moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / nameassignment.cpp

diff --git a/nameassignment.cpp b/nameassignment.cpp
deleted file mode 100644 (file)
index 3d99551..0000000
--- a/nameassignment.cpp
+++ /dev/null
@@ -1,122 +0,0 @@
-
-
-#include "nameassignment.hpp"
-
-//**********************************************************************************************************************
-
-NameAssignment::NameAssignment(string nameMapFile){
-       m = MothurOut::getInstance();
-       m->openInputFile(nameMapFile, fileHandle);
-       
-}
-
-//**********************************************************************************************************************
-
-void NameAssignment::readMap(){
-       try{
-               string firstCol, secondCol, skip;
-       //      int index = 0;
-       
-               
-               map<string, int>::iterator itData;
-               int rowIndex = 0;
-               
-               while(fileHandle){
-                       fileHandle >> firstCol;                         //read from first column
-                       fileHandle >> secondCol;                        //read from second column
-                                               
-                       itData = (*this).find(firstCol);
-                       if (itData == (*this).end()) {
-                       
-                               (*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) {
-               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);
-       }
-}
-
-//**********************************************************************************************************************
-
-ListVector NameAssignment::getListVector(void){
-
-       return list;
-       
-}
-
-//**********************************************************************************************************************
-
-void NameAssignment::print(ostream& out){
-       try {
-               map<string,int>::iterator it;
-//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) {
-               m->errorOut(e, "NameAssignment", "print");
-               exit(1);
-       }
-}
-
-//**********************************************************************************************************************
-
-int NameAssignment::get(string 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);
-       }
-}
-//**********************************************************************************************************************
-