X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=mothurout.cpp;h=37c0916d4c49e1f8ed8ca979c7ff61b7e1a13ef3;hb=5e1ab7456ec5e9e516cfa0fec6afef2c2a03a257;hp=d9df5a078b425b773611d25b2616e3f66a58bddf;hpb=5b72d1cf3fa48730e5bb70d59cced1e43e1fe424;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index d9df5a0..37c0916 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1541,6 +1541,46 @@ vector<string> MothurOut::splitWhiteSpace(string input){
 		exit(1);
 	}
 }
+/***********************************************************************/
+vector<string> MothurOut::splitWhiteSpaceWithQuotes(string input){
+	try {
+        vector<string> pieces;
+        string rest = "";
+        
+        int pos = input.find('\'');
+        int pos2 = input.find('\"');
+        
+        if ((pos == string::npos) && (pos2 == string::npos)) { return splitWhiteSpace(input); } //no quotes to worry about
+        else {
+            for (int i = 0; i < input.length(); i++) {
+                if ((input[i] == '\'') || (input[i] == '\"') || (rest == "\'") || (rest == "\"")) { //grab everything til end or next ' or "
+                    rest += input[i];
+                    for (int j = i+1; j < input.length(); j++) {
+                        if ((input[j] == '\'') || (input[j] == '\"')) {  //then quit
+                            rest += input[j];
+                            i = j+1;
+                            j+=input.length();
+                        }else { rest += input[j]; }
+                    }
+                }else if (!isspace(input[i]))  { rest += input[i];  }
+                else {
+                    if (rest != "") { pieces.push_back(rest);  rest = ""; }
+                    while (i < input.length()) {  //gobble white space
+                        if (isspace(input[i])) { i++; }
+                        else { rest = input[i];  break; } //cout << "next piece buffer = " << nextPiece << endl;
+                    } 
+                }
+            }
+            
+            if (rest != "") { pieces.push_back(rest); }
+        }
+        return pieces;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "splitWhiteSpace");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 int MothurOut::readTax(string namefile, map<string, string>& taxMap) {
 	try {
@@ -2688,6 +2728,35 @@ bool MothurOut::inUsersGroups(string groupname, vector<string> Groups) {
 		exit(1);
 	}	
 }
+/**************************************************************************************************/
+
+bool MothurOut::inUsersGroups(vector<int> set, vector< vector<int> > sets) {
+	try {
+		for (int i = 0; i < sets.size(); i++) {
+			if (set == sets[i]) { return true; }
+		}
+		return false;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "inUsersGroups");
+		exit(1);
+	}	
+}
+/**************************************************************************************************/
+
+bool MothurOut::inUsersGroups(int groupname, vector<int> Groups) {
+	try {
+		for (int i = 0; i < Groups.size(); i++) {
+			if (groupname == Groups[i]) { return true; }
+		}
+		return false;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "inUsersGroups");
+		exit(1);
+	}	
+}
+
 /**************************************************************************************************/
 //returns true if any of the strings in first vector are in second vector
 bool MothurOut::inUsersGroups(vector<string> groupnames, vector<string> Groups) {
@@ -2890,8 +2959,53 @@ 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);
+	}
+}
+/**************************************************************************************************/