Initial revision

[mothur.git] / commandoptionparser.cpp

diff --git a/commandoptionparser.cpp b/commandoptionparser.cpp
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+/*
+ *  commandoptionparser.cpp
+ *  
+ *
+ *  Created by Pat Schloss on 10/23/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#include <string>
+
+using namespace std;
+
+#include "globaldata.hpp"
+#include "commandoptionparser.hpp"
+#include <exception>
+#include <iostream>
+
+//**********************************************************************************************************************
+//This Function parses through the command line and pulls out the command then sends the options to  the parseGlobalData
+CommandOptionParser::CommandOptionParser(string input){
+       try {
+               int openParen = input.find_first_of('(');
+               int closeParen = input.find_last_of(')');
+               string optionString = "";
+               commandString = "";
+       
+               if(openParen != -1 && closeParen != -1){                        
+                       commandString = input.substr(0, openParen);   //commandString contains everything before "("
+                       optionString = input.substr(openParen+1, closeParen-openParen-1); //optionString contains everything between "(" and ")".
+               }
+                                       
+               GlobalData* globaldata = GlobalData::getInstance();
+               globaldata->parseGlobalData(commandString, optionString);                       //parser to separate and check options
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the CommandOptionParser class Function CommandOptionParser. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the CommandOptionParser class function CommandOptionParser. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+
+}
+
+//**********************************************************************************************************************
+
+string CommandOptionParser::getCommandString() {       return commandString;   }
+
+//**********************************************************************************************************************