try {

CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "",false,false); parameters.push_back(ptempdefault);

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);

}

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 parameters are input, output and tempdefault and one is required.\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);

}

try {

abort = false; calledHelp = false;

//allow user to run help

if(option == "help") { help(); abort = true; calledHelp = true; }

else if(option == "citation") { citation(); abort = true; calledHelp = true;}

else {

vector<string> myArray = setParameters();

OptionParser parser(option);

map<string, string> parameters = parser.getParameters();

ValidParameters validParameter;

//check to make sure all parameters are valid for command

for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {

if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }

}

output = validParameter.validFile(parameters, "output", false);

if (output == "not found") { output = ""; }

input = validParameter.validFile(parameters, "input", false);

if (input == "not found") { input = ""; }

tempdefault = validParameter.validFile(parameters, "tempdefault", false);

if (tempdefault == "not found") { tempdefault = ""; }

if ((input == "") && (output == "") && (tempdefault == "")) {

m->mothurOut("You must provide either an input, output or tempdefault for the set.outdir command."); m->mothurOutEndLine(); abort = true;

}

}

}

catch(exception& e) {

m->errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");

exit(1);

}

try {

if (abort == true) { if (calledHelp) { return 0; } return 2; }

commandFactory = CommandFactory::getInstance();

string tag = "";

#ifdef USE_MPI

int pid;

MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are

tag = toString(pid);

#endif

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("outputDir=" + 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)

if (lastChar != "/") { output += "/"; }

#else

if (lastChar != "\\") { output += "\\"; }

#endif

//test to make sure directory exists

output = m->getFullPathName(output);

string outTemp = output + tag + "temp";

ofstream out;

out.open(outTemp.c_str(), ios::trunc);

if(!out) {

m->mothurOut(output + " directory does not exist or is not writable."); m->mothurOutEndLine();

}else{

out.close();

m->mothurRemove(outTemp);

m->mothurOut("outputDir=" + output); m->mothurOutEndLine();

commandFactory->setOutputDirectory(output);

}

}

//redirect input

if ((input == "clear") || (input == "")) { input = ""; commandFactory->setInputDirectory(input); }

else if (input == "default") {

string exepath = m->argv;

input = exepath.substr(0, (exepath.find_last_of('m')));

m->mothurOut("inputDir=" + 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)

if (lastChar != "/") { input += "/"; }

#else

if (lastChar != "\\") { input += "\\"; }

#endif

//test to make sure directory exists

input = m->getFullPathName(input);

string inTemp = input + tag + "temp";

ofstream in;

in.open(inTemp.c_str(), ios::trunc);

if(!in) {

m->mothurOut(input + " directory does not exist or is not writable."); m->mothurOutEndLine();

}else{

in.close();

m->mothurRemove(inTemp);

m->mothurOut("inputDir=" + input); m->mothurOutEndLine();

commandFactory->setInputDirectory(input);

}

}

//set default

if (tempdefault == "clear") {

#ifdef MOTHUR_FILES

string temp = MOTHUR_FILES;

m->mothurOut("tempDefault=" + temp); m->mothurOutEndLine();

m->setDefaultPath(temp);

#else

string temp = "";

m->mothurOut("No default directory defined at compile time."); m->mothurOutEndLine();

m->setDefaultPath(temp);

#endif

}else if (tempdefault == "") { //do nothing

}else if (tempdefault == "default") {

string exepath = m->argv;

tempdefault = exepath.substr(0, (exepath.find_last_of('m')));

m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();

m->setDefaultPath(tempdefault);

}else {

//add / to name if needed

string lastChar = tempdefault.substr(tempdefault.length()-1);

#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)

if (lastChar != "/") { tempdefault += "/"; }

#else

if (lastChar != "\\") { tempdefault += "\\"; }

#endif

//test to make sure directory exists

tempdefault = m->getFullPathName(tempdefault);

string inTemp = tempdefault + tag + "temp";

ofstream in;

in.open(inTemp.c_str(), ios::trunc);

if(!in) {

m->mothurOut(tempdefault + " directory does not exist or is not writable."); m->mothurOutEndLine();

}else{

in.close();

m->mothurRemove(inTemp);

m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();

m->setDefaultPath(tempdefault);

}

}

return 0;

}

catch(exception& e) {

m->errorOut(e, "SetDirectoryCommand", "execute");

exit(1);

}