changing command name classify.shared to classifyrf.shared

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index b551302646c10b813740516eaa65cc46453b4a1d..accdb2962c198988c457dc8f837b8817dc2799f0 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -10,12 +10,13 @@
 #include "mothur.h"
 #include "engine.hpp"
 #include "mothurout.h"
+#include "referencedb.h"
 
 /**************************************************************************************************/
 
 CommandFactory* CommandFactory::_uniqueInstance = 0;
 MothurOut* MothurOut::_uniqueInstance = 0;
-
+ReferenceDB* ReferenceDB::myInstance = 0;
 /***********************************************************************/
 volatile int ctrlc_pressed = 0;
 void ctrlc_handler ( int sig ) {
@@ -45,7 +46,7 @@ int main(int argc, char *argv[]){
 
                m->setFileName(logFileName);
                
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        system("clear");
                #else
                        system("CLS");
@@ -56,7 +57,7 @@ int main(int argc, char *argv[]){
                
                        //add / to name if needed
                        string lastChar = temp.substr(temp.length()-1);
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                if (lastChar != "/") { temp += "/"; }
                        #else
                                if (lastChar != "\\") { temp += "\\"; } 
@@ -87,7 +88,7 @@ int main(int argc, char *argv[]){
                
                if (outputHeader)  {
                        //version
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                #if defined (__APPLE__) || (__MACH__)
                                        m->mothurOutJustToLog("Mac version");
                                        m->mothurOutEndLine(); m->mothurOutEndLine();
@@ -227,7 +228,7 @@ int main(int argc, char *argv[]){
                                outNewLog.close();
                                
                                m->appendFiles(logFileName, newlogFileName);
-                               remove(logFileName.c_str());
+                               m->mothurRemove(logFileName);
                        }
                }else{  
                        newlogFileName = outputDir + logFileName;