try {

CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);

CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);

CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);

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, "GetSAbundCommand", "setParameters");

exit(1);

}

try {

string helpString = "";

helpString += "The get.sabund command parameters is list, rabund and label. list or rabund is required unless a valid current file exists.\n";

helpString += "The label parameter allows you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n";

helpString += "The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n";

helpString += "Example get.sabund().\n";

helpString += "The default value for label is all labels in your inputfile.\n";

helpString += "The get.sabund command outputs a .sabund file containing the labels you selected.\n";

helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";

return helpString;

}

catch(exception& e) {

m->errorOut(e, "GetSAbundCommand", "getHelpString");

exit(1);

}

try {

abort = true; calledHelp = true;

setParameters();

vector<string> tempOutNames;

outputTypes["sabund"] = tempOutNames;

}

catch(exception& e) {

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

exit(1);

}

try {

abort = false; calledHelp = false;

allLines = 1;

//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();

map<string,string>::iterator it;

ValidParameters validParameter;

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

for (it = parameters.begin(); it != parameters.end(); it++) {

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

}

//initialize outputTypes

vector<string> tempOutNames;

outputTypes["sabund"] = tempOutNames;

//if the user changes the input directory command factory will send this info to us in the output parameter

string inputDir = validParameter.validFile(parameters, "inputdir", false);

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

else {

string path;

it = parameters.find("list");

//user has given a template file

if(it != parameters.end()){

path = m->hasPath(it->second);

//if the user has not given a path then, add inputdir. else leave path alone.

if (path == "") { parameters["list"] = inputDir + it->second; }

}

it = parameters.find("rabund");

//user has given a template file

if(it != parameters.end()){

path = m->hasPath(it->second);

//if the user has not given a path then, add inputdir. else leave path alone.

if (path == "") { parameters["rabund"] = inputDir + it->second; }

}

}

//check for required parameters

listfile = validParameter.validFile(parameters, "list", true);

if (listfile == "not open") { listfile = ""; abort = true; }

else if (listfile == "not found") { listfile = ""; }

else { format = "list"; inputfile = listfile; m->setListFile(listfile); }

rabundfile = validParameter.validFile(parameters, "rabund", true);

if (rabundfile == "not open") { rabundfile = ""; abort = true; }

else if (rabundfile == "not found") { rabundfile = ""; }

else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }

//check for optional parameter and set defaults

// ...at some point should added some additional type checking...

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

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

else {

if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }

else { allLines = 1; }

}

if ((listfile == "") && (rabundfile == "")) {

//is there are current file available for any of these?

//give priority to shared, then list, then rabund, then sabund

//if there is a current shared file, use it

listfile = m->getListFile();

if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }

else {

rabundfile = m->getRabundFile();

if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }

else {

m->mothurOut("No valid current files. You must provide a list or rabund file."); m->mothurOutEndLine();

abort = true;

}

}

}

//if the user changes the output directory command factory will send this info to us in the output parameter

outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(inputfile); }

}

}

catch(exception& e) {

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

exit(1);

}

try {

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

filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "sabund";

m->openOutputFile(filename, out);

input = new InputData(inputfile, format);

sabund = input->getSAbundVector();

string lastLabel = sabund->getLabel();

//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.

set<string> processedLabels;

set<string> userLabels = labels;

if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete sabund; delete input; return 0; }

while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {

if(allLines == 1 || labels.count(sabund->getLabel()) == 1){

m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();

sabund->print(out);

if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete sabund; delete input; return 0; }

processedLabels.insert(sabund->getLabel());

userLabels.erase(sabund->getLabel());

}

if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {

string saveLabel = sabund->getLabel();

delete sabund;

sabund = (input->getSAbundVector(lastLabel));

m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();

sabund->print(out);

if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete sabund; delete input; return 0; }

processedLabels.insert(sabund->getLabel());

userLabels.erase(sabund->getLabel());

//restore real lastlabel to save below

sabund->setLabel(saveLabel);

}

lastLabel = sabund->getLabel();

delete sabund;

sabund = (input->getSAbundVector());

}

//output error messages about any remaining user labels

set<string>::iterator it;

bool needToRun = false;

for (it = userLabels.begin(); it != userLabels.end(); it++) {

m->mothurOut("Your file does not include the label " + *it);

if (processedLabels.count(lastLabel) != 1) {

m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();

needToRun = true;

}else {

m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();

}

}

//run last label if you need to

if (needToRun == true) {

if (sabund != NULL) { delete sabund; }

sabund = (input->getSAbundVector(lastLabel));

m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();

sabund->print(out);

delete sabund;

if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete input; return 0; }

}

out.close();

delete input;

m->mothurOutEndLine();

m->mothurOut("Output File Name: "); m->mothurOutEndLine();

m->mothurOut(filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["sabund"].push_back(filename);

m->mothurOutEndLine();

//set sabund file as new current sabundfile

string current = "";

itTypes = outputTypes.find("sabund");

if (itTypes != outputTypes.end()) {

if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }

}

return 0;

}

catch(exception& e) {

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

exit(1);

}