void FastaMap::readFastaFile(string inFileName) {
try {
ifstream in;
- openInputFile(inFileName, in);
+ m->openInputFile(inFileName, in);
string name, sequence, line;
sequence = "";
string temp;
while(!in.eof()){
+ if (m->control_pressed) { break; }
+
Sequence currSeq(in);
name = currSeq.getName();
// data[sequence].groupnumber++;
}
}
- gobble(in);
+ m->gobble(in);
}
in.close();
}
catch(exception& e) {
- errorOut(e, "FastaMap", "readFastaFile");
+ m->errorOut(e, "FastaMap", "readFastaFile");
exit(1);
}
}
void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prints data
ifstream oldNameFile;
- openInputFile(oldNameFileName, oldNameFile);
+ m->openInputFile(oldNameFileName, oldNameFile);
map<string,string> oldNameMap;
string name, list;
while(!oldNameFile.eof()){
+ if (m->control_pressed) { break; }
+
oldNameFile >> name >> list;
oldNameMap[name] = list;
- gobble(oldNameFile);
+ m->gobble(oldNameFile);
}
oldNameFile.close();
ifstream inFASTA;
- openInputFile(inFastaFile, inFASTA);
+ m->openInputFile(inFastaFile, inFASTA);
string sequence;
while(!inFASTA.eof()){
+ if (m->control_pressed) { break; }
+
Sequence currSeq(inFASTA);
name = currSeq.getName();
// data[sequence].groupnumber++;
}
}
- gobble(inFASTA);
+ m->gobble(inFASTA);
}
void FastaMap::printNamesFile(string outFileName){ //prints data
try {
ofstream outFile;
- openOutputFile(outFileName, outFile);
+ m->openOutputFile(outFileName, outFile);
// two column file created with groupname and them list of identical sequence names
for (map<string,group>::iterator it = data.begin(); it != data.end(); it++) {
+ if (m->control_pressed) { break; }
outFile << it->second.groupname << '\t' << it->second.names << endl;
}
outFile.close();
}
catch(exception& e) {
- errorOut(e, "FastaMap", "printNamesFile");
+ m->errorOut(e, "FastaMap", "printNamesFile");
exit(1);
}
}
void FastaMap::printCondensedFasta(string outFileName){ //prints data
try {
ofstream out;
- openOutputFile(outFileName, out);
+ m->openOutputFile(outFileName, out);
//creates a fasta file
for (map<string,group>::iterator it = data.begin(); it != data.end(); it++) {
+ if (m->control_pressed) { break; }
out << ">" << it->second.groupname << endl;
out << it->first << endl;
}
out.close();
}
catch(exception& e) {
- errorOut(e, "FastaMap", "printCondensedFasta");
+ m->errorOut(e, "FastaMap", "printCondensedFasta");
exit(1);
}
}