if (m->control_pressed) { return 0; }
ifstream fileHandle;
- openInputFile(blastfile, fileHandle);
+ m->openInputFile(blastfile, fileHandle);
string firstName, secondName, eScore, currentRow;
string repeatName = "";
if (!hclusterWanted) {
matrix = new SparseMatrix();
}else{
- overlapFile = getRootName(blastfile) + "overlap.dist";
- distFile = getRootName(blastfile) + "hclusterDists.dist";
+ overlapFile = m->getRootName(blastfile) + "overlap.dist";
+ distFile = m->getRootName(blastfile) + "hclusterDists.dist";
- openOutputFile(overlapFile, outOverlap);
- openOutputFile(distFile, outDist);
+ m->openOutputFile(overlapFile, outOverlap);
+ m->openOutputFile(distFile, outDist);
}
if (m->control_pressed) {
if (!fileHandle.eof()) {
//read in line from file
fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
- gobble(fileHandle);
+ m->gobble(fileHandle);
currentRow = firstName;
lengthThisSeq = numBases;
//read in line from file
fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
//cout << firstName << '\t' << secondName << '\t' << percentId << '\t' << numBases << '\t' << mismatch << '\t' << gap << '\t' << startQuery << '\t' << endQuery << '\t' << startRef << '\t' << endRef << '\t' << eScore << '\t' << score << endl;
- gobble(fileHandle);
+ m->gobble(fileHandle);
string temp = firstName + secondName; //to check if this file has repeat lines, ie. is this a blast instead of a blscreen file
int num = 1;
ifstream in;
- openInputFile(blastfile, in);
+ m->openInputFile(blastfile, in);
//ofstream outName;
- //openOutputFile((blastfile + ".tempOutNames"), outName);
+ //m->openOutputFile((blastfile + ".tempOutNames"), outName);
//read first line
in >> prevName;
for (int i = 0; i < 11; i++) { in >> hold; }
- gobble(in);
+ m->gobble(in);
//save name in nameMap
nameMap->push_back(prevName);
in >> name;
for (int i = 0; i < 11; i++) { in >> hold; }
- gobble(in);
+ m->gobble(in);
//is this a new name?
if (name != prevName) {
in.close();
//write out names file
- //string outNames = getRootName(blastfile) + "names";
+ //string outNames = m->getRootName(blastfile) + "names";
//ofstream out;
- //openOutputFile(outNames, out);
+ //m->openOutputFile(outNames, out);
//nameMap->print(out);
//out.close();