- bestfit = findPairs(lines[0]->start, lines[0]->end);
- obsDistance = calcObserved(lines[0]->start, lines[0]->end);
- Qav = findQav(lines[0]->start, lines[0]->end);
- seqCoef = getCoef(lines[0]->start, lines[0]->end);
- expectedDistance = calcExpected(lines[0]->start, lines[0]->end);
- DE = calcDE(lines[0]->start, lines[0]->end);
+ mothurOut("Calculating observed distance... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ vector<float> obsi = calcObserved(querySeqs[i], bestfit[i], windows[i], windowSizes[i]);
+ obsDistance[i] = obsi;
+ }
+ mothurOut("Done."); mothurOutEndLine();
+
+
+
+ mothurOut("Finding variability... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ vector<float> q = findQav(windows[i], windowSizes[i]);
+ Qav[i] = q;
+ }
+ mothurOut("Done."); mothurOutEndLine();
+
+
+
+ mothurOut("Calculating alpha... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ float alpha = getCoef(obsDistance[i], Qav[i]);
+ seqCoef.push_back(alpha);
+ }
+ mothurOut("Done."); mothurOutEndLine();
+
+
+
+ mothurOut("Calculating expected distance... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ vector<float> exp = calcExpected(Qav[i], seqCoef[i]);
+ expectedDistance[i] = exp;
+ }
+ mothurOut("Done."); mothurOutEndLine();
+
+
+
+ mothurOut("Finding deviation... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ float de = calcDE(obsDistance[i], expectedDistance[i]);
+ DE[i] = de;
+
+ it = trimmed[i].begin();
+ float dist = calcDist(querySeqs[i], bestfit[i], it->first, it->second);
+ deviation[i] = dist;
+ }
+ mothurOut("Done."); mothurOutEndLine();