try {

CommandParameter pfasta("fasta", "InputTypes", "", "", "sharedFasta", "none", "none","fasta",false,false); parameters.push_back(pfasta);

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

CommandParameter plist("list", "InputTypes", "", "", "sharedList", "sharedList", "groupList","sharedseq",false,false,true); parameters.push_back(plist);

CommandParameter pshared("shared", "InputTypes", "", "", "sharedList-sharedFasta", "sharedList", "none","sharedseq",false,false,true); parameters.push_back(pshared);

CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "","",false,false); parameters.push_back(poutput);

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

CommandParameter puniquegroups("uniquegroups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(puniquegroups);

CommandParameter psharedgroups("sharedgroups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(psharedgroups);

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, "GetSharedOTUCommand", "setParameters");

exit(1);

}

try {

string helpString = "";

helpString += "The get.sharedseqs command parameters are list, group, shared, label, uniquegroups, sharedgroups, output and fasta. The list and group or shared parameters are required, unless you have valid current files.\n";

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

helpString += "The uniquegroups and sharedgroups parameters allow you to select groups you would like to know the shared info for, and are separated by dashes.\n";

helpString += "If you enter your groups under the uniquegroups parameter mothur will return the otus that contain ONLY sequences from those groups.\n";

helpString += "If you enter your groups under the sharedgroups parameter mothur will return the otus that contain sequences from those groups and may also contain sequences from other groups.\n";

helpString += "If you do not enter any groups then the get.sharedseqs command will return sequences that are unique to all groups in your group or shared file.\n";

helpString += "The fasta parameter allows you to input a fasta file and outputs a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified. It can only be used with a list and group file not the shared file input.\n";

helpString += "The output parameter allows you to output the list of names without the group and bin number added. \n";

helpString += "With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n";

helpString += "The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n";

helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(list=yourListFile, group=yourGroupFile, label=yourLabels, uniquegroups=yourGroups, fasta=yourFastafile, output=yourOutput).\n";

helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=amazon.groups, uniquegroups=forest-pasture, fasta=amazon.fasta, output=accnos).\n";

helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n";

helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\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, "GetSharedOTUCommand", "getHelpString");

exit(1);

}

try {

string pattern = "";

if (type == "fasta") { pattern = "[filename],[distance],[group],shared.fasta"; }

else if (type == "accnos") { pattern = "[filename],[distance],[group],accnos"; }

else if (type == "sharedseqs") { pattern = "[filename],[distance],[group],shared.seqs"; }

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

return pattern;

}

catch(exception& e) {

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

exit(1);

}

try {

abort = true; calledHelp = true;

setParameters();

vector<string> tempOutNames;

outputTypes["fasta"] = tempOutNames;

outputTypes["accnos"] = tempOutNames;

outputTypes["sharedseqs"] = tempOutNames;

}

catch(exception& e) {

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

exit(1);

}

try {

abort = false; calledHelp = false;

unique = true;

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["fasta"] = tempOutNames;

outputTypes["accnos"] = tempOutNames;

outputTypes["sharedseqs"] = 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("fasta");

//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["fasta"] = 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; }

}

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("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; }

}

}

//check for required parameters

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

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

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

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

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

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

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

else { m->setGroupFile(groupfile); }

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

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

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

else { m->setSharedFile(sharedfile); }

fastafile = validParameter.validFile(parameters, "fasta", true);

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

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

else { m->setFastaFile(fastafile); }

if ((sharedfile == "") && (listfile == "")) { //look for currents

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

//give priority to shared, then list

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 {

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

abort = true;

}

}

}else if ((sharedfile != "") && (listfile != "")) {

m->mothurOut("You may enter ONLY ONE of the following: shared or list."); m->mothurOutEndLine(); abort = true;

}

if (listfile != "") {

if (groupfile == ""){

groupfile = m->getGroupFile();

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

else { m->mothurOut("You need to provide a group file if you are going to use the list format."); m->mothurOutEndLine(); abort = true;

}

}

}

if ((sharedfile != "") && (fastafile != "")) { m->mothurOut("You cannot use the fasta file with the shared file."); m->mothurOutEndLine(); abort = true; }

//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; }

}

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

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

else if (output == "default") { output = ""; }

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

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

else {

userGroups = "unique." + groups;

m->splitAtDash(groups, Groups);

}

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

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

else {

userGroups = groups;

m->splitAtDash(groups, Groups);

unique = false;

}

}

}

catch(exception& e) {

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

exit(1);

}

try {

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

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

else {

m->setGroups(Groups);

groupMap = new GroupMap(groupfile);

int error = groupMap->readMap();

if (error == 1) { delete groupMap; return 0; }

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

if (Groups.size() == 0) {

Groups = groupMap->getNamesOfGroups();

