try {

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

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

CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);

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

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

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, "MergeGroupsCommand", "setParameters");

exit(1);

}

try {

string helpString = "";

helpString += "The merge.groups command reads a shared or group file and a design file and merges the groups that are in the same grouping in the design file.\n";

helpString += "The merge.groups command outputs a .shared file. \n";

helpString += "The merge.groups command parameters are shared, group, groups, label and design. The design parameter is required.\n";

helpString += "The design parameter allows you to assign your groups to sets. It is required. \n";

helpString += "The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.\n";

helpString += "The groups parameter allows you to specify which of the groups in your shared or group file 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 merge.groups command should be in the following format: merge.groups(design=yourDesignFile, shared=yourSharedFile).\n";

helpString += "Example merge.groups(design=temp.design, groups=A-B-C, shared=temp.shared).\n";

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

exit(1);

}

try {

string pattern = "";

if (type == "shared") { pattern = "[filename],merge,[extension]"; }

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

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

return pattern;

}

catch(exception& e) {

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

exit(1);

}

try {

abort = true; calledHelp = true;

setParameters();

vector<string> tempOutNames;

outputTypes["shared"] = tempOutNames;

outputTypes["group"] = tempOutNames;

}

catch(exception& e) {

m->errorOut(e, "MergeGroupsCommand", "MetaStatsCommand");

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;

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

map<string,string>::iterator it;

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["shared"] = tempOutNames;

outputTypes["group"] = 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("design");

//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["design"] = 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

designfile = validParameter.validFile(parameters, "design", true);

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

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

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

designfile = m->getDesignFile();

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

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

}else { m->setDesignFile(designfile); }

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

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

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

else { m->setSharedFile(sharedfile); }

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

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

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

else { m->setGroupFile(groupfile); }

//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 = "all"; }

m->splitAtDash(groups, Groups);

m->setGroups(Groups);

if ((sharedfile == "") && (groupfile == "")) {

//give priority to group, then shared

groupfile = m->getGroupFile();

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

else {

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 groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;

}

}

}

}

}

catch(exception& e) {

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

exit(1);

}

try {

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

designMap = new GroupMap(designfile);

designMap->readDesignMap();

if (groupfile != "") { processGroupFile(designMap); }

if (sharedfile != "") { processSharedFile(designMap); }

//reset groups parameter

m->clearGroups();

delete designMap;

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

//set shared file as new current sharedfile

string current = "";

itTypes = outputTypes.find("shared");

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

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

}

itTypes = outputTypes.find("group");

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

if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(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, "MergeGroupsCommand", "execute");

exit(1);

}

try {

map<string, SharedRAbundVector> merged;

map<string, SharedRAbundVector>::iterator it;

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

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

//what grouping does this group belong to

string grouping = designMap->getGroup(thisLookUp[i]->getGroup());

if (grouping == "not found") { m->mothurOut("[ERROR]: " + thisLookUp[i]->getGroup() + " is not in your design file. Ignoring!"); m->mothurOutEndLine(); grouping = "NOTFOUND"; }

else {

//do we already have a member of this grouping?

it = merged.find(grouping);

if (it == merged.end()) { //nope, so create it

merged[grouping] = *thisLookUp[i];

merged[grouping].setGroup(grouping);

}else { //yes, merge it

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

int abund = (it->second).getAbundance(j);

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

(it->second).set(j, abund, grouping);

}

}

}

}

//print new file

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

out << (it->second).getLabel() << '\t' << it->first << '\t';

(it->second).print(out);

}

return 0;

}

catch(exception& e) {

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

exit(1);

}

try {

string thisOutputDir = outputDir;

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

map<string, string> variables;

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

variables["[extension]"] = m->getExtension(sharedfile);

string outputFileName = getOutputFileName("shared", variables);

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

ofstream out;

m->openOutputFile(outputFileName, out);

InputData input(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) { out.close(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); delete designMap; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } 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); }

process(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); }

process(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) { out.close(); m->clearGroups(); delete designMap; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }

//get next line to process

lookup = input.getSharedRAbundVectors();

}

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

process(lookup, out);

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

}

out.close();

return 0;

}

catch(exception& e) {

m->errorOut(e, "MergeGroupsCommand", "processSharedFile");

exit(1);

}

try {

string thisOutputDir = outputDir;

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

map<string, string> variables;

variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));

variables["[extension]"] = m->getExtension(groupfile);

string outputFileName = getOutputFileName("group", variables);

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

ofstream out;

m->openOutputFile(outputFileName, out);

//read groupfile

GroupMap groupMap(groupfile);

groupMap.readMap();

//fill Groups - checks for "all" and for any typo groups

SharedUtil* util = new SharedUtil();

vector<string> nameGroups = groupMap.getNamesOfGroups();

util->setGroups(Groups, nameGroups);

delete util;

vector<string> namesOfSeqs = groupMap.getNamesSeqs();

bool error = false;

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

if (m->control_pressed) { break; }

string thisGroup = groupMap.getGroup(namesOfSeqs[i]);

//are you in a group the user wants

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

string thisGrouping = designMap->getGroup(thisGroup);

if (thisGrouping == "not found") { m->mothurOut("[ERROR]: " + namesOfSeqs[i] + " is from group " + thisGroup + " which is not in your design file, please correct."); m->mothurOutEndLine(); error = true; }

else {

out << namesOfSeqs[i] << '\t' << thisGrouping << endl;

}

}

}

if (error) { m->control_pressed = true; }

out.close();

return 0;

}

catch(exception& e) {

m->errorOut(e, "MergeGroupsCommand", "processGroupFile");

exit(1);

}