added distance search method to classify.seqs

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index 46189271b470a5b58562a66438db48372214720b..bd7ab728c76d311ffe0dc7dcc052a026cfa6e741 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -14,13 +14,16 @@
 /**************************************************************************************************/
 
 GlobalData* GlobalData::_uniqueInstance = 0;
+CommandFactory* CommandFactory::_uniqueInstance = 0;
 
 int main(int argc, char *argv[]){
        try {
                
-               //remove old logfile
-               string logFileName = "mothur.logFile";
-               remove(logFileName.c_str());
+               string log = "mothur.logFile";
+               remove(log.c_str());
+               
+               time_t ltime = time(NULL); /* calendar time */  
+               string logFileName = "mothur." + toString(ltime) + ".logfile";
                
                //version
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
@@ -41,9 +44,9 @@ int main(int argc, char *argv[]){
 
                
                //header
-               mothurOut("mothur v.1.6.0");
+               mothurOut("mothur v.1.7.2");
                mothurOutEndLine();             
-               mothurOut("Last updated: 10/6/2009");
+               mothurOut("Last updated: 12/04/2009");
                mothurOutEndLine();     
                mothurOutEndLine();             
                mothurOut("by");
@@ -58,7 +61,11 @@ int main(int argc, char *argv[]){
                mothurOut("pschloss@umich.edu");
                mothurOutEndLine();             
                mothurOut("http://www.mothur.org");
-               mothurOutEndLine();     
+               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");
@@ -73,7 +80,7 @@ int main(int argc, char *argv[]){
                                
                //srand(54321);
                srand( (unsigned)time( NULL ) );
-
+               
                Engine* mothur;
                bool bail = 0;
                string input;
@@ -88,13 +95,19 @@ int main(int argc, char *argv[]){
                        }
                }
                else{
-                       mothur = new InteractEngine(argv[0]);           
+                       mothur = new InteractEngine(argv[0]);   
                }
-
+               
                while(bail == 0)                {       bail = mothur->getInput();                      }
+               
+               string outputDir = mothur->getOutputDir();
+               logFileName = 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
+               
                delete mothur;
-       
+
                return 0;
        }
        catch(exception& e) {