added classify.shared command and random forest files. added count file to pcr.seqs...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index d9df5a078b425b773611d25b2616e3f66a58bddf..7d40e80ead727205f4bcc00269f78bd7f81057ca 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -2890,8 +2890,53 @@ int MothurOut::removeConfidences(string& tax) {
        }
 }
 /**************************************************************************************************/
-
-
+string MothurOut::removeQuotes(string tax) {
+       try {
+               
+               string taxon;
+               string newTax = "";
+               
+               for (int i = 0; i < tax.length(); i++) {
+                       
+                       if (control_pressed) { return newTax; }
+            
+            if ((tax[i] != '\'') && (tax[i] != '\"')) { newTax += tax[i]; }
+                       
+        }
+               
+               return newTax;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "removeQuotes");
+               exit(1);
+       }
+}
+/**************************************************************************************************/
+// function for calculating standard deviation
+double MothurOut::getStandardDeviation(vector<int>& featureVector){
+    try {
+        //finds sum
+        double average = 0; 
+        for (int i = 0; i < featureVector.size(); i++) { average += featureVector[i]; }
+        average /= (double) featureVector.size();
+        
+        //find standard deviation
+        double stdDev = 0;
+        for (int i = 0; i < featureVector.size(); i++) { //compute the difference of each dist from the mean, and square the result of each
+            stdDev += ((featureVector[i] - average) * (featureVector[i] - average));
+        }
+          
+        stdDev /= (double) featureVector.size(); 
+        stdDev = sqrt(stdDev);
+        
+        return stdDev;
+    }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "getStandardDeviation");
+               exit(1);
+       }
+}
+/**************************************************************************************************/