X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.cpp;h=9ed0dfc5d1645c5c2b65cabdb04063e300634d04;hb=6d12ed0ba66fb35e9e2781fe3ca361e2293f2476;hp=75d03e16d62a4c01b20236b42c00c1e00cd0bfc0;hpb=30c1fd8c45b6f0d66c17f2714dbb58b8ddccdce2;p=mothur.git

diff --git a/mothur.cpp b/mothur.cpp
index 75d03e1..9ed0dfc 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -12,7 +12,6 @@
 #include "globaldata.hpp"
 #include "mothurout.h"
 
-
 /**************************************************************************************************/
 
 GlobalData* GlobalData::_uniqueInstance = 0;
@@ -36,8 +35,7 @@ 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 */  
@@ -58,7 +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
@@ -72,10 +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");
@@ -107,7 +137,10 @@ int main(int argc, char *argv[]){
 		m->mothurOutEndLine();	
 		
 		#ifdef USE_MPI
-			m->mothurOutJustToLog("Using MPI\n");
+			m->mothurOutJustToLog("Using MPI\tversion ");
+			int version, subversion;
+			MPI_Get_version(&version, &subversion);
+			m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
 		#endif
 		
 		//srand(54321);
@@ -116,7 +149,7 @@ int main(int argc, char *argv[]){
 		Engine* mothur;
 		bool bail = 0;
 		string input;
-
+ 
 		if(argc>1){
 			input = argv[1];
 
@@ -141,12 +174,37 @@ int main(int argc, char *argv[]){
 		
 		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();
 		
+		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