X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.cpp;h=75d03e16d62a4c01b20236b42c00c1e00cd0bfc0;hb=30c1fd8c45b6f0d66c17f2714dbb58b8ddccdce2;hp=3bdbfcd0c5e6859a34172c5accf14ebbd28e866a;hpb=a5afca18544555fba2d9c3670ad1f8574916b0a0;p=mothur.git

diff --git a/mothur.cpp b/mothur.cpp
index 3bdbfcd..75d03e1 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -10,72 +10,106 @@
 #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 {
 		
-		//remove old logfile
-		string logFileName = "mothur.logFile";
-		remove(logFileName.c_str());
+		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__)
-				mothurOutJustToLog("Mac version");
-				mothurOutEndLine(); mothurOutEndLine();
+				m->mothurOutJustToLog("Mac version");
+				m->mothurOutEndLine(); m->mothurOutEndLine();
 			#else
-				mothurOutJustToLog("Linux version");
-				mothurOutEndLine(); mothurOutEndLine();
+				m->mothurOutJustToLog("Linux version");
+				>m->mothurOutEndLine(); m->mothurOutEndLine();
 			#endif
 
 		#else
 			system("CLS");
-			mothurOutJustToLog("Windows version");
-			mothurOutEndLine(); mothurOutEndLine();
+			m->mothurOutJustToLog("Windows version");
+			m->mothurOutEndLine(); m->mothurOutEndLine();
 		#endif		
-
+		
+		#ifdef USE_READLINE
+			m->mothurOutJustToLog("Using ReadLine");
+			m->mothurOutEndLine(); m->mothurOutEndLine();
+		#endif
 		
 		//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();	
-
-				
+		m->mothurOut("mothur v.1.8");
+		m->mothurOutEndLine();		
+		m->mothurOut("Last updated: 2/02/2010");
+		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\n");
+		#endif
+		
 		//srand(54321);
 		srand( (unsigned)time( NULL ) );
 		
@@ -87,30 +121,42 @@ int main(int argc, char *argv[]){
 			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]);	
 		}
 		
-		//used to intercept the terminate signal, so instead of terminating mothur it will end a command
-		//void (*prev_fn)(int);
-		//prev_fn = signal(SIGTERM, mothur->terminateCommand(0));
+		while(bail == 0)	{	bail = mothur->getInput();	}
 		
-		//if (prev_fn==SIG_IGN) signal (SIGTERM,SIG_IGN);
-
-		
-		while(bail == 0)		{	bail = mothur->getInput();			}
+		string outputDir = mothur->getOutputDir();
+		string newlogFileName = outputDir + logFileName;
 	
+		//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) {
-		errorOut(e, "mothur", "main");
+		m->errorOut(e, "mothur", "main");
 		exit(1);
 	}
 }