+//**********************************************************************************************************************
+vector<string> SetDirectoryCommand::setParameters(){
+ try {
+ CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "",false,false); parameters.push_back(ptempdefault);
+ CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pdebug);
+ CommandParameter pinput("input", "String", "", "", "", "", "",false,false); parameters.push_back(pinput);
+ CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SetDirectoryCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SetDirectoryCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The set.dir command can be used to direct the output files generated by mothur to a specific place, the directory must exist.\n";
+ helpString += "The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n";
+ helpString += "The set.dir command can also be used to override or set the default location mothur will look for files if it is unable to find them, the directory must exist.\n";
+ helpString += "The set.dir command can also be used to run mothur in debug mode.\n";
+ helpString += "The set.dir command parameters are input, output, tempdefault and debug and one is required.\n";
+ helpString += "To run mothur in debug mode set debug=true. Default debug=false.\n";
+ helpString += "To return the output to the same directory as the input files you may enter: output=clear.\n";
+ helpString += "To return the input to the current working directory you may enter: input=clear.\n";
+ helpString += "To set the output to the directory where mothur.exe is located you may enter: output=default.\n";
+ helpString += "To set the input to the directory where mothur.exe is located you may enter: input=default.\n";
+ helpString += "To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\n";
+ 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";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SetDirectoryCommand", "getHelpString");
+ exit(1);
+ }
+}