//make string for outputfile name

userGroups = "unique.";

for(int i = 0; i < Groups.size(); i++) { userGroups += Groups[i] + "-"; }

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

}else{

//sanity check for group names

SharedUtil util;

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

util.setGroups(Groups, namesOfGroups);

groupMap->setNamesOfGroups(namesOfGroups);

}

//put groups in map to find easier

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

groupFinder[Groups[i]] = Groups[i];

}

if (fastafile != "") {

ifstream inFasta;

m->openInputFile(fastafile, inFasta);

while(!inFasta.eof()) {

if (m->control_pressed) { outputTypes.clear(); inFasta.close(); delete groupMap; return 0; }

Sequence seq(inFasta); m->gobble(inFasta);

if (seq.getName() != "") { seqs.push_back(seq); }

}

inFasta.close();

}

ListVector* lastlist = NULL;

string lastLabel = "";

//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;

ifstream in;

m->openInputFile(listfile, in);

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

while((!in.eof()) && ((allLines == 1) || (userLabels.size() != 0))) {

if (m->control_pressed) {

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

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

delete groupMap; return 0;

}

list = new ListVector(in);

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

m->mothurOut(list->getLabel());

process(list);

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

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

}

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

string saveLabel = list->getLabel();

m->mothurOut(lastlist->getLabel());

process(lastlist);

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

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

//restore real lastlabel to save below

list->setLabel(saveLabel);

}

lastLabel = list->getLabel();

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

lastlist = list;

}

in.close();

//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) {

m->mothurOut(lastlist->getLabel());

process(lastlist);

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

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

}

//reset groups parameter

m->clearGroups();

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

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

}

//set fasta file as new current fastafile

string current = "";

itTypes = outputTypes.find("fasta");

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

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

}

if (output == "accnos") {

itTypes = outputTypes.find("accnos");

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

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

}

}

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, "GetSharedOTUCommand", "execute");

exit(1);

}

try {

map<string, string> fastaMap;

ofstream outNames;

string outputFileNames;

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

map<string, string> variables;

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

variables["[distance]"] = shared->getLabel();

variables["[group]"] = userGroups;

if (output != "accnos") { outputFileNames = getOutputFileName("sharedseqs", variables); }

else { outputFileNames = getOutputFileName("accnos", variables); }

m->openOutputFile(outputFileNames, outNames);

bool wroteSomething = false;

int num = 0;

//go through each bin, find out if shared

vector<string> binLabels = shared->getLabels();

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

if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; }

bool uniqueOTU = true;

map<string, int> atLeastOne;

for (int f = 0; f < Groups.size(); f++) {

atLeastOne[Groups[f]] = 0;

}

vector<string> namesOfSeqsInThisBin;

string names = shared->get(i);

vector<string> binNames;

m->splitAtComma(names, binNames);

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

string name = binNames[j];

//find group

string seqGroup = groupMap->getGroup(name);

if (output != "accnos") {

namesOfSeqsInThisBin.push_back((name + "|" + seqGroup + "|" + binLabels[i]));

}else { namesOfSeqsInThisBin.push_back(name); }

if (seqGroup == "not found") { m->mothurOut(name + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1); }

//is this seq in one of hte groups we care about

it = groupFinder.find(seqGroup);

if (it == groupFinder.end()) { uniqueOTU = false; } //you have a sequence from a group you don't want

else { atLeastOne[seqGroup]++; }

}

//make sure you have at least one seq from each group you want

bool sharedByAll = true;

map<string, int>::iterator it2;

for (it2 = atLeastOne.begin(); it2 != atLeastOne.end(); it2++) {

if (it2->second == 0) { sharedByAll = false; }

}

//if the user wants unique bins and this is unique then print

//or this the user wants shared bins and this bin is shared then print

if ((unique && uniqueOTU && sharedByAll) || (!unique && sharedByAll)) {

wroteSomething = true;

num++;

//output list of names

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

outNames << namesOfSeqsInThisBin[j] << endl;

if (fastafile != "") {

if (output != "accnos") {

string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('|'));

seqName = seqName.substr(0,seqName.find_last_of('|'));

fastaMap[seqName] = namesOfSeqsInThisBin[j]; //fastaMap needs to contain just the seq name for output later

}else {

fastaMap[namesOfSeqsInThisBin[j]] = namesOfSeqsInThisBin[j];

}

}

}

}

}

outNames.close();

if (!wroteSomething) {

m->mothurRemove(outputFileNames);

string outputString = "\t" + toString(num) + " - No otus shared by groups";

string groupString = "";

for (int h = 0; h < Groups.size(); h++) {

groupString += " " + Groups[h];

}

outputString += groupString + ".";

m->mothurOut(outputString); m->mothurOutEndLine();

