//**********************************************************************************************************************
int SharedCommand::createSharedFromBiom() {
try {
//getting output filename
string filename = biomfile;
if (outputDir == "") { outputDir += util.hasPath(filename); }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(filename));
filename = getOutputFileName("shared",variables);
outputNames.push_back(filename); outputTypes["shared"].push_back(filename);
ofstream out;
util.openOutputFile(filename, out);
/*{
"id":"/Users/SarahsWork/Desktop/release/temp.job2.shared-unique",
"format": "Biological Observation Matrix 0.9.1",
"format_url": "http://biom-format.org",
"type": "OTU table",
"generated_by": "mothur1.24.0",
"date": "Tue Apr 17 13:12:07 2012", */
ifstream in;
util.openInputFile(biomfile, in);
string matrixFormat = "";
int numRows = 0;
int numCols = 0;
int shapeNumRows = 0;
int shapeNumCols = 0;
vector<string> otuNames;
vector<string> groupNames;
map<string, string> fileLines;
vector<string> names;
int countOpenBrace = 0;
int countClosedBrace = 0;
int openParen = -1; //account for opening brace
int closeParen = 0;
bool ignoreCommas = false;
bool atComma = false;
string line = "";
string matrixElementType = "";
while (!in.eof()) { //split file by tags, so each "line" will have something like "id":"/Users/SarahsWork/Desktop/release/final.tx.1.subsample.1.pick.shared-1"
if (m->getControl_pressed()) { break; }
char c = in.get(); util.gobble(in);
if (c == '[') { countOpenBrace++; }
else if (c == ']') { countClosedBrace++; }
else if (c == '{') { openParen++; }
else if (c == '}') { closeParen++; }
else if ((!ignoreCommas) && (c == ',')) { atComma = true; }
if ((countOpenBrace != countClosedBrace) && (countOpenBrace != countClosedBrace)) { ignoreCommas = true; }
else if ((countOpenBrace == countClosedBrace) && (countOpenBrace == countClosedBrace)) { ignoreCommas = false; }
if (atComma && !ignoreCommas) {
if (fileLines.size() == 0) { //clip first {
line = line.substr(1);
}
string tag = getTag(line);
fileLines[tag] = line;
line = "";
atComma = false;
ignoreCommas = false;
}else { line += c; }
}
if (line != "") {
line = line.substr(0, line.length()-1);
string tag = getTag(line);
fileLines[tag] = line;
}
in.close();
string biomType;
map<string, string>::iterator it;
it = fileLines.find("type");
if (it == fileLines.end()) { m->mothurOut("[ERROR]: you file does not have a type provided.\n"); }
else {
string thisLine = it->second;
biomType = getTag(thisLine);
// if ((biomType != "OTU table") && (biomType != "OTUtable") && (biomType != "Taxon table") && (biomType != "Taxontable")) { m->mothurOut("[ERROR]: " + biomType + " is not a valid biom type for mothur. Only types allowed are OTU table and Taxon table.\n"); m->setControl_pressed(true); }
}
if (m->getControl_pressed()) { out.close(); util.mothurRemove(filename); return 0; }
it = fileLines.find("matrix_type");
if (it == fileLines.end()) { m->mothurOut("[ERROR]: you file does not have a matrix_type provided.\n"); }
else {
string thisLine = it->second;
matrixFormat = getTag(thisLine);
if ((matrixFormat != "sparse") && (matrixFormat != "dense")) { m->mothurOut("[ERROR]: " + matrixFormat + " is not a valid biom matrix_type for mothur. Types allowed are sparse and dense.\n"); m->setControl_pressed(true); }
}
if (m->getControl_pressed()) { out.close(); util.mothurRemove(filename); return 0; }
it = fileLines.find("matrix_element_type");
if (it == fileLines.end()) { m->mothurOut("[ERROR]: you file does not have a matrix_element_type provided.\n"); }
else {
string thisLine = it->second;
matrixElementType = getTag(thisLine);
if ((matrixElementType != "int") && (matrixElementType != "float")) { m->mothurOut("[ERROR]: " + matrixElementType + " is not a valid biom matrix_element_type for mothur. Types allowed are int and float.\n"); m->setControl_pressed(true); }
if (matrixElementType == "float") { m->mothurOut("[WARNING]: the shared file only uses integers, any float values will be rounded down to the nearest integer.\n"); }
}
if (m->getControl_pressed()) { out.close(); util.mothurRemove(filename); return 0; }
it = fileLines.find("rows");
if (it == fileLines.end()) { m->mothurOut("[ERROR]: you file does not have a rows provided.\n"); }
else {
string thisLine = it->second;
if ((biomType == "Taxon table") || (biomType == "Taxontable")) {
string mapFilename = getOutputFileName("map",variables);
outputNames.push_back(mapFilename); outputTypes["map"].push_back(mapFilename);
ofstream outMap;
util.openOutputFile(mapFilename, outMap);
vector<string> taxonomies = readRows(thisLine, numRows);
string snumBins = toString(numRows);
for (int i = 0; i < numRows; i++) {
//if there is a bin label use it otherwise make one
string binLabel = "OTU";
string sbinNumber = toString(i+1);
if (sbinNumber.length() < snumBins.length()) {
int diff = snumBins.length() - sbinNumber.length();
for (int h = 0; h < diff; h++) { binLabel += "0"; }
}
binLabel += sbinNumber;
otuNames.push_back(binLabel);
outMap << otuNames[i] << '\t' << taxonomies[i] << endl;
}
outMap.close();
}else{ otuNames = readRows(thisLine, numRows); }
}
if (m->getControl_pressed()) { out.close(); util.mothurRemove(filename); return 0; }
it = fileLines.find("columns");
if (it == fileLines.end()) { m->mothurOut("[ERROR]: you file does not have a columns provided.\n"); }
else {
string thisLine = it->second;
//read sample names
groupNames = readRows(thisLine, numCols);
//if users selected groups, then remove the groups not wanted.
