try {

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

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

CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psabund);

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

CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);

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

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

CommandParameter pnseqs("nseqs", "Number", "", "0", "", "", "",false,true); parameters.push_back(pnseqs);

CommandParameter pbygroup("bygroup", "Boolean", "", "f", "", "", "",false,true); parameters.push_back(pbygroup);

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, "RemoveRareCommand", "setParameters");

exit(1);

}

try {

string helpString = "";

helpString += "The remove.rare command parameters are list, rabund, sabund, shared, group, label, groups, bygroup and nseqs.\n";

helpString += "The remove.rare command reads one of the following file types: list, rabund, sabund or shared file. It outputs a new file after removing the rare otus.\n";

helpString += "The groups parameter allows you to specify which of the groups you would like analyzed. Default=all. You may separate group names with dashes.\n";

helpString += "The label parameter is used to analyze specific labels in your input. default=all. You may separate label names with dashes.\n";

helpString += "The bygroup parameter is only valid with the shared file. default=f, meaning remove any OTU that has nseqs or fewer sequences across all groups.\n";

helpString += "bygroups=T means remove any OTU that has nseqs or fewer sequences in each group (if groupA has 1 sequence and group B has 100 sequences in OTUZ and nseqs=1, then set the groupA count for OTUZ to 0 and keep groupB's count at 100.) \n";

helpString += "The nseqs parameter allows you to set the cutoff for an otu to be deemed rare. It is required.\n";

helpString += "The remove.rare command should be in the following format: remove.rare(shared=yourSharedFile, nseqs=yourRareCutoff).\n";

helpString += "Example remove.rare(shared=amazon.fn.shared, nseqs=2).\n";

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

return helpString;

}

catch(exception& e) {

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

exit(1);

}

try {

abort = true; calledHelp = true;

setParameters();

vector<string> tempOutNames;

outputTypes["rabund"] = tempOutNames;

outputTypes["sabund"] = tempOutNames;

outputTypes["list"] = tempOutNames;

outputTypes["group"] = tempOutNames;

outputTypes["shared"] = tempOutNames;

}

catch(exception& e) {

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

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();

ValidParameters validParameter;

map<string,string>::iterator it;

//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["rabund"] = tempOutNames;

outputTypes["sabund"] = tempOutNames;

outputTypes["list"] = tempOutNames;

outputTypes["group"] = tempOutNames;

outputTypes["shared"] = tempOutNames;

//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 = ""; }

//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("group");

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

}

it = parameters.find("sabund");

//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["sabund"] = 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; }

}

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; }

}

}

//check for file parameters

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

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

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

else { m->setListFile(listfile); }

sabundfile = validParameter.validFile(parameters, "sabund", true);

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

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

else { m->setSabundFile(sabundfile); }

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

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

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

else { m->setRabundFile(rabundfile); }

groupfile = validParameter.validFile(parameters, "group", true);

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

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

else { m->setGroupFile(groupfile); }

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

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

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

else { m->setSharedFile(sharedfile); }

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

//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

sharedfile = m->getSharedFile();

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

else {

listfile = m->getListFile();

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

else {

rabundfile = m->getRabundFile();

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

else {

sabundfile = m->getSabundFile();

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

else {

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

abort = true;

}

}

}

}

}

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

if (groups == "not found") { groups = "all"; }

m->splitAtDash(groups, Groups);

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

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

else {

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

else { allLines = 1; }

}

string temp = validParameter.validFile(parameters, "nseqs", false);

if (temp == "not found") { m->mothurOut("nseqs is a required parameter."); m->mothurOutEndLine(); abort = true; }

else { m->mothurConvert(temp, nseqs); }

temp = validParameter.validFile(parameters, "bygroup", false); if (temp == "not found") { temp = "f"; }

byGroup = m->isTrue(temp);

if (byGroup && (sharedfile == "")) { m->mothurOut("The byGroup parameter is only valid with a shared file."); m->mothurOutEndLine(); }

if ((groupfile != "") && (listfile == "")) { m->mothurOut("A groupfile is only valid with a list file."); m->mothurOutEndLine(); groupfile = ""; }

}

}

catch(exception& e) {

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

exit(1);

}

try {

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

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

//read through the correct file and output lines you want to keep

if (sabundfile != "") { processSabund(); }

if (rabundfile != "") { processRabund(); }

if (listfile != "") { processList(); }

if (sharedfile != "") { processShared(); }

if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }

if (outputNames.size() != 0) {

m->mothurOutEndLine();

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

for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }

m->mothurOutEndLine();

//set rabund file as new current rabundfile

string current = "";

itTypes = outputTypes.find("rabund");

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

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

}

itTypes = outputTypes.find("sabund");

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

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

}

itTypes = outputTypes.find("group");

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

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

}

itTypes = outputTypes.find("list");

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

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

}

itTypes = outputTypes.find("shared");

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

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

}

}

return 0;

