try {

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

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

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

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

CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);

CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);

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

CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "","",true,false,true); parameters.push_back(pcalc);

CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);

CommandParameter psize("size", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psize);

CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pgroupmode);

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, "SummaryCommand", "setParameters");

exit(1);

}

try {

string helpString = "";

ValidCalculators validCalculator;

helpString += "The summary.single command parameters are list, sabund, rabund, shared, subsample, iters, label, calc, abund and groupmode. list, sabund, rabund or shared is required unless you have a valid current file.\n";

helpString += "The summary.single command should be in the following format: \n";

helpString += "summary.single(label=yourLabel, calc=yourEstimators).\n";

helpString += "Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n";

helpString += validCalculator.printCalc("summary");

helpString += "The subsample parameter allows you to enter the size of the sample or you can set subsample=T and mothur will use the size of your smallest group in the case of a shared file. With a list, sabund or rabund file you must provide a subsample size.\n";

helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";

helpString += "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n";

helpString += "If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=true).\n";

helpString += "The label parameter is used to analyze specific labels in your input.\n";

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

return helpString;

}

catch(exception& e) {

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

exit(1);

}

try {

string pattern = "";

if (type == "summary") { pattern = "[filename],summary-[filename],[tag],summary"; }

else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }

return pattern;

}

catch(exception& e) {

m->errorOut(e, "SummaryCommand", "getOutputPattern");

exit(1);

}

try {

abort = true; calledHelp = true;

setParameters();

vector<string> tempOutNames;

outputTypes["summary"] = tempOutNames;

}

catch(exception& e) {

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

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

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

}

//initialize outputTypes

vector<string> tempOutNames;

outputTypes["summary"] = 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; }

}

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("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("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; }

}

}

//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); }

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

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

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

else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }

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); }

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

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

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

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

else {

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 {

sabundfile = m->getSabundFile();

if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; 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 before you can use the collect.single command."); 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); }

//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; }

}

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

if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }

else {

if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }

}

m->splitAtDash(calc, Estimators);

if (m->inUsersGroups("citation", Estimators)) {

ValidCalculators validCalc; validCalc.printCitations(Estimators);

//remove citation from list of calcs

for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }

}

string temp;

temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }

m->mothurConvert(temp, abund);

temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }

m->mothurConvert(temp, size);

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

groupMode = m->isTrue(temp);

temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }

m->mothurConvert(temp, iters);

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

if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; }

else {

if (m->isTrue(temp)) { subsample = true; subsampleSize = -1; } //we will set it to smallest group later

else { subsample = false; subsampleSize = -1; }

}

if (subsample == false) { iters = 0; }

else {

//if you did not set a samplesize and are not using a sharedfile

if ((subsampleSize == -1) && (format != "sharedfile")) { m->mothurOut("[ERROR]: If you want to subsample with a list, rabund or sabund file, you must provide the sample size. You can do this by setting subsample=yourSampleSize.\n"); abort=true; }

}

}

}

catch(exception& e) {

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

exit(1);

}

try {

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

if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); }

else { inputFileNames = parseSharedFile(sharedfile); format = "rabund"; }

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

int numLines = 0;

int numCols = 0;

map<string, string> groupIndex;

for (int p = 0; p < inputFileNames.size(); p++) {

numLines = 0;

numCols = 0;

map<string, string> variables;

variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));

string fileNameRoot = getOutputFileName("summary",variables);

variables["[tag]"] = "ave-std";

string fileNameAve = getOutputFileName("summary",variables);

outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);

if (inputFileNames.size() > 1) {

m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();

groupIndex[fileNameRoot] = groups[p];

}

sumCalculators.clear();

ValidCalculators validCalculator;

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

if (validCalculator.isValidCalculator("summary", Estimators[i]) == true) {

if(Estimators[i] == "sobs"){

sumCalculators.push_back(new Sobs());

}else if(Estimators[i] == "chao"){

sumCalculators.push_back(new Chao1());

}else if(Estimators[i] == "coverage"){

sumCalculators.push_back(new Coverage());

