m->setFileName(logFileName);
-
- //version
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
system("clear");
- #if defined (__APPLE__) || (__MACH__)
- m->mothurOutJustToLog("Mac version");
- m->mothurOutEndLine(); m->mothurOutEndLine();
- #else
- m->mothurOutJustToLog("Linux version");
- m->mothurOutEndLine(); m->mothurOutEndLine();
- #endif
-
#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)
#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();
+ #ifdef USE_MPI
+ int version, subversion;
+ MPI_Get_version(&version, &subversion);
#endif
//get releaseDate from Make
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();
+ //will make the gui output "pretty"
+ bool guiMode = false;
+ if (argc>1) {
+ string guiInput = argv[1];
+ if (guiInput[0] == '+') { guiMode = true; }
+ }
- #ifdef USE_MPI
- m->mothurOutJustToLog("Using MPI\tversion ");
- int version, subversion;
- MPI_Get_version(&version, &subversion);
- m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
- #endif
+ if (!guiMode) {
+ //version
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__)
+ m->mothurOutJustToLog("Mac version");
+ m->mothurOutEndLine(); m->mothurOutEndLine();
+ #else
+ m->mothurOutJustToLog("Linux version");
+ m->mothurOutEndLine(); m->mothurOutEndLine();
+ #endif
+
+ #else
+ m->mothurOutJustToLog("Windows version");
+ m->mothurOutEndLine(); m->mothurOutEndLine();
+ #endif
+
+ #ifdef USE_READLINE
+ m->mothurOutJustToLog("Using ReadLine");
+ m->mothurOutEndLine(); m->mothurOutEndLine();
+ #endif
+
+ #ifdef MOTHUR_FILES
+ 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." + 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 ");
+ m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
+ #endif
+ }
//srand(54321);
srand( (unsigned)time( NULL ) );
if(argc>1){
input = argv[1];
+ //m->mothurOut("input = " + input); m->mothurOutEndLine();
if (input[0] == '#') {
m->mothurOutJustToLog("Script Mode");
m->mothurOutEndLine(); m->mothurOutEndLine();
mothur = new ScriptEngine(argv[0], argv[1]);
+ }else if (input[0] == '+') {
+ mothur = new ScriptEngine(argv[0], argv[1]);
+ m->gui = true;
}else{
m->mothurOutJustToLog("Batch Mode");
m->mothurOutEndLine(); m->mothurOutEndLine();
}else {
ofstream outNewLog;
m->openOutputFileAppend(newlogFileName, outNewLog);
- outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
+
+ if (!m->gui) {
+ outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
+ }
outNewLog.close();
m->appendFiles(logFileName, newlogFileName);