moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index eb5e8f92c105f708d56a6d4ce681e94aaa0453c3..18d8d437c619a1a38386d21dc511de75db73e946 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -82,7 +82,7 @@ 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);
@@ -192,11 +192,11 @@ 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{