//for each window
float sum = 0.0; //sum = sum from 1 to m of (oi-ei)^2
- for (int m = 0; m < obs.size(); m++) { sum += ((obs[m] - exp[m]) * (obs[m] - exp[m])); }
+ int numZeros = 0;
+ for (int m = 0; m < obs.size(); m++) {
- float de = sqrt((sum / (obs.size() - 1)));
+ //if (obs[m] != 0.0) {
+ sum += ((obs[m] - exp[m]) * (obs[m] - exp[m]));
+ //}else { numZeros++; }
+
+ }
+
+ float de = sqrt((sum / (obs.size() - 1 - numZeros)));
return de;
}
//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++){
float de = calcDE(obsi, exp);
float dist = calcDist(query, subject, front, back);
-
+ //o << i << '\t' << j << '\t' << dist << '\t' << de << endl;
dist = ceil(dist);
quanMember newScore(de, i, j);
exit(1);
}
}
-
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareQuanMembers(quanMember left, quanMember right){
+ return (left.score < right.score);
+}
//***************************************************************************************************************
//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...
-vector< vector<float> > DeCalculator::removeObviousOutliers(vector< vector<quanMember> >& quantiles, int num) {
+void DeCalculator::removeObviousOutliers(vector< vector<quanMember> >& quantiles, int num) {
try {
- vector< vector<float> > quan;
- quan.resize(100);
-
- /*vector<quanMember> contributions;
- vector<int> seen; //seen[0] is the number of outliers that template seqs[0] was part of.
- seen.resize(num,0);
-
- //find contributions
+
for (int i = 0; i < quantiles.size(); i++) {
//find mean of this quantile score
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;
+
//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)) {
-
- }else {
- //add to contributions
- contributions.push_back(quantiles[i][j]);
- seen[quantiles[i][j].member1]++;
- seen[quantiles[i][j].member2]++;
+ temp.push_back(quantiles[i][j]);
}
}
+
+ quantiles[i] = temp;
}
+/*
//find contributer with most offending score related to it
int largestContrib = findLargestContrib(seen);
}
*/
- return quan;
+
}
catch(exception& e) {
errorOut(e, "DeCalculator", "removeObviousOutliers");