adding mothurout.h and .cpp to repo

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index 5142ca22eabb2d6a3121e6dc2701cb4a04fe9f1f..7cd77a1c2fd8fec087e740a7340f4a74c19ea801 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -10,39 +10,136 @@
 #include "mothur.h"
 #include "engine.hpp"
 #include "globaldata.hpp"
+#include "mothurout.h"
 
-using namespace std;
+/**************************************************************************************************/
 
 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 {
+               
+               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__)
+                               m->mothurOutJustToLog("Mac version");
+                               m->mothurOutEndLine(); m->mothurOutEndLine();
+                       #else
+                               m->mothurOutJustToLog("Linux version");
+                               >m->mothurOutEndLine(); m->mothurOutEndLine();
+                       #endif
+
+               #else
+                       system("CLS");
+                       m->mothurOutJustToLog("Windows version");
+                       m->mothurOutEndLine(); m->mothurOutEndLine();
+               #endif          
+               
+               #ifdef USE_READLINE
+                       m->mothurOutJustToLog("Using ReadLine");
+                       m->mothurOutEndLine(); m->mothurOutEndLine();
+               #endif
+               
+               //header
+               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);
                srand( (unsigned)time( NULL ) );
-
-               Engine* dotur;
+               
+               Engine* mothur;
                bool bail = 0;
+               string input;
 
                if(argc>1){
-                       dotur = new BatchEngine(argv[1]);
+                       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{
-                       dotur = new InteractEngine();           
+                       m->mothurOutJustToLog("Interactive Mode");
+                       m->mothurOutEndLine(); m->mothurOutEndLine();
+                       
+                       mothur = new InteractEngine(argv[0]);   
                }
-
-               while(bail == 0)                {       bail = dotur->getInput();                       }
-       
-               delete dotur;
+               
+               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) {
-               cout << "Standard Error: " << e.what() << " has occurred in the dotur class Function main. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the dotur class function main. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "mothur", "main");
                exit(1);
        }
 }
 
+/**************************************************************************************************/
+