X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.cpp;h=bd7ab728c76d311ffe0dc7dcc052a026cfa6e741;hb=c3f0a9c8f932b923f3a6fbbf143e8f4b85fd6f5f;hp=2b3f8f5146d7b1c47e8af3845ec9dfdba58fb355;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/mothur.cpp b/mothur.cpp
index 2b3f8f5..bd7ab72 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -6,48 +6,115 @@
  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
  *
  */
-#include <string>
-#include <iostream>
-#include <iomanip>
-#include <fstream>
-#include <sstream>
-#include <exception>
-
+ 
+#include "mothur.h"
 #include "engine.hpp"
 #include "globaldata.hpp"
 
-using namespace std;
+/**************************************************************************************************/
 
 GlobalData* GlobalData::_uniqueInstance = 0;
+CommandFactory* CommandFactory::_uniqueInstance = 0;
 
 int main(int argc, char *argv[]){
 	try {
-	//	srand(54321);
-		srand( (unsigned)time( NULL ) );
+		
+		string log = "mothur.logFile";
+		remove(log.c_str());
+		
+		time_t ltime = time(NULL); /* calendar time */  
+		string logFileName = "mothur." + toString(ltime) + ".logfile";
+		
+		//version
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			system("clear");
+			#if defined (__APPLE__) || (__MACH__)
+				mothurOutJustToLog("Mac version");
+				mothurOutEndLine(); mothurOutEndLine();
+			#else
+				mothurOutJustToLog("Linux version");
+				mothurOutEndLine(); mothurOutEndLine();
+			#endif
+
+		#else
+			system("CLS");
+			mothurOutJustToLog("Windows version");
+			mothurOutEndLine(); mothurOutEndLine();
+		#endif		
 
-		Engine* dotur;
+		
+		//header
+		mothurOut("mothur v.1.7.2");
+		mothurOutEndLine();		
+		mothurOut("Last updated: 12/04/2009");
+		mothurOutEndLine();	
+		mothurOutEndLine();		
+		mothurOut("by");
+		mothurOutEndLine();		
+		mothurOut("Patrick D. Schloss");
+		mothurOutEndLine();
+		mothurOutEndLine();			
+		mothurOut("Department of Microbiology & Immunology");
+		mothurOutEndLine();	
+		mothurOut("University of Michigan");
+		mothurOutEndLine();			
+		mothurOut("pschloss@umich.edu");
+		mothurOutEndLine();		
+		mothurOut("http://www.mothur.org");
+		mothurOutEndLine();
+		mothurOutEndLine();
+		mothurOut("When using, please cite:");
+		mothurOutEndLine();
+		mothurOut("Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.");
+		mothurOutEndLine();	
+		mothurOutEndLine();		
+		mothurOut("Distributed under the GNU General Public License");
+		mothurOutEndLine();
+		mothurOutEndLine();			
+		mothurOut("Type 'help()' for information on the commands that are available");
+		mothurOutEndLine();
+		mothurOutEndLine();			
+		mothurOut("Type 'quit()' to exit program");
+		mothurOutEndLine();	
+
+				
+		//srand(54321);
+		srand( (unsigned)time( NULL ) );
+		
+		Engine* mothur;
 		bool bail = 0;
+		string input;
 
 		if(argc>1){
-			dotur = new BatchEngine(argv[1]);
+			input = argv[1];
+
+			if (input[0] == '#') {
+				mothur = new ScriptEngine(argv[0], argv[1]);
+			}else{
+				mothur = new BatchEngine(argv[0], argv[1]);
+			}
 		}
 		else{
-			dotur = new InteractEngine();		
+			mothur = new InteractEngine(argv[0]);	
 		}
-
-		while(bail == 0)		{	bail = dotur->getInput();			}
-	
-		delete dotur;
+		
+		while(bail == 0)		{	bail = mothur->getInput();			}
+		
+		string outputDir = mothur->getOutputDir();
+		logFileName = outputDir + logFileName;
 	
+		//need this because mothur.h makes the logfile, but doesn't know where to put it
+		rename(log.c_str(), logFileName.c_str()); //logfile with timestamp
+		
+		delete mothur;
+
 		return 0;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the dotur class Function main. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the dotur class function main. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "mothur", "main");
 		exit(1);
 	}
 }
 
+/**************************************************************************************************/
+