X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.cpp;h=9ed0dfc5d1645c5c2b65cabdb04063e300634d04;hb=a537fefa3bd2c2eba7d532249375b6a11b295e25;hp=4f91c2e90a0b52aa8c3f51140e857660e8ba038f;hpb=84f93a9e670eb7f7e69e0468b9be4c53890c07f2;p=mothur.git

diff --git a/mothur.cpp b/mothur.cpp
index 4f91c2e..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.1.9");
+		m->mothurOut("mothur v." + mothurVersion);
 		m->mothurOutEndLine();		
-		m->mothurOut("Last updated: 4/16/2010");
+		m->mothurOut("Last updated: " + releaseDate);
 		m->mothurOutEndLine();	
 		m->mothurOutEndLine();		
 		m->mothurOut("by");
@@ -119,7 +149,7 @@ int main(int argc, char *argv[]){
 		Engine* mothur;
 		bool bail = 0;
 		string input;
-
+ 
 		if(argc>1){
 			input = argv[1];
 
@@ -161,11 +191,11 @@ int main(int argc, char *argv[]){
 
 			}else {
 				ofstream outNewLog;
-				openOutputFileAppend(newlogFileName, outNewLog);
+				m->openOutputFileAppend(newlogFileName, outNewLog);
 				outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
 				outNewLog.close();
 				
-				appendFiles(logFileName, newlogFileName);
+				m->appendFiles(logFileName, newlogFileName);
 				remove(logFileName.c_str());
 			}
 		}else{