+ #else
+ system("CLS");
+ m->mothurOutJustToLog("Windows version");
+ m->mothurOutEndLine(); m->mothurOutEndLine();
+ #endif
+
+ #ifdef USE_READLINE
+ m->mothurOutJustToLog("Using ReadLine");
+ 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 = m->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
+
+ //get releaseDate from Make
+ string releaseDate = RELEASE_DATE;
+ string mothurVersion = VERSION;
+ m->setReleaseDate(releaseDate);
+ m->setVersion(mothurVersion);
+
+ //header
+ m->mothurOut("mothur v." + mothurVersion);
+ m->mothurOutEndLine();
+ m->mothurOut("Last updated: " + releaseDate);
+ 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();
+
+ #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 ) );
+
+ Engine* mothur;
+ bool bail = 0;
+ string input;
+