changes for 1.11

[mothur.git] / decalc.cpp

diff --git a/decalc.cpp b/decalc.cpp
index 4e80c65d29aa7c8d6a2354db95027c3365c7962d..2e214bffe969181c9f83061edc69a491610fe8a8 100644 (file)
--- a/decalc.cpp
+++ b/decalc.cpp
@@ -381,9 +381,9 @@ vector<float>  DeCalculator::findQav(vector<int> window, int size, vector<float>
 }
 //***************************************************************************************************************
 //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);
@@ -428,9 +428,9 @@ vector< vector<quanMember> > DeCalculator::getQuantiles(vector<Sequence*> seqs,
        //cout << i << '\t' <<  j << '\t' << dist << '\t' << de << endl;                        
                                dist = ceil(dist);
                                
-                               quanMember newScore(de, i, j);
+                               //quanMember newScore(de, i, j);
                                
-                               quan[dist].push_back(newScore);
+                               quan[dist].push_back(de);
 
                                delete subject;
                        }
@@ -454,23 +454,23 @@ inline bool compareQuanMembers(quanMember left, quanMember right){
 } 
 //***************************************************************************************************************
 //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);
+                       sort(quantiles[i].begin(), quantiles[i].end());
                        
-                       vector<quanMember> temp;
+                       vector<float> temp;
                        if (quantiles[i].size() != 0) {
-                               float high = quantiles[i][int(quantiles[i].size() * 0.99)].score;
-                               float low =  quantiles[i][int(quantiles[i].size() * 0.01)].score;
+                               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].score > low) && (quantiles[i][j].score < high)) {
+                                       if ((quantiles[i][j] > low) && (quantiles[i][j] < high)) {
                                                temp.push_back(quantiles[i][j]);
                                        }
                                }