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 same directory as the mothur.exe you may enter: input=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");
//redirect output
if ((output == "clear") || (output == "")) { output = ""; commandFactory->setOutputDirectory(output); }
- else {
+ else if (output == "default") {
+ GlobalData* globaldata = GlobalData::getInstance();
+ string exepath = globaldata->argv;
+ output = exepath.substr(0, (exepath.find_last_of('m')));
+
+ m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();
+ commandFactory->setOutputDirectory(output);
+ }else {
//add / to name if needed
string lastChar = output.substr(output.length()-1);
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//redirect input
if ((input == "clear") || (input == "")) { input = ""; commandFactory->setInputDirectory(input); }
- else {
+ else if (input == "default") {
+ GlobalData* globaldata = GlobalData::getInstance();
+ string exepath = globaldata->argv;
+ input = exepath.substr(0, (exepath.find_last_of('m')));
+
+ m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();
+ commandFactory->setInputDirectory(input);
+ }else {
//add / to name if needed
string lastChar = input.substr(input.length()-1);
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
m->setDefaultPath(temp);
#endif
}else if (tempdefault == "") { //do nothing
+ }else if (tempdefault == "default") {
+ GlobalData* globaldata = GlobalData::getInstance();
+ string exepath = globaldata->argv;
+ tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
+
+ m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();
+ m->setDefaultPath(tempdefault);
}else {
//add / to name if needed
string lastChar = tempdefault.substr(tempdefault.length()-1);