X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.cpp;h=bd7ab728c76d311ffe0dc7dcc052a026cfa6e741;hb=c3f0a9c8f932b923f3a6fbbf143e8f4b85fd6f5f;hp=ab4fea0e09482b3c8c988ade3e244fa4c8504750;hpb=c99f3846e7a7b6f06ab46508baa5409204ad6290;p=mothur.git

diff --git a/mothur.cpp b/mothur.cpp
index ab4fea0..bd7ab72 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -19,9 +19,8 @@ CommandFactory* CommandFactory::_uniqueInstance = 0;
 int main(int argc, char *argv[]){
 	try {
 		
-		//remove old logfile
-//		string log = "mothur.logFile";
-//		remove(log.c_str());
+		string log = "mothur.logFile";
+		remove(log.c_str());
 		
 		time_t ltime = time(NULL); /* calendar time */  
 		string logFileName = "mothur." + toString(ltime) + ".logfile";
@@ -99,19 +98,16 @@ int main(int argc, char *argv[]){
 			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));
-		
-		//if (prev_fn==SIG_IGN) signal (SIGTERM,SIG_IGN);
-
-		
 		while(bail == 0)		{	bail = mothur->getInput();			}
-	
-		delete mothur;
 		
-//		rename(log.c_str(), logFileName.c_str()); //logfile with timestamp
+		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) {