X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.cpp;h=cb72ac635299285b9fe0775833e6fed18ae1369d;hb=e189982e0a9b7352ad57cc38ccee675f128be22e;hp=2b3f8f5146d7b1c47e8af3845ec9dfdba58fb355;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/mothur.cpp b/mothur.cpp
index 2b3f8f5..cb72ac6 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -1,53 +1,171 @@
-/*
- *  interface.cpp
- *  
- *
- *  Created by Pat Schloss on 8/14/08.
- *  Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- */
-#include <string>
-#include <iostream>
-#include <iomanip>
-#include <fstream>
-#include <sstream>
-#include <exception>
-
-#include "engine.hpp"
-#include "globaldata.hpp"
-
-using namespace std;
-
-GlobalData* GlobalData::_uniqueInstance = 0;
-
-int main(int argc, char *argv[]){
-	try {
-	//	srand(54321);
-		srand( (unsigned)time( NULL ) );
-
-		Engine* dotur;
-		bool bail = 0;
-
-		if(argc>1){
-			dotur = new BatchEngine(argv[1]);
-		}
-		else{
-			dotur = new InteractEngine();		
-		}
-
-		while(bail == 0)		{	bail = dotur->getInput();			}
-	
-		delete dotur;
-	
-		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";
-		exit(1);
-	}
-}
-
+/*
+ *  interface.cpp
+ *  
+ *
+ *  Created by Pat Schloss on 8/14/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ */
+ 
+#include "mothur.h"
+#include "engine.hpp"
+#include "globaldata.hpp"
+#include "mothurout.h"
+
+
+/**************************************************************************************************/
+
+GlobalData* GlobalData::_uniqueInstance = 0;
+CommandFactory* CommandFactory::_uniqueInstance = 0;
+MothurOut* MothurOut::_uniqueInstance = 0;
+
+/***********************************************************************/
+volatile int ctrlc_pressed = 0;
+void ctrlc_handler ( int sig ) {
+	MothurOut* m = MothurOut::getInstance();
+    ctrlc_pressed = 1;
+	m->control_pressed = ctrlc_pressed;
+	
+	if (m->executing) { //if mid command quit execution, else quit mothur
+		m->mothurOutEndLine(); m->mothurOut("quitting command...");  m->mothurOutEndLine();
+	}else{
+		m->mothurOut("quitting mothur");  m->mothurOutEndLine();
+		exit(1);
+	}
+}
+/***********************************************************************/
+int main(int argc, char *argv[]){
+	MothurOut* m = MothurOut::getInstance();
+	try {
+		
+		signal(SIGINT, ctrlc_handler );
+				
+		time_t ltime = time(NULL); /* calendar time */  
+		string logFileName = "mothur." + toString(ltime) + ".logfile";
+		
+		#ifdef USE_MPI
+			MPI_Init(&argc, &argv); 
+		#endif
+
+		m->setFileName(logFileName);
+		
+				
+		//version
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			system("clear");
+			#if defined (__APPLE__) || (__MACH__)
+				m->mothurOutJustToLog("Mac version");
+				m->mothurOutEndLine(); m->mothurOutEndLine();
+			#else
+				m->mothurOutJustToLog("Linux version");
+				>m->mothurOutEndLine(); m->mothurOutEndLine();
+			#endif
+
+		#else
+			system("CLS");
+			m->mothurOutJustToLog("Windows version");
+			m->mothurOutEndLine(); m->mothurOutEndLine();
+		#endif		
+		
+		#ifdef USE_READLINE
+			m->mothurOutJustToLog("Using ReadLine");
+			m->mothurOutEndLine(); m->mothurOutEndLine();
+		#endif
+		
+		//header
+		m->mothurOut("mothur v.1.9");
+		m->mothurOutEndLine();		
+		m->mothurOut("Last updated: 4/09/2010");
+		m->mothurOutEndLine();	
+		m->mothurOutEndLine();		
+		m->mothurOut("by");
+		m->mothurOutEndLine();		
+		m->mothurOut("Patrick D. Schloss");
+		m->mothurOutEndLine();
+		m->mothurOutEndLine();			
+		m->mothurOut("Department of Microbiology & Immunology");
+		m->mothurOutEndLine();	
+		m->mothurOut("University of Michigan");
+		m->mothurOutEndLine();			
+		m->mothurOut("pschloss@umich.edu");
+		m->mothurOutEndLine();		
+		m->mothurOut("http://www.mothur.org");
+		m->mothurOutEndLine();
+		m->mothurOutEndLine();
+		m->mothurOut("When using, please cite:");
+		m->mothurOutEndLine();
+		m->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.");
+		m->mothurOutEndLine();	
+		m->mothurOutEndLine();		
+		m->mothurOut("Distributed under the GNU General Public License");
+		m->mothurOutEndLine();
+		m->mothurOutEndLine();			
+		m->mothurOut("Type 'help()' for information on the commands that are available");
+		m->mothurOutEndLine();
+		m->mothurOutEndLine();			
+		m->mothurOut("Type 'quit()' to exit program");
+		m->mothurOutEndLine();	
+		
+		#ifdef USE_MPI
+			m->mothurOutJustToLog("Using MPI\tversion ");
+			int version, subversion;
+			MPI_Get_version(&version, &subversion);
+			m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
+		#endif
+		
+		//srand(54321);
+		srand( (unsigned)time( NULL ) );
+		
+		Engine* mothur;
+		bool bail = 0;
+		string input;
+
+		if(argc>1){
+			input = argv[1];
+
+			if (input[0] == '#') {
+				m->mothurOutJustToLog("Script Mode");
+				m->mothurOutEndLine(); m->mothurOutEndLine();
+
+				mothur = new ScriptEngine(argv[0], argv[1]);
+			}else{
+				m->mothurOutJustToLog("Batch Mode");
+				m->mothurOutEndLine(); m->mothurOutEndLine();
+				
+				mothur = new BatchEngine(argv[0], argv[1]);
+			}
+		}
+		else{
+			m->mothurOutJustToLog("Interactive Mode");
+			m->mothurOutEndLine(); m->mothurOutEndLine();
+			
+			mothur = new InteractEngine(argv[0]);	
+		}
+		
+		while(bail == 0)	{	bail = mothur->getInput();	}
+		
+		string outputDir = mothur->getOutputDir();
+		string newlogFileName = outputDir + logFileName;
+		
+		//closes logfile so we can rename
+		m->closeLog();
+	
+		//need this because m->mothurOut makes the logfile, but doesn't know where to put it
+		rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
+		
+		delete mothur;
+		
+		#ifdef USE_MPI
+			MPI_Finalize();
+		#endif
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "mothur", "main");
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/
+