-void SetDirectoryCommand::help(){
- try {
- m->mothurOut("The set.dir command can be used to direct the output files generated by mothur to a specific place, the directory must exist.\n");
- m->mothurOut("The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n");
- m->mothurOut("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");
- m->mothurOut("The set.dir command parameters are input, output and tempdefault and one is required.\n");
- m->mothurOut("To return the output to the same directory as the input files you may enter: output=clear.\n");
- m->mothurOut("To return the input to the current working directory you may enter: input=clear.\n");
- m->mothurOut("To set the output to the directory where mothur.exe is located you may enter: output=default.\n");
- m->mothurOut("To set the input to the directory where mothur.exe is located you may enter: input=default.\n");
- m->mothurOut("To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\n");
- m->mothurOut("To set the tempdefault to the directory where mothur.exe is located you may enter: tempdefault=default.\n");
- m->mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory, tempdefault=yourTempDefault).\n");
- m->mothurOut("Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "SetDirectoryCommand", "help");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-SetDirectoryCommand::~SetDirectoryCommand(){}
-
-//**********************************************************************************************************************
-