X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.cpp;h=bd7ab728c76d311ffe0dc7dcc052a026cfa6e741;hb=c3f0a9c8f932b923f3a6fbbf143e8f4b85fd6f5f;hp=a676c83aff566f8c2dbbaa05bef8519c4aff494b;hpb=ef3f6d42fe720cd6d91419e5e32f8c04d8765010;p=mothur.git

diff --git a/mothur.cpp b/mothur.cpp
index a676c83..bd7ab72 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -14,13 +14,16 @@
 /**************************************************************************************************/
 
 GlobalData* GlobalData::_uniqueInstance = 0;
+CommandFactory* CommandFactory::_uniqueInstance = 0;
 
 int main(int argc, char *argv[]){
 	try {
 		
-		//remove old logfile
-		string logFileName = "mothur.logFile";
-		remove(logFileName.c_str());
+		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)
@@ -41,9 +44,9 @@ int main(int argc, char *argv[]){
 
 		
 		//header
-		mothurOut("mothur v.1.6.0");
+		mothurOut("mothur v.1.7.2");
 		mothurOutEndLine();		
-		mothurOut("Last updated: 11/20/2009");
+		mothurOut("Last updated: 12/04/2009");
 		mothurOutEndLine();	
 		mothurOutEndLine();		
 		mothurOut("by");
@@ -58,7 +61,11 @@ int main(int argc, char *argv[]){
 		mothurOut("pschloss@umich.edu");
 		mothurOutEndLine();		
 		mothurOut("http://www.mothur.org");
-		mothurOutEndLine();	
+		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");
@@ -73,7 +80,7 @@ int main(int argc, char *argv[]){
 				
 		//srand(54321);
 		srand( (unsigned)time( NULL ) );
-
+		
 		Engine* mothur;
 		bool bail = 0;
 		string input;
@@ -88,13 +95,19 @@ int main(int argc, char *argv[]){
 			}
 		}
 		else{
-			mothur = new InteractEngine(argv[0]);		
+			mothur = new InteractEngine(argv[0]);	
 		}
-
+		
 		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) {