changes while testing

[mothur.git] / nameassignment.cpp

diff --git a/nameassignment.cpp b/nameassignment.cpp
index c31468c36cbd422a5d8aa72a99cbfc02f7abb5ff..1e42111e574baacf2eb2f5c3407416c9029f9041 100644 (file)
--- a/nameassignment.cpp
+++ b/nameassignment.cpp
@@ -5,37 +5,58 @@
 //**********************************************************************************************************************
 
 NameAssignment::NameAssignment(string nameMapFile){
-       
-       openInputFile(nameMapFile, fileHandle);
+       m = MothurOut::getInstance();
+       m->openInputFile(nameMapFile, fileHandle);
        
 }
-
+//**********************************************************************************************************************
+NameAssignment::NameAssignment(){ m = MothurOut::getInstance(); }
 //**********************************************************************************************************************
 
 void NameAssignment::readMap(){
        try{
                string firstCol, secondCol, skip;
        //      int index = 0;
-       
-       
-//             map<string, string> data;
+        
+               
+               map<string, int>::iterator itData;
                int rowIndex = 0;
-
+               
                while(fileHandle){
-                       fileHandle >> firstCol;                         //read from first column
+                       fileHandle >> firstCol; m->gobble(fileHandle);                  //read from first column
                        fileHandle >> secondCol;                        //read from second column
+                                               
+                       itData = (*this).find(firstCol);
+                       if (itData == (*this).end()) {
                        
-//                     data[firstCol] = secondCol;                     //store data in map
-
-                       list.push_back(secondCol);              //adds data's value to list
-                       (*this)[firstCol] = rowIndex++;
-                       gobble(fileHandle);
+                               (*this)[firstCol] = rowIndex++;
+                               list.push_back(secondCol);              //adds data's value to list
+                               reverse[rowIndex] = firstCol;
+                               
+                       }else{  m->mothurOut(firstCol + " is already in namesfile. I will use first definition."); m->mothurOutEndLine();  }
+                       
+                       m->gobble(fileHandle);
                }
                fileHandle.close();
        
        }
        catch(exception& e) {
-               errorOut(e, "NameAssignment", "readMap");
+               m->errorOut(e, "NameAssignment", "readMap");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+void NameAssignment::push_back(string name) {
+       try{
+       
+               int num = (*this).size();
+               (*this)[name] = num;
+               reverse[num] = name;
+               
+               list.push_back(name);
+       }
+       catch(exception& e) {
+               m->errorOut(e, "NameAssignment", "push_back");
                exit(1);
        }
 }
@@ -50,15 +71,17 @@ ListVector NameAssignment::getListVector(void){
 
 //**********************************************************************************************************************
 
-void NameAssignment::print(void){
+void NameAssignment::print(ostream& out){
        try {
                map<string,int>::iterator it;
+//cout << (*this).size() << endl;
                for(it = (*this).begin(); it!=(*this).end(); it++){
-                       mothurOut(it->first + "\t" + toString(it->second)); mothurOutEndLine();  //prints out keys and values of the map this.
+                       out << it->first << '\t' <<  it->second << endl;  //prints out keys and values of the map this.
+                       //out << it->first << '\t' <<  it->first << endl;
                }
        }
        catch(exception& e) {
-               errorOut(e, "NameAssignment", "print");
+               m->errorOut(e, "NameAssignment", "print");
                exit(1);
        }
 }
@@ -66,10 +89,35 @@ void NameAssignment::print(void){
 //**********************************************************************************************************************
 
 int NameAssignment::get(string key){
-       
-       return  (*this)[key];   
-
+       try {
+               map<string, int>::iterator itGet = (*this).find(key);
+               
+               //if you can't find it
+               if (itGet == (*this).end()) { return -1; }
+               
+               return  (*this)[key];   
+       }
+       catch(exception& e) {
+               m->errorOut(e, "NameAssignment", "get");
+               exit(1);
+       }
 }
+//**********************************************************************************************************************
 
+string NameAssignment::get(int key){
+       try {
+       
+               map<int, string>::iterator itGet = reverse.find(key);
+       
+               if (itGet == reverse.end()) { return "not found"; }
+       
+               return  reverse[key];   
+       
+       }
+       catch(exception& e) {
+               m->errorOut(e, "NameAssignment", "get");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************