Merge remote-tracking branch 'origin/master'

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index d9df5a078b425b773611d25b2616e3f66a58bddf..124fbb876b38def3d61f1bf425ef15f36237fa5f 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1183,7 +1183,7 @@ string MothurOut::sortFile(string distFile, string outputDir){
 
                        string firstName, secondName;
                        float dist;
-                       while (input) {
+                       while (!input.eof()) {
                                input >> firstName >> secondName >> dist;
                                output << dist << '\t' << firstName << '\t' << secondName << endl;
                                gobble(input);
@@ -1199,16 +1199,17 @@ string MothurOut::sortFile(string distFile, string outputDir){
                
                        //read in sorted file and put distance at end again
                        ifstream input2;
+            ofstream output2;
                        openInputFile(tempOutfile, input2);
-                       openOutputFile(outfile, output);
+                       openOutputFile(outfile, output2);
                
-                       while (input2) {
+            while (!input2.eof()) {
                                input2 >> dist >> firstName >> secondName;
-                               output << firstName << '\t' << secondName << '\t' << dist << endl;
+                               output2 << firstName << '\t' << secondName << '\t' << dist << endl;
                                gobble(input2);
                        }
                        input2.close();
-                       output.close();
+                       output2.close();
                
                        //remove temp files
                        mothurRemove(tempDistFile);
@@ -1541,6 +1542,46 @@ 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 {
@@ -2430,6 +2471,9 @@ void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
 //This function parses the estimator options and puts them in a vector
 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
        try {
+        
+        if (symbol == '-') { splitAtDash(estim, container); return; }
+        
                string individual = "";
                int estimLength = estim.size();
                for(int i=0;i<estimLength;i++){
@@ -2688,6 +2732,35 @@ 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 +2963,53 @@ 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);
+       }
+}
+/**************************************************************************************************/