removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index a95c381658009f988e6caff879181a9412851c3d..74e7e731cc391441280d202bb6913019e0fd0538 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -14,7 +14,6 @@
 
 /**************************************************************************************************/
 
-GlobalData* GlobalData::_uniqueInstance = 0;
 CommandFactory* CommandFactory::_uniqueInstance = 0;
 MothurOut* MothurOut::_uniqueInstance = 0;
 
@@ -35,8 +34,7 @@ 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 */  
@@ -82,7 +80,7 @@ int main(int argc, char *argv[]){
                                if (lastChar != "\\") { temp += "\\"; } 
                        #endif
                        
-                       temp = getFullPathName(temp);
+                       temp = m->getFullPathName(temp);
                        m->setDefaultPath(temp);
                        
                        m->mothurOutJustToLog("Using default file location " + temp);
@@ -97,10 +95,16 @@ int main(int argc, char *argv[]){
                        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.1.12.0");
+               m->mothurOut("mothur v." + mothurVersion);
                m->mothurOutEndLine();          
-               m->mothurOut("Last updated: 7/23/2010");
+               m->mothurOut("Last updated: " + releaseDate);
                m->mothurOutEndLine();  
                m->mothurOutEndLine();          
                m->mothurOut("by");
@@ -144,7 +148,7 @@ int main(int argc, char *argv[]){
                Engine* mothur;
                bool bail = 0;
                string input;
-
+ 
                if(argc>1){
                        input = argv[1];
 
@@ -186,11 +190,11 @@ 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{