working on pam

[mothur.git] / nameassignment.cpp

diff --git a/nameassignment.cpp b/nameassignment.cpp
index 1f2feacff2ebd5eca6d137b23c12cfc416521def..1e42111e574baacf2eb2f5c3407416c9029f9041 100644 (file)
--- a/nameassignment.cpp
+++ b/nameassignment.cpp
@@ -1,59 +1,62 @@
-using namespace std;
 
-#include <string>
-#include <map>
-#include <exception>
 
 #include "nameassignment.hpp"
 
 //**********************************************************************************************************************
 
 NameAssignment::NameAssignment(string nameMapFile){
-       
-       openInputFile(nameMapFile, fileHandle);
+       m = MothurOut::getInstance();
+       m->openInputFile(nameMapFile, fileHandle);
        
 }
-
+//**********************************************************************************************************************
+NameAssignment::NameAssignment(){ m = MothurOut::getInstance(); }
 //**********************************************************************************************************************
 
-void NameAssignment::readMap(int colA, int colB){
+void NameAssignment::readMap(){
        try{
                string firstCol, secondCol, skip;
        //      int index = 0;
-       
-               int skipNCols = colB-colA-1;
-       
-               map<string, string> data;
-       
-               while(fileHandle){
-                       fileHandle >> firstCol;                         //read from first column
+        
                
-                       for(int i=0;i<skipNCols;i++){           //allows for anticipated file format
-                               fileHandle >> skip;
-                       }
+               map<string, int>::iterator itData;
+               int rowIndex = 0;
                
+               while(fileHandle){
+                       fileHandle >> firstCol; m->gobble(fileHandle);                  //read from first column
                        fileHandle >> secondCol;                        //read from second column
-               
-                       data[firstCol] = secondCol;                     //store data in map
-               
-                       gobble(fileHandle);
+                                               
+                       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();
        
-               int rowIndex = 0;
-               map<string, string>::iterator it = data.begin();
-               for(it;it!=data.end();it++){
-                       list.push_back(it->second);             //adds data's value to list
-                       (*this)[it->first] = rowIndex;
-                       rowIndex++;
-               }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the NameAssignment class Function readMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "NameAssignment", "readMap");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the NameAssignment class function readMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+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);
        }
 }
@@ -68,19 +71,17 @@ ListVector NameAssignment::getListVector(void){
 
 //**********************************************************************************************************************
 
-void NameAssignment::print(void){
+void NameAssignment::print(ostream& out){
        try {
-               map<string,int>::iterator it = (*this).begin();
-               for(it;it!=(*this).end();it++){
-                       cout << it->first << '\t' << it->second << endl;  //prints out keys and values of the map this.
+               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) {
-               cout << "Standard Error: " << e.what() << " has occurred in the NameAssignment class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the NameAssignment class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "NameAssignment", "print");
                exit(1);
        }
 }
@@ -88,10 +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);
+       }
+}
 //**********************************************************************************************************************