working on pam

[mothur.git] / nameassignment.cpp

diff --git a/nameassignment.cpp b/nameassignment.cpp
index 42d374d0b9e74842e4d3f289c75ae61645556ebd..1e42111e574baacf2eb2f5c3407416c9029f9041 100644 (file)
--- a/nameassignment.cpp
+++ b/nameassignment.cpp
@@ -6,31 +6,36 @@
 
 NameAssignment::NameAssignment(string nameMapFile){
        m = MothurOut::getInstance();
-       openInputFile(nameMapFile, fileHandle);
+       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
-                       reverse[rowIndex] = firstCol;
-                       (*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();
        
@@ -72,6 +77,7 @@ void NameAssignment::print(ostream& out){
 //cout << (*this).size() << endl;
                for(it = (*this).begin(); it!=(*this).end(); it++){
                        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) {
@@ -83,16 +89,35 @@ void NameAssignment::print(ostream& out){
 //**********************************************************************************************************************
 
 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 {
        
-       return  reverse[key];   
-
+               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);
+       }
 }
 //**********************************************************************************************************************