changing command name classify.shared to classifyrf.shared

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index 45be11d8adbb0a74fa5412298e803991f1877fd9..accdb2962c198988c457dc8f837b8817dc2799f0 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -9,14 +9,14 @@
  
 #include "mothur.h"
 #include "engine.hpp"
-#include "globaldata.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 ) {
@@ -46,7 +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");
@@ -57,7 +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 += "\\"; } 
@@ -79,15 +79,16 @@ int main(int argc, char *argv[]){
                m->setVersion(mothurVersion);
                
                //will make the gui output "pretty"
-               bool guiMode = false;
+               bool outputHeader = true;
                if (argc>1) {
                        string guiInput = argv[1];
-                       if (guiInput[0] == '+') { guiMode = true; }
+                       if (guiInput[0] == '+') { outputHeader = false; }
+                       if (guiInput[0] == '-') { outputHeader = false; }
                }
                
-               if (!guiMode) {
+               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();
@@ -162,13 +163,13 @@ int main(int argc, char *argv[]){
                //srand(54321);
                srand( (unsigned)time( NULL ) );
                
-               Engine* mothur;
+               Engine* mothur = NULL;
                bool bail = 0;
                string input;
  
                if(argc>1){
                        input = argv[1];
-                       m->mothurOut("input = " + input); m->mothurOutEndLine();
+                       //m->mothurOut("input = " + input); m->mothurOutEndLine();
 
                        if (input[0] == '#') {
                                m->mothurOutJustToLog("Script Mode");
@@ -178,6 +179,12 @@ int main(int argc, char *argv[]){
                        }else if (input[0] == '+') {
                                        mothur = new ScriptEngine(argv[0], argv[1]);
                                        m->gui = true;
+                       }else if (input == "-version") {
+                               m->mothurOut("Mothur version=" + mothurVersion + "\nRelease Date=" + releaseDate); m->mothurOutEndLine(); m->mothurOutEndLine(); m->closeLog();
+                               #ifdef USE_MPI
+                                       MPI_Finalize();
+                               #endif
+                               return 0;
                        }else{
                                m->mothurOutJustToLog("Batch Mode");
                                m->mothurOutEndLine(); m->mothurOutEndLine();
@@ -215,11 +222,13 @@ int main(int argc, char *argv[]){
                                
                                if (!m->gui) {
                                        outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
+                               }else {
+                                       outNewLog << endl;
                                }
                                outNewLog.close();
                                
                                m->appendFiles(logFileName, newlogFileName);
-                               remove(logFileName.c_str());
+                               m->mothurRemove(logFileName);
                        }
                }else{  
                        newlogFileName = outputDir + logFileName;
@@ -228,7 +237,7 @@ int main(int argc, char *argv[]){
                }
                
                                
-               delete mothur;
+               if (mothur != NULL) { delete mothur; }
                
                #ifdef USE_MPI
                        MPI_Finalize();