}else {

m->mothurOut("\t" + toString(num)); m->mothurOutEndLine();

outputNames.push_back(outputFileNames);

if (output != "accnos") { outputTypes["sharedseqs"].push_back(outputFileNames); }

else { outputTypes["accnos"].push_back(outputFileNames); }

}

//if fasta file provided output new fasta file

if ((fastafile != "") && wroteSomething) {

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

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

string outputFileFasta = getOutputFileName("fasta", variables);

ofstream outFasta;

m->openOutputFile(outputFileFasta, outFasta);

outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);

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

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

//if this is a sequence we want, output it

it = fastaMap.find(seqs[k].getName());

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

if (output != "accnos") {

outFasta << ">" << it->second << endl;

}else {

outFasta << ">" << it->first << endl;

}

outFasta << seqs[k].getAligned() << endl;

}

}

outFasta.close();

}

return 0;

}

catch(exception& e) {

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

exit(1);

}

try {

InputData input(sharedfile, "sharedfile");

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

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

if (Groups.size() == 0) {

Groups = m->getGroups();

//make string for outputfile name

userGroups = "unique.";

for(int i = 0; i < Groups.size(); i++) { userGroups += Groups[i] + "-"; }

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

}else {

//sanity check for group names

SharedUtil util;

vector<string> allGroups = m->getAllGroups();

util.setGroups(Groups, allGroups);

}

//put groups in map to find easier

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

groupFinder[Groups[i]] = Groups[i];

}

//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 < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }

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

}

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

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

process(lookup);

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());

process(lookup);

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

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

//restore real lastlabel to save below

lookup[0]->setLabel(saveLabel);

}

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

//get next line to process

//prevent memory leak

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

lookup = input.getSharedRAbundVectors();

}

if (m->control_pressed) {

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

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

process(lookup);

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

}

//reset groups parameter

m->clearGroups();

return 0;

}

catch(exception& e) {

m->errorOut(e, "GetSharedOTUCommand", "runShared");

exit(1);

}

try {

string outputFileNames;

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

map<string, string> variables;

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

variables["[distance]"] = lookup[0]->getLabel();

variables["[group]"] = userGroups;

if (output != "accnos") { outputFileNames = getOutputFileName("sharedseqs", variables); }

else { outputFileNames = getOutputFileName("accnos", variables); }

ofstream outNames;

m->openOutputFile(outputFileNames, outNames);

bool wroteSomething = false;

int num = 0;

//go through each bin, find out if shared

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

if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; }

bool uniqueOTU = true;

map<string, int> atLeastOne;

for (int f = 0; f < Groups.size(); f++) { atLeastOne[Groups[f]] = 0; }

set<string> namesOfGroupsInThisBin;

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

string seqGroup = lookup[j]->getGroup();

string name = m->currentSharedBinLabels[i];

if (lookup[j]->getAbundance(i) != 0) {

if (output != "accnos") {

namesOfGroupsInThisBin.insert(name + "|" + seqGroup + "|" + toString(lookup[j]->getAbundance(i)));

}else { namesOfGroupsInThisBin.insert(name); }

//is this seq in one of the groups we care about

it = groupFinder.find(seqGroup);

if (it == groupFinder.end()) { uniqueOTU = false; } //you have sequences from a group you don't want

else { atLeastOne[seqGroup]++; }

}

}

//make sure you have at least one seq from each group you want

bool sharedByAll = true;

map<string, int>::iterator it2;

for (it2 = atLeastOne.begin(); it2 != atLeastOne.end(); it2++) {

if (it2->second == 0) { sharedByAll = false; }

}

//if the user wants unique bins and this is unique then print

//or this the user wants shared bins and this bin is shared then print

if ((unique && uniqueOTU && sharedByAll) || (!unique && sharedByAll)) {

wroteSomething = true;

num++;

//output list of names

for (set<string>::iterator itNames = namesOfGroupsInThisBin.begin(); itNames != namesOfGroupsInThisBin.end(); itNames++) {

outNames << (*itNames) << endl;

}

}

}

outNames.close();

if (!wroteSomething) {

m->mothurRemove(outputFileNames);

string outputString = "\t" + toString(num) + " - No otus shared by groups";

string groupString = "";

for (int h = 0; h < Groups.size(); h++) {

groupString += " " + Groups[h];

}

outputString += groupString + ".";

m->mothurOut(outputString); m->mothurOutEndLine();

}else {

m->mothurOut("\t" + toString(num)); m->mothurOutEndLine();

outputNames.push_back(outputFileNames);

if (output != "accnos") { outputTypes["sharedseqs"].push_back(outputFileNames); }

else { outputTypes["accnos"].push_back(outputFileNames); }

}

return 0;

}

catch(exception& e) {

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

exit(1);

}