}else if(Estimators[i] == "geometric"){

sumCalculators.push_back(new Geom());

}else if(Estimators[i] == "logseries"){

sumCalculators.push_back(new LogSD());

}else if(Estimators[i] == "qstat"){

sumCalculators.push_back(new QStat());

}else if(Estimators[i] == "bergerparker"){

sumCalculators.push_back(new BergerParker());

}else if(Estimators[i] == "bstick"){

sumCalculators.push_back(new BStick());

}else if(Estimators[i] == "ace"){

if(abund < 5)

abund = 10;

sumCalculators.push_back(new Ace(abund));

}else if(Estimators[i] == "jack"){

sumCalculators.push_back(new Jackknife());

}else if(Estimators[i] == "shannon"){

sumCalculators.push_back(new Shannon());

}else if(Estimators[i] == "shannoneven"){

sumCalculators.push_back(new ShannonEven());

}else if(Estimators[i] == "npshannon"){

sumCalculators.push_back(new NPShannon());

}else if(Estimators[i] == "heip"){

sumCalculators.push_back(new Heip());

}else if(Estimators[i] == "smithwilson"){

sumCalculators.push_back(new SmithWilson());

}else if(Estimators[i] == "simpson"){

sumCalculators.push_back(new Simpson());

}else if(Estimators[i] == "simpsoneven"){

sumCalculators.push_back(new SimpsonEven());

}else if(Estimators[i] == "invsimpson"){

sumCalculators.push_back(new InvSimpson());

}else if(Estimators[i] == "bootstrap"){

sumCalculators.push_back(new Bootstrap());

}else if (Estimators[i] == "nseqs") {

sumCalculators.push_back(new NSeqs());

}else if (Estimators[i] == "goodscoverage") {

sumCalculators.push_back(new GoodsCoverage());

}else if (Estimators[i] == "efron") {

sumCalculators.push_back(new Efron(size));

}else if (Estimators[i] == "boneh") {

sumCalculators.push_back(new Boneh(size));

}else if (Estimators[i] == "solow") {

sumCalculators.push_back(new Solow(size));

}else if (Estimators[i] == "shen") {

sumCalculators.push_back(new Shen(size, abund));

}

}

}

//if the users entered no valid calculators don't execute command

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

ofstream outputFileHandle;

m->openOutputFile(fileNameRoot, outputFileHandle);

outputFileHandle << "label";

ofstream outAve;

if (subsample) {

m->openOutputFile(fileNameAve, outAve);

outputNames.push_back(fileNameAve); outputTypes["summary"].push_back(fileNameAve);

outAve << "label\tmethod";

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

if (inputFileNames.size() > 1) {

groupIndex[fileNameAve] = groups[p];

}

}

input = new InputData(inputFileNames[p], format);

sabund = input->getSAbundVector();

string lastLabel = sabund->getLabel();

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

if(sumCalculators[i]->getCols() == 1){

outputFileHandle << '\t' << sumCalculators[i]->getName();

if (subsample) { outAve << '\t' << sumCalculators[i]->getName(); }

numCols++;

}

else{

outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";

if (subsample) { outAve << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci"; }

numCols += 3;

}

}

outputFileHandle << endl;

if (subsample) { outAve << endl; }

//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) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }

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

if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }

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

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

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

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

process(sabund, outputFileHandle, outAve);

if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }

numLines++;

}

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());

process(sabund, outputFileHandle, outAve);

if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }

numLines++;

//restore real lastlabel to save below

sabund->setLabel(saveLabel);

}

lastLabel = sabund->getLabel();

delete sabund;

sabund = input->getSAbundVector();

}

if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete input; 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();

process(sabund, outputFileHandle, outAve);

if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }

numLines++;

delete sabund;

}

outputFileHandle.close();

if (subsample) { outAve.close(); }

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

delete input;

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

}

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

//create summary file containing all the groups data for each label - this function just combines the info from the files already created.

