added sets to amova and homova commands. added oligos to make.contigs. added metadat...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 2debf843f7910e6e0d61c9092cd366f1be5b2161..37c0916d4c49e1f8ed8ca979c7ff61b7e1a13ef3 100644 (file)
--- 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 {
@@ -2114,6 +2154,32 @@ 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 {
@@ -2662,6 +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) {
@@ -2864,8 +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);
+       }
+}
+/**************************************************************************************************/