created mothurOut class to handle logfiles

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index 7acf3894e150f24a8eaaa5bc72f0e752bab4ecc6..ba058ba3fde6d2dd2d25458f88be358f1c7c0408 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -10,76 +10,81 @@
 #include "mothur.h"
 #include "engine.hpp"
 #include "globaldata.hpp"
+#include "mothurout.h"
 
 /**************************************************************************************************/
 
 GlobalData* GlobalData::_uniqueInstance = 0;
 CommandFactory* CommandFactory::_uniqueInstance = 0;
+MothurOut* MothurOut::_uniqueInstance = 0;
 
 int main(int argc, char *argv[]){
+       MothurOut* m = MothurOut::getInstance();
        try {
                
-               string log = "mothur.logFile";
-               remove(log.c_str());
+               //string log = "mothur.logFile";
+               //remove(log.c_str());
                
                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
-                       mothurOutJustToLog("Using ReadLine");
-                       mothurOutEndLine(); mothurOutEndLine();
+                       m->mothurOutJustToLog("Using ReadLine");
+                       m->mothurOutEndLine(); m->mothurOutEndLine();
                #endif
                
                //header
-               mothurOut("mothur v.1.8");
-               mothurOutEndLine();             
-               mothurOut("Last updated: 2/02/2010");
-               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);
@@ -93,20 +98,20 @@ int main(int argc, char *argv[]){
                        input = argv[1];
 
                        if (input[0] == '#') {
-                               mothurOutJustToLog("Script Mode");
-                               mothurOutEndLine(); mothurOutEndLine();
+                               m->mothurOutJustToLog("Script Mode");
+                               m->mothurOutEndLine(); m->mothurOutEndLine();
 
                                mothur = new ScriptEngine(argv[0], argv[1]);
                        }else{
-                               mothurOutJustToLog("Batch Mode");
-                               mothurOutEndLine(); mothurOutEndLine();
+                               m->mothurOutJustToLog("Batch Mode");
+                               m->mothurOutEndLine(); m->mothurOutEndLine();
                                
                                mothur = new BatchEngine(argv[0], argv[1]);
                        }
                }
                else{
-                       mothurOutJustToLog("Interactive Mode");
-                       mothurOutEndLine(); mothurOutEndLine();
+                       m->mothurOutJustToLog("Interactive Mode");
+                       m->mothurOutEndLine(); m->mothurOutEndLine();
                        
                        mothur = new InteractEngine(argv[0]);   
                }
@@ -114,17 +119,17 @@ int main(int argc, char *argv[]){
                while(bail == 0)                {       bail = mothur->getInput();                      }
                
                string outputDir = mothur->getOutputDir();
-               logFileName = outputDir + logFileName;
+               string newlogFileName = outputDir + logFileName;
        
-               //need this because mothur.h makes the logfile, but doesn't know where to put it
-               rename(log.c_str(), logFileName.c_str()); //logfile with timestamp
+               //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);
        }
 }