X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.cpp;h=a95c381658009f988e6caff879181a9412851c3d;hb=e0fbf58358a72f20352cf2a43922ab6b5bdf0cf8;hp=623601207afe90ae92a691646110eac2e9a18f79;hpb=30f2d98fffb579b870c8969ddcc1dfc61ccbb70a;p=mothur.git

diff --git a/mothur.cpp b/mothur.cpp
index 6236012..a95c381 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -12,7 +12,6 @@
 #include "globaldata.hpp"
 #include "mothurout.h"
 
-
 /**************************************************************************************************/
 
 GlobalData* GlobalData::_uniqueInstance = 0;
@@ -58,7 +57,7 @@ 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 +71,36 @@ 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 = 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
+		
 		//header
-		m->mothurOut("mothur v.1.8");
+		m->mothurOut("mothur v.1.12.0");
 		m->mothurOutEndLine();		
-		m->mothurOut("Last updated: 2/02/2010");
+		m->mothurOut("Last updated: 7/23/2010");
 		m->mothurOutEndLine();	
 		m->mothurOutEndLine();		
 		m->mothurOut("by");
@@ -144,12 +169,37 @@ 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;
+				openOutputFileAppend(newlogFileName, outNewLog);
+				outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
+				outNewLog.close();
+				
+				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