokens;
const int SIZE=500000;
char buffer[SIZE];
std::ifstream pFile (filename.c_str(),std::ios::in);
if(!pFile){
std::cout <<"Problems opening file" <<filename<<std::endl;
exit(0);
}
std::string tmp_string;
int doFirstRow =1;
int itemsInFirstRow=0;
int numRows =0;
while(!pFile.eof()){
pFile.getline(buffer,SIZE);
tmp_string = std::string(buffer);
if(doFirstRow){
//if file has a emptystart line
itemsInFirstRow = get_lexemes(tmp_string,tokens,delim);
if (itemsInFirstRow==0)
continue;
// printf("items in first rwo:%d\n",itemsInFirstRow);
doFirstRow=0;
numRows++;
}
else{
int nItems = get_lexemes(tmp_string,tokens,delim);
//if line is empty
if(nItems==0)
continue;
numRows++;
if(nItems!=itemsInFirstRow){
printf("row length mismatch at line:%d numitems is:%d shouldn't be:%d\t will exit\n",numRows,itemsInFirstRow,nItems);
exit(0);
}
}
}
iMatrix *data_ = allocIntMatrix(numRows,itemsInFirstRow);
//now we have a token array of string coerce the types now
typecast_stringarray_to_int_matrix(tokens,data_);
//copy(tokens.begin(), tokens.end(), ostream_iterator<string>(cout, ", "));
printf("\t-> Dimension of genotype datafile is (%d,%d)\n",data_->x,data_->y);
return data_;
}
iMatrix *readmatrix_filty_memory(std::string filename,const std::string delim=",;: \t"){
///@param filename A filename to read.@param delim A string of delimiters.
std::vector<std::string> tokens;
const int SIZE = MAX_ELEMS_PER_LINE;//defined in conf.h
char buffer[SIZE];
std::ifstream pFile (filename.c_str(),std::ios::in);
if(!pFile){
fileError(filename);
exit(0);
}
std::string tmp_string;
int doFirstRow =1;
int itemsInFirstRow=0;
int numRows =0;
while(!pFile.eof()){
pFile.getline(buffer,SIZE);
tmp_string = std::string(buffer);
if(doFirstRow){
//if file has a emptystart line
itemsInFirstRow = get_lexemes(tmp_string,tokens,delim);
if (itemsInFirstRow==0)
continue;
// printf("items in first rwo:%d\n",itemsInFirstRow);
doFirstRow=0;
numRows++;
}
else{
int nItems = get_lexemes(tmp_string,tokens,delim);
//if line is empty
if(nItems==0)
continue;
numRows++;
if(nItems!=itemsInFirstRow){
printf("row length mismatch at line:%d numitems is:%d shouldn't be:%d\t will exit\n",numRows,itemsInFirstRow,nItems);
exit(0);
}
}
}
flush_print("\r\t-> File has been read in now, will now typecheck... ");
iMatrix *data_ = allocIntMatrix(numRows,itemsInFirstRow);
//now we have a token array of string coerce the types now
typecast_stringarray_to_int_matrix(tokens,data_);
//copy(tokens.begin(), tokens.end(), ostream_iterator<string>(cout, ", "));
return data_;
}
