changed dups parameter to dereplicate in chimera.uchime.

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 2debf843f7910e6e0d61c9092cd366f1be5b2161..7d40e80ead727205f4bcc00269f78bd7f81057ca 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -2114,6 +2114,32 @@ int MothurOut::getNumChar(string line, char c){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+bool MothurOut::isSubset(vector<string> bigset, vector<string> subset) {
+       try {
+               
+        
+               if (subset.size() > bigset.size()) { return false;  }
+               
+               //check if each guy in suset is also in bigset
+               for (int i = 0; i < subset.size(); i++) {
+                       bool match = false;
+                       for (int j = 0; j < bigset.size(); j++) {
+                               if (subset[i] == bigset[j]) { match = true; break; }
+                       }
+                       
+                       //you have a guy in subset that had no match in bigset
+                       if (match == false) { return false; }
+               }
+               
+               return true;
+        
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "isSubset");
+               exit(1);
+       }
+}
 /***********************************************************************/
 int MothurOut::mothurRemove(string filename){
        try {
@@ -2864,8 +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);
+       }
+}
+/**************************************************************************************************/