try {

CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);

CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);

CommandParameter pscale("scale", "Multiple", "totalgroup-totalotu-averagegroup-averageotu", "totalgroup", "", "", "",false,false); parameters.push_back(pscale);

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, "GetRelAbundCommand", "setParameters");

exit(1);

}

try {

string helpString = "";

helpString += "The get.relabund command parameters are shared, groups, scale and label. shared is required, unless you have a valid current file.\n";

helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n";

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

helpString += "The scale parameter allows you to select what scale you would like to use. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.\n";

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

helpString += "Example get.relabund(groups=A-B-C, scale=averagegroup).\n";

helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";

helpString += "The get.relabund command outputs a .relabund file.\n";

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

return helpString;

}

catch(exception& e) {

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

exit(1);

}

try {

abort = true; calledHelp = true;

setParameters();

vector<string> tempOutNames;

outputTypes["relabund"] = tempOutNames;

}

catch(exception& e) {

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

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["relabund"] = 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("shared");

//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["shared"] = inputDir + it->second; }

}

}

//get shared file

sharedfile = validParameter.validFile(parameters, "shared", true);

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

else if (sharedfile == "not found") {

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

sharedfile = m->getSharedFile();

if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }

else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }

}else { m->setSharedFile(sharedfile); }

//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(sharedfile); }

//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; }

}

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

if (groups == "not found") { groups = ""; pickedGroups = false; }

else {

pickedGroups = true;

m->splitAtDash(groups, Groups);

m->setGroups(Groups);

}

scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "totalgroup"; }

if ((scale != "totalgroup") && (scale != "totalotu") && (scale != "averagegroup") && (scale != "averageotu")) {

m->mothurOut(scale + " is not a valid scaling option for the get.relabund command. Choices are totalgroup, totalotu, averagegroup, averageotu."); m->mothurOutEndLine(); abort = true;

}

}

}

catch(exception& e) {

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

exit(1);

}

try {

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

string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "relabund";

ofstream out;

m->openOutputFile(outputFileName, out);

out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);

input = new InputData(sharedfile, "sharedfile");

lookup = input->getSharedRAbundVectors();

string lastLabel = lookup[0]->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;

//as long as you are not at the end of the file or done wih the lines you want

while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {

if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }

if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){

m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();

if (!m->printedHeaders) { lookup[0]->printHeaders(out); }

getRelAbundance(lookup, out);

processedLabels.insert(lookup[0]->getLabel());

userLabels.erase(lookup[0]->getLabel());

}

if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {

string saveLabel = lookup[0]->getLabel();

for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }

lookup = input->getSharedRAbundVectors(lastLabel);

m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();

if (!m->printedHeaders) { lookup[0]->printHeaders(out); }

getRelAbundance(lookup, out);

processedLabels.insert(lookup[0]->getLabel());

userLabels.erase(lookup[0]->getLabel());

//restore real lastlabel to save below

lookup[0]->setLabel(saveLabel);

}

lastLabel = lookup[0]->getLabel();

//prevent memory leak

for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }

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

//get next line to process

lookup = input->getSharedRAbundVectors();

}

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

//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) {

for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }

lookup = input->getSharedRAbundVectors(lastLabel);

m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();

if (!m->printedHeaders) { lookup[0]->printHeaders(out); }

getRelAbundance(lookup, out);

for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }

}

//reset groups parameter

m->clearGroups();

delete input;

out.close();

if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0;}

m->mothurOutEndLine();

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

m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["relabund"].push_back(outputFileName);

m->mothurOutEndLine();

//set relabund file as new current relabundfile

string current = "";

itTypes = outputTypes.find("relabund");

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

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

}

return 0;

}

catch(exception& e) {

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

exit(1);

}

try {

for (int i = 0; i < thisLookUp.size(); i++) {

out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t' << thisLookUp[i]->getNumBins() << '\t';

for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) {

if (m->control_pressed) { return 0; }

int abund = thisLookUp[i]->getAbundance(j);

float relabund = 0.0;

if (scale == "totalgroup") {

relabund = abund / (float) thisLookUp[i]->getNumSeqs();

}else if (scale == "totalotu") {

//calc the total in this otu

int totalOtu = 0;

for (int l = 0; l < thisLookUp.size(); l++) { totalOtu += thisLookUp[l]->getAbundance(j); }

relabund = abund / (float) totalOtu;

}else if (scale == "averagegroup") {

relabund = abund / (float) (thisLookUp[i]->getNumSeqs() / (float) thisLookUp[i]->getNumBins());

}else if (scale == "averageotu") {

//calc the total in this otu

int totalOtu = 0;

for (int l = 0; l < thisLookUp.size(); l++) { totalOtu += thisLookUp[l]->getAbundance(j); }

float averageOtu = totalOtu / (float) thisLookUp.size();

relabund = abund / (float) averageOtu;

}else{ m->mothurOut(scale + " is not a valid scaling option."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }

out << relabund << '\t';

}

out << endl;

}

return 0;

}

catch(exception& e) {

m->errorOut(e, "GetRelAbundCommand", "getRelAbundance");

exit(1);

}