added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index 5941663f8e063ba3ee6664ba47ee2cc3c7860522..d4177e3368be8d836374e935b9e884d6ff26c5f4 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -14,13 +14,17 @@
 /**************************************************************************************************/
 
 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)
@@ -95,17 +99,15 @@ 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();                      }
+               
+               string outputDir = mothur->getOutputDir();
+               logFileName = outputDir + logFileName;
        
                delete mothur;
-       
+               
+//             rename(log.c_str(), logFileName.c_str()); //logfile with timestamp
+               
                return 0;
        }
        catch(exception& e) {