}

catch(exception& e) {

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

exit(1);

}

try {

string thisOutputDir = outputDir;

if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }

string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);

string outputGroupFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);

ofstream out, outGroup;

m->openOutputFile(outputFileName, out);

bool wroteSomething = false;

//you must provide a label because the names in the listfile need to be consistent

string thisLabel = "";

if (allLines) { m->mothurOut("For the listfile you must select one label, using first label in your listfile."); m->mothurOutEndLine(); }

else if (labels.size() > 1) { m->mothurOut("For the listfile you must select one label, using " + (*labels.begin()) + "."); m->mothurOutEndLine(); thisLabel = *labels.begin(); }

else { thisLabel = *labels.begin(); }

InputData input(listfile, "list");

ListVector* list = input.getListVector();

//get first one or the one we want

if (thisLabel != "") {

//use smart distancing

set<string> userLabels; userLabels.insert(thisLabel);

set<string> processedLabels;

string lastLabel = list->getLabel();

while((list != NULL) && (userLabels.size() != 0)) {

if(userLabels.count(list->getLabel()) == 1){

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

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

break;

}

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

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

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

delete list;

list = input.getListVector(lastLabel);

break;

}

lastLabel = list->getLabel();

delete list;

list = input.getListVector();

}

if (userLabels.size() != 0) {

m->mothurOut("Your file does not include the label " + thisLabel + ". I will use " + lastLabel + "."); m->mothurOutEndLine();

list = input.getListVector(lastLabel);

}

}

//if groupfile is given then use it

GroupMap* groupMap;

if (groupfile != "") {

groupMap = new GroupMap(groupfile); groupMap->readMap();

SharedUtil util;

vector<string> namesGroups = groupMap->getNamesOfGroups();

util.setGroups(Groups, namesGroups);

m->openOutputFile(outputGroupFileName, outGroup);

}

if (list != NULL) {

//make a new list vector

ListVector newList;

newList.setLabel(list->getLabel());

//for each bin

for (int i = 0; i < list->getNumBins(); i++) {

if (m->control_pressed) { if (groupfile != "") { delete groupMap; outGroup.close(); m->mothurRemove(outputGroupFileName); } out.close(); m->mothurRemove(outputFileName); return 0; }

//parse out names that are in accnos file

string binnames = list->get(i);

vector<string> names;

string saveBinNames = binnames;

m->splitAtComma(binnames, names);

vector<string> newGroupFile;

if (groupfile != "") {

vector<string> newNames;

saveBinNames = "";

for(int k = 0; k < names.size(); k++) {

string group = groupMap->getGroup(names[k]);

if (m->inUsersGroups(group, Groups)) {

newGroupFile.push_back(names[k] + "\t" + group);

newNames.push_back(names[k]);

saveBinNames += names[k] + ",";

}

}

names = newNames;

saveBinNames = saveBinNames.substr(0, saveBinNames.length()-1);

}

if (names.size() > nseqs) { //keep bin

newList.push_back(saveBinNames);

for(int k = 0; k < newGroupFile.size(); k++) { outGroup << newGroupFile[k] << endl; }

}

}

//print new listvector

if (newList.getNumBins() != 0) {

wroteSomething = true;

newList.print(out);

}

}

out.close();

if (groupfile != "") { outGroup.close(); outputTypes["group"].push_back(outputGroupFileName); outputNames.push_back(outputGroupFileName); }

if (wroteSomething == false) { m->mothurOut("Your file contains only rare sequences."); m->mothurOutEndLine(); }

outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);

return 0;

}

catch(exception& e) {

m->errorOut(e, "RemoveRareCommand", "processList");

exit(1);

}

try {

string thisOutputDir = outputDir;

if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); }

string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "pick" + m->getExtension(sabundfile);

outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName);

ofstream out;

m->openOutputFile(outputFileName, out);

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

InputData input(sabundfile, "sabund");

SAbundVector* sabund = input.getSAbundVector();

string lastLabel = sabund->getLabel();

set<string> processedLabels;

set<string> userLabels = labels;

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

if (m->control_pressed) { delete sabund; out.close(); return 0; }

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

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

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

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

if (sabund->getMaxRank() > nseqs) {

for(int i = 1; i <=nseqs; i++) { sabund->set(i, 0); }

}else { sabund->clear(); }

if (sabund->getNumBins() > 0) { sabund->print(out); }

}

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();

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

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

if (sabund->getMaxRank() > nseqs) {

for(int i = 1; i <=nseqs; i++) { sabund->set(i, 0); }

}else { sabund->clear(); }

if (sabund->getNumBins() > 0) { sabund->print(out); }

//restore real lastlabel to save below

sabund->setLabel(saveLabel);

}

lastLabel = sabund->getLabel();

delete sabund;

sabund = input.getSAbundVector();

}

if (m->control_pressed) { out.close(); 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) {

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

sabund = input.getSAbundVector(lastLabel);