if ((sharedfile != "") && (groupMode)) { vector<string> comboNames = createGroupSummaryFile(numLines, numCols, outputNames, groupIndex); for (int i = 0; i < comboNames.size(); i++) { outputNames.push_back(comboNames[i]); } }

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

return 0;

}

catch(exception& e) {

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

exit(1);

}

try {

//calculator -> data -> values

vector< vector< vector<double> > > results; results.resize(sumCalculators.size());

outputFileHandle << sabund->getLabel();

SubSample sample;

for (int thisIter = 0; thisIter < iters+1; thisIter++) {

SAbundVector* thisIterSabund = sabund;

//we want the summary results for the whole dataset, then the subsampling

if ((thisIter > 0) && subsample) { //subsample sabund and run it

//copy sabund since getSample destroys it

RAbundVector rabund = sabund->getRAbundVector();

SAbundVector* newSabund = new SAbundVector();

*newSabund = rabund.getSAbundVector();

sample.getSample(newSabund, subsampleSize);

thisIterSabund = newSabund;

}

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

vector<double> data = sumCalculators[i]->getValues(thisIterSabund);

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

if (thisIter == 0) {

outputFileHandle << '\t';

sumCalculators[i]->print(outputFileHandle);

}else {

//some of the calc have hci and lci need to make room for that

if (results[i].size() == 0) { results[i].resize(data.size()); }

//save results for ave and std.

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

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

results[i][j].push_back(data[j]);

}

}

}

//cleanup memory

if ((thisIter > 0) && subsample) { delete thisIterSabund; }

}

outputFileHandle << endl;

if (subsample) {

outAve << sabund->getLabel() << '\t' << "ave\t";

//find ave and std for this label and output

//will need to modify the createGroupSummary to combine results and not mess with the .summary file.

//calcs -> values

vector< vector<double> > calcAverages; calcAverages.resize(sumCalculators.size());

for (int i = 0; i < calcAverages.size(); i++) { calcAverages[i].resize(results[i].size(), 0); }

for (int thisIter = 0; thisIter < iters; thisIter++) { //sum all groups dists for each calculator

for (int i = 0; i < calcAverages.size(); i++) { //initialize sums to zero.

for (int j = 0; j < calcAverages[i].size(); j++) {

calcAverages[i][j] += results[i][j][thisIter];

}

}

}

for (int i = 0; i < calcAverages.size(); i++) { //finds average.

for (int j = 0; j < calcAverages[i].size(); j++) {

calcAverages[i][j] /= (float) iters;

outAve << calcAverages[i][j] << '\t';

}

}

//find standard deviation

vector< vector<double> > stdDev; stdDev.resize(sumCalculators.size());

for (int i = 0; i < stdDev.size(); i++) { stdDev[i].resize(results[i].size(), 0); }

for (int thisIter = 0; thisIter < iters; thisIter++) { //compute the difference of each dist from the mean, and square the result of each

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

for (int j = 0; j < stdDev[i].size(); j++) {

stdDev[i][j] += ((results[i][j][thisIter] - calcAverages[i][j]) * (results[i][j][thisIter] - calcAverages[i][j]));

}

}

}

outAve << endl << sabund->getLabel() << '\t' << "std\t";

for (int i = 0; i < stdDev.size(); i++) { //finds average.

for (int j = 0; j < stdDev[i].size(); j++) {

stdDev[i][j] /= (float) iters;

stdDev[i][j] = sqrt(stdDev[i][j]);

outAve << stdDev[i][j] << '\t';

}

}

outAve << endl;

}

return 0;

}

catch(exception& e) {

m->errorOut(e, "SummaryCommand", "process");

exit(1);

}

try {

vector<string> filenames;

map<string, ofstream*> filehandles;

map<string, ofstream*>::iterator it3;

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

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

string sharedFileRoot = m->getRootName(filename);

/******************************************************/

if (subsample) {

if (subsampleSize == -1) { //user has not set size, set size = smallest samples size

subsampleSize = lookup[0]->getNumSeqs();

for (int i = 1; i < lookup.size(); i++) {

int thisSize = lookup[i]->getNumSeqs();

if (thisSize < subsampleSize) { subsampleSize = thisSize; }

}

}else {

m->clearGroups();

vector<string> Groups;

vector<SharedRAbundVector*> temp;

