X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.cpp;h=9ed0dfc5d1645c5c2b65cabdb04063e300634d04;hb=fd5f17bcbe5fadab2c525f3d1fcfd1d79a60ae72;hp=a3eef76a2766d5ae69c824b0ee4cf4b5e3f14a51;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/mothur.cpp b/mothur.cpp
index a3eef76..9ed0dfc 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -35,15 +35,19 @@ void ctrlc_handler ( int sig ) {
 /***********************************************************************/
 int main(int argc, char *argv[]){
 	MothurOut* m = MothurOut::getInstance();
-	try {
-		
+	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");
@@ -52,7 +56,7 @@ int main(int argc, char *argv[]){
 				m->mothurOutEndLine(); m->mothurOutEndLine();
 			#else
 				m->mothurOutJustToLog("Linux version");
-				>m->mothurOutEndLine(); m->mothurOutEndLine();
+				m->mothurOutEndLine(); m->mothurOutEndLine();
 			#endif
 
 		#else
@@ -66,10 +70,42 @@ int main(int argc, char *argv[]){
 			m->mothurOutEndLine(); m->mothurOutEndLine();
 		#endif
 		
+		#ifdef MOTHUR_FILES
+			string temp = MOTHUR_FILES; 
+			
+			//add / to name if needed
+			string lastChar = temp.substr(temp.length()-1);
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				if (lastChar != "/") { temp += "/"; }
+			#else
+				if (lastChar != "\\") { temp += "\\"; }	
+			#endif
+			
+			temp = m->getFullPathName(temp);
+			m->setDefaultPath(temp);
+			
+			m->mothurOutJustToLog("Using default file location " + temp);
+			m->mothurOutEndLine(); m->mothurOutEndLine();
+		#endif
+		
+		#ifdef BIT_VERSION
+			m->mothurOutJustToLog("Running 64Bit Version");
+			m->mothurOutEndLine(); m->mothurOutEndLine();
+		#else
+			m->mothurOutJustToLog("Running 32Bit Version");
+			m->mothurOutEndLine(); m->mothurOutEndLine();
+		#endif
+		
+		//get releaseDate from Make
+		string releaseDate = RELEASE_DATE; 
+		string mothurVersion = VERSION; 
+		m->setReleaseDate(releaseDate);
+		m->setVersion(mothurVersion);
+		
 		//header
-		m->mothurOut("mothur v.1.8");
+		m->mothurOut("mothur v." + mothurVersion);
 		m->mothurOutEndLine();		
-		m->mothurOut("Last updated: 2/02/2010");
+		m->mothurOut("Last updated: " + releaseDate);
 		m->mothurOutEndLine();	
 		m->mothurOutEndLine();		
 		m->mothurOut("by");
@@ -99,15 +135,21 @@ int main(int argc, char *argv[]){
 		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];
 
@@ -130,16 +172,45 @@ int main(int argc, char *argv[]){
 			mothur = new InteractEngine(argv[0]);	
 		}
 		
-		while(bail == 0)		{	bail = mothur->getInput();			}
+		while(bail == 0)	{	bail = mothur->getInput();	}
+		
+		//closes logfile so we can rename
+		m->closeLog();
 		
 		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
+		string tempLog = mothur->getLogFileName();
+		bool append = mothur->getAppend();
 		
-		delete mothur;
+		string newlogFileName;
+		if (tempLog != "") {
+			newlogFileName = outputDir + tempLog;
+			
+			if (!append) {	
+				//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
 
+			}else {
+				ofstream outNewLog;
+				m->openOutputFileAppend(newlogFileName, outNewLog);
+				outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
+				outNewLog.close();
+				
+				m->appendFiles(logFileName, newlogFileName);
+				remove(logFileName.c_str());
+			}
+		}else{  
+			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) {