//***************************************************************************************************************
-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);
}
*/
//this follows wigeon, but we may want to consider that it chops off the end values if the sequence cannot be evenly divided into steps
- for (int m = front; m < (back - size) ; m+=increment) { win.push_back(m); }
+ for (int i = front; i < (back - size) ; i+=increment) { win.push_back(i); }
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "findWindows");
+ m->errorOut(e, "DeCalculator", "findWindows");
exit(1);
}
}
vector<float> temp;
//int gaps = 0;
- for (int m = 0; m < window.size(); m++) {
+ for (int i = 0; i < window.size(); i++) {
- string seqFrag = query->getAligned().substr(window[m], size);
- string seqFragsub = subject->getAligned().substr(window[m], size);
+ string seqFrag = query->getAligned().substr(window[i], size);
+ string seqFragsub = subject->getAligned().substr(window[i], size);
int diff = 0;
for (int b = 0; b < seqFrag.length(); b++) {
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);
}
}
//for each window
vector<float> queryExpected;
- for (int m = 0; m < qav.size(); m++) {
+ for (int j = 0; j < qav.size(); j++) {
- float expected = qav[m] * coef;
+ float expected = qav[j] * coef;
queryExpected.push_back(expected);
}
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "calcExpected");
+ m->errorOut(e, "DeCalculator", "calcExpected");
exit(1);
}
}
try {
//for each window
- float sum = 0.0; //sum = sum from 1 to m of (oi-ei)^2
+ float sum = 0.0; //sum = sum from 1 to i of (oi-ei)^2
int numZeros = 0;
- for (int m = 0; m < obs.size(); m++) {
+ for (int j = 0; j < obs.size(); j++) {
- //if (obs[m] != 0.0) {
- sum += ((obs[m] - exp[m]) * (obs[m] - exp[m]));
+ //if (obs[j] != 0.0) {
+ sum += ((obs[j] - exp[j]) * (obs[j] - exp[j]));
//}else { numZeros++; }
}
return de;
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "calcDE");
+ m->errorOut(e, "DeCalculator", "calcDE");
exit(1);
}
}
try {
vector<float> prob;
- string freqfile = getRootName(filename) + "freq";
+ string freqfile = m->getRootName(filename) + "freq";
ofstream outFreq;
- openOutputFile(freqfile, outFreq);
+ m->openOutputFile(freqfile, outFreq);
+
+ outFreq << "#" << m->getVersion() << endl;
string length = toString(seqs.size()); //if there are 5000 seqs in the template then set precision to 3
int precision = length.length() - 1;
//find base with highest frequency
int highest = 0;
- for (int m = 0; m < freq.size(); m++) { if (freq[m] > highest) { highest = freq[m]; } }
+ for (int j = 0; j < freq.size(); j++) { if (freq[j] > highest) { highest = freq[j]; } }
float highFreq = highest / (float) (seqs.size());
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "calcFreq");
+ m->errorOut(e, "DeCalculator", "calcFreq");
exit(1);
}
}
vector<float> averages;
//for each window find average
- for (int m = 0; m < window.size(); m++) {
+ for (int i = 0; i < window.size(); i++) {
float average = 0.0;
//while you are in the window for this sequence
int count = 0;
- for (int j = window[m]; j < (window[m]+size); j++) {
+ for (int j = window[i]; j < (window[i]+size); j++) {
average += probabilityProfile[j];
count++;
}
return averages;
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "findQav");
+ m->errorOut(e, "DeCalculator", "findQav");
exit(1);
}
}
//***************************************************************************************************************
//seqs have already been masked
-vector< vector<quanMember> > DeCalculator::getQuantiles(vector<Sequence*> seqs, vector<int> windowSizesTemplate, int window, vector<float> probProfile, int increment, int start, int end) {
+vector< vector<float> > DeCalculator::getQuantiles(vector<Sequence*> seqs, vector<int> windowSizesTemplate, int window, vector<float> probProfile, int increment, int start, int end) {
try {
- vector< vector<quanMember> > quan;
+ vector< vector<float> > quan;
//percentage of mismatched pairs 1 to 100
quan.resize(100);
-//ofstream o;
-//string out = "getQuantiles.out";
-//openOutputFile(out, o);
-
+
//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;
float de = calcDE(obsi, exp);
float dist = calcDist(query, subject, front, back);
- //o << i << '\t' << j << '\t' << dist << '\t' << de << endl;
+ //cout << i << '\t' << j << '\t' << dist << '\t' << de << endl;
dist = ceil(dist);
- quanMember newScore(de, i, j);
-
- quan[dist].push_back(newScore);
+ //quanMember newScore(de, i, j);
+ quan[dist].push_back(de);
+
delete subject;
}
delete query;
}
+
return quan;
}
catch(exception& e) {
- errorOut(e, "DeCalculator", "getQuantiles");
+ m->errorOut(e, "DeCalculator", "getQuantiles");
exit(1);
}
}
}
//***************************************************************************************************************
//this was going to be used by pintail to increase the sensitivity of the chimera detection, but it wasn't quite right. may want to revisit in the future...
-void DeCalculator::removeObviousOutliers(vector< vector<quanMember> >& quantiles, int num) {
+void DeCalculator::removeObviousOutliers(vector< vector<float> >& quantiles, int num) {
try {
for (int i = 0; i < quantiles.size(); i++) {
-
- //find mean of this quantile score
- sort(quantiles[i].begin(), quantiles[i].end(), compareQuanMembers);
- float high = quantiles[i][int(quantiles[i].size() * 0.99)].score;
- float low = quantiles[i][int(quantiles[i].size() * 0.01)].score;
-
- vector<quanMember> temp;
+ //find mean of this quantile score
+ sort(quantiles[i].begin(), quantiles[i].end());
- //look at each value in quantiles to see if it is an outlier
- for (int j = 0; j < quantiles[i].size(); j++) {
- //is this score between 1 and 99%
- if ((quantiles[i][j].score > low) && (quantiles[i][j].score < high)) {
- temp.push_back(quantiles[i][j]);
+ vector<float> temp;
+ if (quantiles[i].size() != 0) {
+ float high = quantiles[i][int(quantiles[i].size() * 0.99)];
+ float low = quantiles[i][int(quantiles[i].size() * 0.01)];
+
+ //look at each value in quantiles to see if it is an outlier
+ for (int j = 0; j < quantiles[i].size(); j++) {
+ //is this score between 1 and 99%
+ if ((quantiles[i][j] > low) && (quantiles[i][j] < high)) {
+ temp.push_back(quantiles[i][j]);
+ }
}
}
-
quantiles[i] = temp;
}
//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);
}
}
i++;
}
+ if (numWanted > dists.size()) { m->mothurOut("numwanted is larger than the number of template sequences, adjusting numwanted."); m->mothurOutEndLine(); numWanted = dists.size(); }
+
//cout << numWanted << endl;
for (int i = 0; i < numWanted; i++) {
//cout << dists[i].seq->getName() << '\t' << dists[i].dist << endl;
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);
}