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

if (lookup[i]->getNumSeqs() < subsampleSize) {

m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();

delete lookup[i];

}else {

Groups.push_back(lookup[i]->getGroup());

temp.push_back(lookup[i]);

}

}

lookup = temp;

m->setGroups(Groups);

}

if (lookup.size() < 1) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; delete input; return filenames; }

}

/******************************************************/

//clears file before we start to write to it below

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

m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));

filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));

}

ofstream* temp;

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

temp = new ofstream;

filehandles[lookup[i]->getGroup()] = temp;

groups.push_back(lookup[i]->getGroup());

}

while(lookup[0] != NULL) {

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

RAbundVector rav = lookup[i]->getRAbundVector();

m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));

rav.print(*(filehandles[lookup[i]->getGroup()]));

(*(filehandles[lookup[i]->getGroup()])).close();

}

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

lookup = input->getSharedRAbundVectors();

}

//free memory

for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {

delete it3->second;

}

delete input;

return filenames;

}

catch(exception& e) {

m->errorOut(e, "SummaryCommand", "parseSharedFile");

exit(1);

}

try {

//open each groups summary file

vector<string> newComboNames;

map<string, map<string, vector<string> > > files;

map<string, string> filesTypesLabels;

map<string, int> filesTypesNumLines;

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

vector<string> thisFilesLines;

ifstream temp;

m->openInputFile(outputNames[i], temp);

//read through first line - labels

string labelsLine = m->getline(temp);

vector<string> theseLabels = m->splitWhiteSpace(labelsLine);

string newLabel = "";

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

if (j == 1) { newLabel += "group\t" + theseLabels[j] + '\t';

}else{ newLabel += theseLabels[j] + '\t'; }

}

m->gobble(temp);

int stop = numLines;

if (theseLabels.size() != numCols+1) { stop = numLines*2; }

//for each label

for (int k = 0; k < stop; k++) {

string thisLine = "";

string tempLabel;

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

temp >> tempLabel;

//save for later

if (j == 1) { thisLine += groupIndex[outputNames[i]] + "\t" + tempLabel + "\t"; }

else{ thisLine += tempLabel + "\t"; }

}

thisLine += "\n";

thisFilesLines.push_back(thisLine);

m->gobble(temp);

}

string extension = m->getExtension(outputNames[i]);

if (theseLabels.size() != numCols+1) { extension = ".ave-std" + extension; }

string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;

m->mothurRemove(combineFileName); //remove old file

filesTypesLabels[extension] = newLabel;

filesTypesNumLines[extension] = stop;

map<string, map<string, vector<string> > >::iterator itFiles = files.find(extension);

if (itFiles != files.end()) { //add new files info to existing type

files[extension][outputNames[i]] = thisFilesLines;

}else {

map<string, vector<string> > thisFile;

thisFile[outputNames[i]] = thisFilesLines;

files[extension] = thisFile;

}

temp.close();

m->mothurRemove(outputNames[i]);

}

for (map<string, map<string, vector<string> > >::iterator itFiles = files.begin(); itFiles != files.end(); itFiles++) {

if (m->control_pressed) { break; }

string extension = itFiles->first;

map<string, vector<string> > thisType = itFiles->second;

string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;

newComboNames.push_back(combineFileName);

//open combined file

ofstream out;

m->openOutputFile(combineFileName, out);

//output label line to new file

out << filesTypesLabels[extension] << endl;

//for each label

for (int k = 0; k < filesTypesNumLines[extension]; k++) {

//grab summary data for each group

for (map<string, vector<string> >::iterator itType = thisType.begin(); itType != thisType.end(); itType++) {

out << (itType->second)[k];

}

}

outputNames.clear();

out.close();

}

//return combine file name

return newComboNames;

}

catch(exception& e) {

m->errorOut(e, "SummaryCommand", "createGroupSummaryFile");

exit(1);

}