added zap method to classify.seqs and changed bayesian method name to wang.

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 1a3bf79f50dad4e0a66e9910bb4abfe8c2cff944..7d40e80ead727205f4bcc00269f78bd7f81057ca 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -939,7 +939,7 @@ string MothurOut::getFullPathName(string fileName){
                                }
                        
                                for (int i = index; i >= 0; i--) {
-                                       newFileName = dirs[i] +  "\\" + newFileName;            
+                                       newFileName = dirs[i] +  "\\\\" + newFileName;          
                                }
                                
                                return newFileName;
@@ -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 {
@@ -2431,30 +2457,29 @@ void MothurOut::splitAtDash(string& estim, vector<string>& container) {
        try {
                string individual = "";
                int estimLength = estim.size();
+               bool prevEscape = false;
                for(int i=0;i<estimLength;i++){
-                       if(estim[i] == '-'){
-                               container.push_back(individual);
-                               individual = "";                                
+                       if(prevEscape){
+                               individual += estim[i];
+                               prevEscape = false;
                        }
                        else{
-                               individual += estim[i];
+                               if(estim[i] == '\\'){
+                                       prevEscape = true;
+                               }
+                               else if(estim[i] == '-'){
+                                       container.push_back(individual);
+                                       individual = "";
+                                       prevEscape = false;                             
+                               }
+                               else{
+                                       individual += estim[i];
+                                       prevEscape = false;
+                               }
                        }
                }
                container.push_back(individual);
-
-       
-       /*      string individual;
-               
-               while (estim.find_first_of('-') != -1) {
-                       individual = estim.substr(0,estim.find_first_of('-'));
-                       if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
-                               estim = estim.substr(estim.find_first_of('-')+1, estim.length());
-                               container.push_back(individual);
-                       }
-               }
-               //get last one
-               container.push_back(estim); */
-       }
+       }
        catch(exception& e) {
                errorOut(e, "MothurOut", "splitAtDash");
                exit(1);
@@ -2467,29 +2492,29 @@ void MothurOut::splitAtDash(string& estim, set<string>& container) {
        try {
                string individual = "";
                int estimLength = estim.size();
+               bool prevEscape = false;
                for(int i=0;i<estimLength;i++){
-                       if(estim[i] == '-'){
-                               container.insert(individual);
-                               individual = "";                                
+                       if(prevEscape){
+                               individual += estim[i];
+                               prevEscape = false;
                        }
                        else{
-                               individual += estim[i];
+                               if(estim[i] == '\\'){
+                                       prevEscape = true;
+                               }
+                               else if(estim[i] == '-'){
+                                       container.insert(individual);
+                                       individual = "";
+                                       prevEscape = false;                             
+                               }
+                               else{
+                                       individual += estim[i];
+                                       prevEscape = false;
+                               }
                        }
                }
                container.insert(individual);
-
-       //      string individual;
-               
-       //      while (estim.find_first_of('-') != -1) {
-       //              individual = estim.substr(0,estim.find_first_of('-'));
-       //              if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
-       //                      estim = estim.substr(estim.find_first_of('-')+1, estim.length());
-       //                      container.insert(individual);
-       //              }
-       //      }
-               //get last one
-       //      container.insert(estim);
-       
+        
        }
        catch(exception& e) {
                errorOut(e, "MothurOut", "splitAtDash");
@@ -2500,19 +2525,32 @@ void MothurOut::splitAtDash(string& estim, set<string>& container) {
 //This function parses the line options and puts them in a set
 void MothurOut::splitAtDash(string& estim, set<int>& container) {
        try {
-               string individual;
+               string individual = "";
                int lineNum;
-               
-               while (estim.find_first_of('-') != -1) {
-                       individual = estim.substr(0,estim.find_first_of('-'));
-                       if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
-                               estim = estim.substr(estim.find_first_of('-')+1, estim.length());
-                               convert(individual, lineNum); //convert the string to int
-                               container.insert(lineNum);
+               int estimLength = estim.size();
+               bool prevEscape = false;
+               for(int i=0;i<estimLength;i++){
+                       if(prevEscape){
+                               individual += estim[i];
+                               prevEscape = false;
+                       }
+                       else{
+                               if(estim[i] == '\\'){
+                                       prevEscape = true;
+                               }
+                               else if(estim[i] == '-'){
+                                       convert(individual, lineNum); //convert the string to int
+                                       container.insert(lineNum);
+                                       individual = "";
+                                       prevEscape = false;                             
+                               }
+                               else{
+                                       individual += estim[i];
+                                       prevEscape = false;
+                               }
                        }
                }
-               //get last one
-               convert(estim, lineNum); //convert the string to int
+               convert(individual, lineNum); //convert the string to int
                container.insert(lineNum);
        }
        catch(exception& e) {
@@ -2852,8 +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);
+       }
+}
+/**************************************************************************************************/