added name option to read.tree for use in unifrac and parimony commands

[mothur.git] / nameassignment.cpp

diff --git a/nameassignment.cpp b/nameassignment.cpp
index cd9ef4e0381a0a8ec384482b26d1966bb3388763..bc088f45924f4af9db951e81882376cd64fbc8f0 100644 (file)
--- a/nameassignment.cpp
+++ b/nameassignment.cpp
@@ -1,4 +1,4 @@
-using namespace std;
+
 
 #include "nameassignment.hpp"
 
@@ -12,44 +12,46 @@ NameAssignment::NameAssignment(string nameMapFile){
 
 //**********************************************************************************************************************
 
-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;
        
+//             map<string, string> data;
+               int rowIndex = 0;
+
                while(fileHandle){
                        fileHandle >> firstCol;                         //read from first column
-               
-                       for(int i=0;i<skipNCols;i++){           //allows for anticipated file format
-                               fileHandle >> skip;
-                       }
-               
                        fileHandle >> secondCol;                        //read from second column
-               
-                       data[firstCol] = secondCol;                     //store data in map
-               
+                       
+//                     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);
                }
                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";
+               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) {
+               errorOut(e, "NameAssignment", "push_back");
                exit(1);
        }
 }
@@ -64,19 +66,16 @@ 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.
                }
        }
        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";
+               errorOut(e, "NameAssignment", "print");
                exit(1);
        }
 }
@@ -88,6 +87,12 @@ int NameAssignment::get(string key){
        return  (*this)[key];   
 
 }
+//**********************************************************************************************************************
 
+string NameAssignment::get(int key){
+       
+       return  reverse[key];   
+
+}
 //**********************************************************************************************************************