1.12.1

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index a3eef76a2766d5ae69c824b0ee4cf4b5e3f14a51..c413cedeef8dac80a552349a48129dfb54d50a1d 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -42,8 +42,13 @@ int main(int argc, char *argv[]){
                time_t ltime = time(NULL); /* calendar time */  
                string logFileName = "mothur." + toString(ltime) + ".logfile";
                
+               #ifdef USE_MPI
+                       MPI_Init(&argc, &argv); 
+               #endif
+
                m->setFileName(logFileName);
                
+                               
                //version
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                        system("clear");
@@ -52,7 +57,7 @@ int main(int argc, char *argv[]){
                                m->mothurOutEndLine(); m->mothurOutEndLine();
                        #else
                                m->mothurOutJustToLog("Linux version");
-                               >m->mothurOutEndLine(); m->mothurOutEndLine();
+                               m->mothurOutEndLine(); m->mothurOutEndLine();
                        #endif
 
                #else
@@ -66,10 +71,36 @@ int main(int argc, char *argv[]){
                        m->mothurOutEndLine(); m->mothurOutEndLine();
                #endif
                
+               #ifdef MOTHUR_FILES
+                       string temp = MOTHUR_FILES; 
+                       
+                       //add / to name if needed
+                       string lastChar = temp.substr(temp.length()-1);
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                               if (lastChar != "/") { temp += "/"; }
+                       #else
+                               if (lastChar != "\\") { temp += "\\"; } 
+                       #endif
+                       
+                       temp = getFullPathName(temp);
+                       m->setDefaultPath(temp);
+                       
+                       m->mothurOutJustToLog("Using default file location " + temp);
+                       m->mothurOutEndLine(); m->mothurOutEndLine();
+               #endif
+               
+               #ifdef BIT_VERSION
+                       m->mothurOutJustToLog("Running 64Bit Version");
+                       m->mothurOutEndLine(); m->mothurOutEndLine();
+               #else
+                       m->mothurOutJustToLog("Running 32Bit Version");
+                       m->mothurOutEndLine(); m->mothurOutEndLine();
+               #endif
+               
                //header
-               m->mothurOut("mothur v.1.8");
+               m->mothurOut("mothur v.1.12.1");
                m->mothurOutEndLine();          
-               m->mothurOut("Last updated: 2/02/2010");
+               m->mothurOut("Last updated: 7/29/2010");
                m->mothurOutEndLine();  
                m->mothurOutEndLine();          
                m->mothurOut("by");
@@ -99,8 +130,14 @@ int main(int argc, char *argv[]){
                m->mothurOutEndLine();                  
                m->mothurOut("Type 'quit()' to exit program");
                m->mothurOutEndLine();  
-
-                               
+               
+               #ifdef USE_MPI
+                       m->mothurOutJustToLog("Using MPI\tversion ");
+                       int version, subversion;
+                       MPI_Get_version(&version, &subversion);
+                       m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
+               #endif
+               
                //srand(54321);
                srand( (unsigned)time( NULL ) );
                
@@ -130,16 +167,45 @@ int main(int argc, char *argv[]){
                        mothur = new InteractEngine(argv[0]);   
                }
                
-               while(bail == 0)                {       bail = mothur->getInput();                      }
+               while(bail == 0)        {       bail = mothur->getInput();      }
+               
+               //closes logfile so we can rename
+               m->closeLog();
                
                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
+               string tempLog = mothur->getLogFileName();
+               bool append = mothur->getAppend();
                
-               delete mothur;
+               string newlogFileName;
+               if (tempLog != "") {
+                       newlogFileName = outputDir + tempLog;
+                       
+                       if (!append) {  
+                               //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
 
+                       }else {
+                               ofstream outNewLog;
+                               openOutputFileAppend(newlogFileName, outNewLog);
+                               outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
+                               outNewLog.close();
+                               
+                               appendFiles(logFileName, newlogFileName);
+                               remove(logFileName.c_str());
+                       }
+               }else{  
+                       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;
+               
+               #ifdef USE_MPI
+                       MPI_Finalize();
+               #endif
+               
                return 0;
        }
        catch(exception& e) {