//***************************************************************************************************************
-void DeCalculator::setMask(string m) {
+void DeCalculator::setMask(string ms) {
try {
- seqMask = m;
+ seqMask = ms;
int count = 0;
maskMap.clear();
}
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "setMask");
+ m->errorOut(e, "DeCalculator", "setMask");
exit(1);
}
}
seq->setUnaligned(tempQuery);
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "runMask");
+ m->errorOut(e, "DeCalculator", "runMask");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "trimSeqs");
+ m->errorOut(e, "DeCalculator", "trimSeqs");
exit(1);
}
}
if (size == 0) { if (cutoff > 1200) { size = 300; }
else{ size = (cutoff / 4); } }
else if (size > (cutoff / 4)) {
- mothurOut("You have selected too large a window size for sequence " + query->getName() + ". I will choose an appropriate window size."); mothurOutEndLine();
+ m->mothurOut("You have selected too large a window size for sequence " + query->getName() + ". I will choose an appropriate window size."); m->mothurOutEndLine();
size = (cutoff / 4);
}
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "findWindows");
+ m->errorOut(e, "DeCalculator", "findWindows");
exit(1);
}
}
return temp;
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "calcObserved");
+ m->errorOut(e, "DeCalculator", "calcObserved");
exit(1);
}
}
return dist;
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "calcDist");
+ m->errorOut(e, "DeCalculator", "calcDist");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "calcExpected");
+ m->errorOut(e, "DeCalculator", "calcExpected");
exit(1);
}
}
return de;
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "calcDE");
+ m->errorOut(e, "DeCalculator", "calcDE");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "calcFreq");
+ m->errorOut(e, "DeCalculator", "calcFreq");
exit(1);
}
}
return averages;
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "findQav");
+ m->errorOut(e, "DeCalculator", "findQav");
exit(1);
}
}
//for each sequence
for(int i = start; i < end; i++){
- mothurOut("Processing sequence " + toString(i)); mothurOutEndLine();
+ m->mothurOut("Processing sequence " + toString(i)); m->mothurOutEndLine();
Sequence* query = new Sequence(seqs[i]->getName(), seqs[i]->getAligned());
//compare to every other sequence in template
Sequence* subject = new Sequence(seqs[j]->getName(), seqs[j]->getAligned());
+ if (m->control_pressed) { delete query; delete subject; return quan; }
+
map<int, int> trim;
map<int, int>::iterator it;
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "getQuantiles");
+ m->errorOut(e, "DeCalculator", "getQuantiles");
exit(1);
}
}
//while you still have guys to eliminate
while (contributions.size() > 0) {
- mothurOut("Removing scores contributed by sequence " + toString(largestContrib) + " in your template file."); mothurOutEndLine();
+ m->mothurOut("Removing scores contributed by sequence " + toString(largestContrib) + " in your template file."); m->mothurOutEndLine();
//remove from quantiles all scores that were made using this largestContrib
for (int i = 0; i < quantiles.size(); i++) {
for(int i = 0; i < marked.size(); i++) {
if (marked[i] > high) {
- mothurOut("Removing scores contributed by sequence " + toString(marked[i]) + " in your template file."); mothurOutEndLine();
+ m->mothurOut("Removing scores contributed by sequence " + toString(marked[i]) + " in your template file."); m->mothurOutEndLine();
for (int i = 0; i < quantiles.size(); i++) {
removeContrib(marked[i], quantiles[i]);
}
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "removeObviousOutliers");
+ m->errorOut(e, "DeCalculator", "removeObviousOutliers");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "sortContrib");
+ m->errorOut(e, "DeCalculator", "sortContrib");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "findLargestContribs");
+ m->errorOut(e, "DeCalculator", "findLargestContribs");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "removeContrib");
+ m->errorOut(e, "DeCalculator", "removeContrib");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "findAverage");
+ m->errorOut(e, "DeCalculator", "findAverage");
exit(1);
}
}
return coef;
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "getCoef");
+ m->errorOut(e, "DeCalculator", "getCoef");
exit(1);
}
}
return seqsMatches;
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "findClosest");
+ m->errorOut(e, "DeCalculator", "findClosest");
exit(1);
}
}
return seqsMatch;
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "findClosest");
+ m->errorOut(e, "DeCalculator", "findClosest");
exit(1);
}
}
if (pos < rearPos) { rearPos = pos; }
//check to make sure that is not whole seq
- if ((rearPos - frontPos - 1) <= 0) { mothurOut("Error, when I trim your sequences, the entire sequence is trimmed."); mothurOutEndLine(); exit(1); }
+ if ((rearPos - frontPos - 1) <= 0) { m->mothurOut("Error, when I trim your sequences, the entire sequence is trimmed."); m->mothurOutEndLine(); exit(1); }
//cout << query->getName() << " front = " << frontPos << " rear = " << rearPos << endl;
//trim query
string newAligned = query->getAligned();
return trimmedPos;
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "trimSequences");
+ m->errorOut(e, "DeCalculator", "trimSequences");
exit(1);
}