Initial revision

[mothur.git] / nameassignment.cpp

diff --git a/nameassignment.cpp b/nameassignment.cpp
new file mode 100644 (file)
index 0000000..1f2feac
--- /dev/null
+++ b/nameassignment.cpp
@@ -0,0 +1,97 @@
+using namespace std;
+
+#include <string>
+#include <map>
+#include <exception>
+
+#include "nameassignment.hpp"
+
+//**********************************************************************************************************************
+
+NameAssignment::NameAssignment(string nameMapFile){
+       
+       openInputFile(nameMapFile, fileHandle);
+       
+}
+
+//**********************************************************************************************************************
+
+void NameAssignment::readMap(int colA, int colB){
+       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;
+                       }
+               
+                       fileHandle >> secondCol;                        //read from second column
+               
+                       data[firstCol] = secondCol;                     //store data in map
+               
+                       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";
+               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";
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************
+
+ListVector NameAssignment::getListVector(void){
+
+       return list;
+       
+}
+
+//**********************************************************************************************************************
+
+void NameAssignment::print(void){
+       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.
+               }
+       }
+       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";
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************
+
+int NameAssignment::get(string key){
+       
+       return  (*this)[key];   
+
+}
+
+//**********************************************************************************************************************
+