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

if (sabund->getMaxRank() > nseqs) {

for(int i = 1; i <=nseqs; i++) { sabund->set(i, 0); }

}else { sabund->clear(); }

if (sabund->getNumBins() > 0) { sabund->print(out); }

delete sabund;

}

return 0;

}

catch(exception& e) {

m->errorOut(e, "RemoveRareCommand", "processSabund");

exit(1);

}

try {

string thisOutputDir = outputDir;

if (outputDir == "") { thisOutputDir += m->hasPath(rabundfile); }

string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + "pick" + m->getExtension(rabundfile);

outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName);

ofstream out;

m->openOutputFile(outputFileName, out);

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

InputData input(rabundfile, "rabund");

RAbundVector* rabund = input.getRAbundVector();

string lastLabel = rabund->getLabel();

set<string> processedLabels;

set<string> userLabels = labels;

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

if (m->control_pressed) { delete rabund; out.close(); return 0; }

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

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

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

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

RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());

for (int i = 0; i < rabund->getNumBins(); i++) {

if (rabund->get(i) > nseqs) {

newRabund.push_back(rabund->get(i));

}

}

if (newRabund.getNumBins() > 0) { newRabund.print(out); }

}

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

string saveLabel = rabund->getLabel();

delete rabund;

rabund = input.getRAbundVector(lastLabel);

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

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

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

RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());

for (int i = 0; i < rabund->getNumBins(); i++) {

if (rabund->get(i) > nseqs) {

newRabund.push_back(rabund->get(i));

}

}

if (newRabund.getNumBins() > 0) { newRabund.print(out); }

//restore real lastlabel to save below

rabund->setLabel(saveLabel);

}

lastLabel = rabund->getLabel();

delete rabund;

rabund = input.getRAbundVector();

}

if (m->control_pressed) { out.close(); 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) {

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

rabund = input.getRAbundVector(lastLabel);

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

RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());

for (int i = 0; i < rabund->getNumBins(); i++) {

if (rabund->get(i) > nseqs) {

newRabund.push_back(rabund->get(i));

}

}

if (newRabund.getNumBins() > 0) { newRabund.print(out); }

delete rabund;

}

return 0;

}

catch(exception& e) {

m->errorOut(e, "RemoveRareCommand", "processRabund");

exit(1);

}

try {

m->setGroups(Groups);

string thisOutputDir = outputDir;

if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }

string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "pick" + m->getExtension(sharedfile);

outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);

ofstream out;

m->openOutputFile(outputFileName, out);

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

InputData input(sharedfile, "sharedfile");

vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();

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

set<string> processedLabels;

set<string> userLabels = labels;

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

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

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

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

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

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

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

processLookup(lookup, out);

}

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();

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

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

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

processLookup(lookup, out);

//restore real lastlabel to save below

lookup[0]->setLabel(saveLabel);

}

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

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

lookup = input.getSharedRAbundVectors();

}

if (m->control_pressed) { out.close(); 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); }

processLookup(lookup, out);

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

}

return 0;

}

catch(exception& e) {

m->errorOut(e, "RemoveRareCommand", "processSabund");

exit(1);

}

try {

vector<SharedRAbundVector> newRabunds; newRabunds.resize(lookup.size());

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

newRabunds[i].setGroup(lookup[i]->getGroup());

newRabunds[i].setLabel(lookup[i]->getLabel());

}

if (byGroup) {

//for each otu

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

bool allZero = true;

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

//for each group

for (int j = 0; j < lookup.size(); j++) {

//are you rare?

if (lookup[j]->getAbundance(i) > nseqs) {

newRabunds[j].push_back(lookup[j]->getAbundance(i), newRabunds[j].getGroup());

allZero = false;

}else {

newRabunds[j].push_back(0, newRabunds[j].getGroup());

}

}

//eliminates zero otus

if (allZero) { for (int j = 0; j < newRabunds.size(); j++) { newRabunds[j].pop_back(); } }

}

}else {

//for each otu

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

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

int totalAbund = 0;

//get total otu abundance

for (int j = 0; j < lookup.size(); j++) {

newRabunds[j].push_back(lookup[j]->getAbundance(i), newRabunds[j].getGroup());

totalAbund += lookup[j]->getAbundance(i);

}

//eliminates otus below rare cutoff

if (totalAbund <= nseqs) { for (int j = 0; j < newRabunds.size(); j++) { newRabunds[j].pop_back(); } }

}

}

//do we have any otus above the rare cutoff

if (newRabunds[0].getNumBins() != 0) {

for (int j = 0; j < newRabunds.size(); j++) {

out << newRabunds[j].getLabel() << '\t' << newRabunds[j].getGroup() << '\t';

newRabunds[j].print(out);

}

}

return 0;

}

catch(exception& e) {

m->errorOut(e, "RemoveRareCommand", "processLookup");

exit(1);

}