if (Groups.size() == 0) { Groups = groupNames; }
else { groupNames = Groups; }
//set fileroot
fileroot = outputDir + util.getRootName(util.getSimpleName(biomfile));
}
if (m->getControl_pressed()) { out.close(); util.mothurRemove(filename); return 0; }
it = fileLines.find("shape");
if (it == fileLines.end()) { m->mothurOut("[ERROR]: you file does not have a shape provided.\n"); }
else {
string thisLine = it->second;
getDims(thisLine, shapeNumRows, shapeNumCols);
//check shape
if (shapeNumCols != numCols) { m->mothurOut("[ERROR]: shape indicates " + toString(shapeNumCols) + " columns, but I only read " + toString(numCols) + " columns.\n"); m->setControl_pressed(true); }
if (shapeNumRows != numRows) { m->mothurOut("[ERROR]: shape indicates " + toString(shapeNumRows) + " rows, but I only read " + toString(numRows) + " rows.\n"); m->setControl_pressed(true); }
}
if (m->getControl_pressed()) { out.close(); util.mothurRemove(filename); return 0; }
bool printHeaders = true;
it = fileLines.find("data");
if (it == fileLines.end()) { m->mothurOut("[ERROR]: you file does not have a data provided.\n"); }
else {
string thisLine = it->second;
//read data
SharedRAbundVectors* lookup = readData(matrixFormat, thisLine, matrixElementType, groupNames, otuNames.size());
lookup->setOTUNames(otuNames);
lookup->eliminateZeroOTUS();
m->mothurOutEndLine(); m->mothurOut(lookup->getLabel()+"\n");
printSharedData(lookup, out, printHeaders);
}
if (m->getControl_pressed()) { util.mothurRemove(filename); return 0; }
return 0;
}
catch(exception& e) {
m->errorOut(e, "SharedCommand", "createSharedFromBiom");
exit(1);
}
}
//**********************************************************************************************************************
int SharedCommand::createSharedFromListGroup() {
try {
GroupMap* groupMap = NULL;
CountTable* countTable = NULL;
pickedGroups = false;
if (groupfile != "") {
groupMap = new GroupMap(groupfile);
int groupError = groupMap->readMap();
if (groupError == 1) { delete groupMap; return 0; }
vector<string> allGroups = groupMap->getNamesOfGroups();
if (Groups.size() == 0) { Groups = allGroups; }
else { pickedGroups = true; }
}else{
countTable = new CountTable();
countTable->readTable(countfile, true, false);
vector<string> allGroups = countTable->getNamesOfGroups();
if (Groups.size() == 0) { Groups = allGroups; }
else { pickedGroups = true; }
}
int numGroups = Groups.size();
if (m->getControl_pressed()) { return 0; }
ofstream out;
string filename = "";
if (!pickedGroups) {
string filename = listfile;
if (outputDir == "") { outputDir += util.hasPath(filename); }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(filename));
filename = getOutputFileName("shared",variables);
outputNames.push_back(filename); outputTypes["shared"].push_back(filename);
util.openOutputFile(filename, out);
}
//set fileroot
fileroot = outputDir + util.getRootName(util.getSimpleName(listfile));
map<string, string> variables;
variables["[filename]"] = fileroot;
string errorOff = "no error";
InputData input(listfile, "shared", Groups);
SharedListVector* SharedList = input.getSharedListVector();
string lastLabel = SharedList->getLabel();
SharedRAbundVectors* lookup;
if (m->getControl_pressed()) {
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
out.close(); if (!pickedGroups) { util.mothurRemove(filename); }
return 0;
}
//sanity check
vector<string> namesSeqs;
int numGroupNames = 0;
if (current->getGroupMode() == "group") { namesSeqs = groupMap->getNamesSeqs(); numGroupNames = groupMap->getNumSeqs(); }
else { namesSeqs = countTable->getNamesOfSeqs(); numGroupNames = countTable->getNumUniqueSeqs(); }
int error = ListGroupSameSeqs(namesSeqs, SharedList);
if ((!pickedGroups) && (SharedList->getNumSeqs() != numGroupNames)) { //if the user has not specified any groups and their files don't match exit with error
m->mothurOut("Your group file contains " + toString(numGroupNames) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct.\n"); m->setControl_pressed(true);
out.close(); if (!pickedGroups) { util.mothurRemove(filename); } //remove blank shared file you made
//delete memory
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
return 0;
}
if (error == 1) { m->setControl_pressed(true); }
//if user has specified groups make new groupfile for them
if ((pickedGroups) && (current->getGroupMode() == "group")) { //make new group file
string groups = "";
if (numGroups < 4) {
for (int i = 0; i < numGroups-1; i++) {
groups += Groups[i] + ".";
}
