added get.otus and remove.otus commands

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index eb5e8f92c105f708d56a6d4ce681e94aaa0453c3..9ed0dfc5d1645c5c2b65cabdb04063e300634d04 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -35,8 +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 */  
@@ -82,7 +81,7 @@ 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);
@@ -150,7 +149,7 @@ int main(int argc, char *argv[]){
                Engine* mothur;
                bool bail = 0;
                string input;
-
+ 
                if(argc>1){
                        input = argv[1];
 
@@ -192,11 +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{