fixed splash page citation

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index 8d0e507a8f35bc7d9ee8664765194c546d736c1b..1c0c98f9f1caf4cec5de25f4c66ce7f9a3a3af8f 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -17,14 +17,79 @@ GlobalData* GlobalData::_uniqueInstance = 0;
 
 int main(int argc, char *argv[]){
        try {
+               
+               //remove old logfile
+               string logFileName = "mothur.logFile";
+               remove(logFileName.c_str());
+               
+               //version
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       system("clear");
+                       #if defined (__APPLE__) || (__MACH__)
+                               mothurOutJustToLog("Mac version");
+                               mothurOutEndLine(); mothurOutEndLine();
+                       #else
+                               mothurOutJustToLog("Linux version");
+                               mothurOutEndLine(); mothurOutEndLine();
+                       #endif
+
+               #else
+                       system("CLS");
+                       mothurOutJustToLog("Windows version");
+                       mothurOutEndLine(); 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();     
+
+                               
                //srand(54321);
                srand( (unsigned)time( NULL ) );
 
                Engine* mothur;
                bool bail = 0;
+               string input;
 
                if(argc>1){
-                       mothur = new BatchEngine(argv[0], argv[1]);
+                       input = argv[1];
+
+                       if (input[0] == '#') {
+                               mothur = new ScriptEngine(argv[0], argv[1]);
+                       }else{
+                               mothur = new BatchEngine(argv[0], argv[1]);
+                       }
                }
                else{
                        mothur = new InteractEngine(argv[0]);           
@@ -37,11 +102,7 @@ int main(int argc, char *argv[]){
                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";
+               errorOut(e, "mothur", "main");
                exit(1);
        }
 }