helpString += "To set the tempdefault to the directory where mothur.exe is located you may enter: tempdefault=default.\n";
helpString += "The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory, tempdefault=yourTempDefault).\n";
helpString += "Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n";
- helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n";
return helpString;
}
catch(exception& e) {
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"output","input","tempdefault","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
commandFactory = CommandFactory::getInstance();
+ m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();
+
//redirect output
if ((output == "clear") || (output == "")) { output = ""; commandFactory->setOutputDirectory(output); }
else if (output == "default") {
string exepath = m->argv;
output = exepath.substr(0, (exepath.find_last_of('m')));
- m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();
+ m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
commandFactory->setOutputDirectory(output);
}else {
//add / to name if needed
}else{
out.close();
remove(outTemp.c_str());
- m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();
+ m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
commandFactory->setOutputDirectory(output);
}
}
string exepath = m->argv;
input = exepath.substr(0, (exepath.find_last_of('m')));
- m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();
+ m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
commandFactory->setInputDirectory(input);
}else {
//add / to name if needed
}else{
in.close();
remove(inTemp.c_str());
- m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();
+ m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
commandFactory->setInputDirectory(input);
}
}
if (tempdefault == "clear") {
#ifdef MOTHUR_FILES
string temp = MOTHUR_FILES;
- m->mothurOut("Resetting default directory to " + temp); m->mothurOutEndLine();
+ m->mothurOut("tempDefault=" + temp); m->mothurOutEndLine();
m->setDefaultPath(temp);
#else
string temp = "";
string exepath = m->argv;
tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
- m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();
+ m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
m->setDefaultPath(tempdefault);
}else {
//add / to name if needed
if (lastChar != "\\") { tempdefault += "\\"; }
#endif
- m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();
+ m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
m->setDefaultPath(tempdefault);
}