Revert to previous commit

[mothur.git] / nameassignment.cpp

diff --git a/nameassignment.cpp b/nameassignment.cpp
new file mode 100644 (file)
index 0000000..3d99551
--- /dev/null
+++ b/nameassignment.cpp
@@ -0,0 +1,122 @@
+
+
+#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);
+       }
+}
+//**********************************************************************************************************************
+