adding mothurout.h and .cpp to repo

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index 4e064b142d896cb1060d98c9574e42a4355a9efb..7cd77a1c2fd8fec087e740a7340f4a74c19ea801 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -10,69 +10,88 @@
 #include "mothur.h"
 #include "engine.hpp"
 #include "globaldata.hpp"
+#include "mothurout.h"
 
 /**************************************************************************************************/
 
 GlobalData* GlobalData::_uniqueInstance = 0;
+CommandFactory* CommandFactory::_uniqueInstance = 0;
+MothurOut* MothurOut::_uniqueInstance = 0;
 
+/***********************************************************************/
+volatile int ctrlc_pressed = 0;
+void ctrlc_handler ( int sig ) {
+       MothurOut* m = MothurOut::getInstance();
+    ctrlc_pressed = 1;
+       m->control_pressed = ctrlc_pressed;
+}
+/***********************************************************************/
 int main(int argc, char *argv[]){
+       MothurOut* m = MothurOut::getInstance();
        try {
                
-               //remove old logfile
-               string logFileName = "mothur.logFile";
-               remove(logFileName.c_str());
+               signal(SIGINT, ctrlc_handler );
+                               
+               time_t ltime = time(NULL); /* calendar time */  
+               string logFileName = "mothur." + toString(ltime) + ".logfile";
+               
+               m->setFileName(logFileName);
                
                //version
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                        system("clear");
                        #if defined (__APPLE__) || (__MACH__)
-                               mothurOutJustToLog("Mac version");
-                               mothurOutEndLine(); mothurOutEndLine();
+                               m->mothurOutJustToLog("Mac version");
+                               m->mothurOutEndLine(); m->mothurOutEndLine();
                        #else
-                               mothurOutJustToLog("Linux version");
-                               mothurOutEndLine(); mothurOutEndLine();
+                               m->mothurOutJustToLog("Linux version");
+                               >m->mothurOutEndLine(); m->mothurOutEndLine();
                        #endif
 
                #else
                        system("CLS");
-                       mothurOutJustToLog("Windows version");
-                       mothurOutEndLine(); mothurOutEndLine();
+                       m->mothurOutJustToLog("Windows version");
+                       m->mothurOutEndLine(); m->mothurOutEndLine();
                #endif          
-
+               
+               #ifdef USE_READLINE
+                       m->mothurOutJustToLog("Using ReadLine");
+                       m->mothurOutEndLine(); m->mothurOutEndLine();
+               #endif
                
                //header
-               mothurOut("mothur v.1.7.0");
-               mothurOutEndLine();             
-               mothurOut("Last updated: 11/23/2009");
-               mothurOutEndLine();     
-               mothurOutEndLine();             
-               mothurOut("by");
-               mothurOutEndLine();             
-               mothurOut("Patrick D. Schloss");
-               mothurOutEndLine();
-               mothurOutEndLine();                     
-               mothurOut("Department of Microbiology & Immunology");
-               mothurOutEndLine();     
-               mothurOut("University of Michigan");
-               mothurOutEndLine();                     
-               mothurOut("pschloss@umich.edu");
-               mothurOutEndLine();             
-               mothurOut("http://www.mothur.org");
-               mothurOutEndLine();
-               mothurOutEndLine();
-               mothurOut("When using, please cite:");
-               mothurOutEndLine();
-               mothurOut("Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.");
-               mothurOutEndLine();     
-               mothurOutEndLine();             
-               mothurOut("Distributed under the GNU General Public License");
-               mothurOutEndLine();
-               mothurOutEndLine();                     
-               mothurOut("Type 'help()' for information on the commands that are available");
-               mothurOutEndLine();
-               mothurOutEndLine();                     
-               mothurOut("Type 'quit()' to exit program");
-               mothurOutEndLine();     
+               m->mothurOut("mothur v.1.8");
+               m->mothurOutEndLine();          
+               m->mothurOut("Last updated: 2/02/2010");
+               m->mothurOutEndLine();  
+               m->mothurOutEndLine();          
+               m->mothurOut("by");
+               m->mothurOutEndLine();          
+               m->mothurOut("Patrick D. Schloss");
+               m->mothurOutEndLine();
+               m->mothurOutEndLine();                  
+               m->mothurOut("Department of Microbiology & Immunology");
+               m->mothurOutEndLine();  
+               m->mothurOut("University of Michigan");
+               m->mothurOutEndLine();                  
+               m->mothurOut("pschloss@umich.edu");
+               m->mothurOutEndLine();          
+               m->mothurOut("http://www.mothur.org");
+               m->mothurOutEndLine();
+               m->mothurOutEndLine();
+               m->mothurOut("When using, please cite:");
+               m->mothurOutEndLine();
+               m->mothurOut("Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.");
+               m->mothurOutEndLine();  
+               m->mothurOutEndLine();          
+               m->mothurOut("Distributed under the GNU General Public License");
+               m->mothurOutEndLine();
+               m->mothurOutEndLine();                  
+               m->mothurOut("Type 'help()' for information on the commands that are available");
+               m->mothurOutEndLine();
+               m->mothurOutEndLine();                  
+               m->mothurOut("Type 'quit()' to exit program");
+               m->mothurOutEndLine();  
 
                                
                //srand(54321);
@@ -86,30 +105,38 @@ int main(int argc, char *argv[]){
                        input = argv[1];
 
                        if (input[0] == '#') {
+                               m->mothurOutJustToLog("Script Mode");
+                               m->mothurOutEndLine(); m->mothurOutEndLine();
+
                                mothur = new ScriptEngine(argv[0], argv[1]);
                        }else{
+                               m->mothurOutJustToLog("Batch Mode");
+                               m->mothurOutEndLine(); m->mothurOutEndLine();
+                               
                                mothur = new BatchEngine(argv[0], argv[1]);
                        }
                }
                else{
+                       m->mothurOutJustToLog("Interactive Mode");
+                       m->mothurOutEndLine(); m->mothurOutEndLine();
+                       
                        mothur = new InteractEngine(argv[0]);   
                }
                
-               //used to intercept the terminate signal, so instead of terminating mothur it will end a command
-               //void (*prev_fn)(int);
-               //prev_fn = signal(SIGTERM, mothur->terminateCommand(0));
-               
-               //if (prev_fn==SIG_IGN) signal (SIGTERM,SIG_IGN);
-
-               
                while(bail == 0)                {       bail = mothur->getInput();                      }
+               
+               string outputDir = mothur->getOutputDir();
+               string newlogFileName = outputDir + logFileName;
        
+               //need this because m->mothurOut makes the logfile, but doesn't know where to put it
+               rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
+               
                delete mothur;
-       
+
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "mothur", "main");
+               m->errorOut(e, "mothur", "main");
                exit(1);
        }
 }