groups+=Groups[numGroups-1];
}else { groups = "merge"; }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(listfile));
variables["[group]"] = groups;
string newGroupFile = getOutputFileName("group",variables);
outputTypes["group"].push_back(newGroupFile);
outputNames.push_back(newGroupFile);
ofstream outGroups;
util.openOutputFile(newGroupFile, outGroups);
vector<string> names = groupMap->getNamesSeqs();
string groupName;
for (int i = 0; i < names.size(); i++) {
groupName = groupMap->getGroup(names[i]);
if (isValidGroup(groupName, Groups)) {
outGroups << names[i] << '\t' << groupName << endl;
}
}
outGroups.close();
}
//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;
bool printHeaders = true;
while((SharedList != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->getControl_pressed()) {
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
if (!pickedGroups) { out.close(); util.mothurRemove(filename); }
return 0;
}
if(allLines == 1 || labels.count(SharedList->getLabel()) == 1){
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup->getLabel()+"\n");
if (m->getControl_pressed()) {
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
delete lookup;
if (!pickedGroups) { out.close(); util.mothurRemove(filename); }
return 0;
}
//if picked groups must split the shared file by label
if (pickedGroups) {
string filename = listfile;
if (outputDir == "") { outputDir += util.hasPath(filename); }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(filename));
variables["[distance]"] = lookup->getLabel();
filename = getOutputFileName("shared",variables);
outputNames.push_back(filename); outputTypes["shared"].push_back(filename);
ofstream out2;
util.openOutputFile(filename, out2);
lookup->eliminateZeroOTUS();
printSharedData(lookup, out2, printHeaders);
out2.close();
}else {
printSharedData(lookup, out, printHeaders); //prints info to the .shared file
}
delete lookup;
processedLabels.insert(SharedList->getLabel());
userLabels.erase(SharedList->getLabel());
}
if ((util.anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) ) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = SharedList->getLabel();
delete SharedList;
SharedList = input.getSharedListVector(lastLabel); //get new list vector to process
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup->getLabel()+"\n");
if (m->getControl_pressed()) {
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
delete lookup;
if (!pickedGroups) { out.close(); util.mothurRemove(filename); }
return 0;
}
//if picked groups must split the shared file by label
if (pickedGroups) {
string filename = listfile;
if (outputDir == "") { outputDir += util.hasPath(filename); }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(filename));
variables["[distance]"] = lookup->getLabel();
filename = getOutputFileName("shared",variables);
outputNames.push_back(filename); outputTypes["shared"].push_back(filename);
ofstream out2;
util.openOutputFile(filename, out2);
lookup->eliminateZeroOTUS();
printSharedData(lookup, out2, printHeaders);
out2.close();
}else {
printSharedData(lookup, out, printHeaders); //prints info to the .shared file
}
delete lookup;
processedLabels.insert(SharedList->getLabel());
userLabels.erase(SharedList->getLabel());
//restore real lastlabel to save below
SharedList->setLabel(saveLabel);
}
lastLabel = SharedList->getLabel();
delete SharedList;
SharedList = input.getSharedListVector(); //get new list vector to process
}
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
if (processedLabels.count(lastLabel) != 1) {
needToRun = true;
}
}
//run last label if you need to
if (needToRun ) {
if (SharedList != NULL) { delete SharedList; }
SharedList = input.getSharedListVector(lastLabel); //get new list vector to process
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup->getLabel()+"\n");
if (m->getControl_pressed()) {
if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
if (!pickedGroups) { out.close(); util.mothurRemove(filename); }
return 0;
}
//if picked groups must split the shared file by label
if (pickedGroups) {
string filename = listfile;
if (outputDir == "") { outputDir += util.hasPath(filename); }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(filename));
variables["[distance]"] = lookup->getLabel();
filename = getOutputFileName("shared",variables);
outputNames.push_back(filename); outputTypes["shared"].push_back(filename);
ofstream out2;
util.openOutputFile(filename, out2);
lookup->eliminateZeroOTUS();
printSharedData(lookup, out2, printHeaders);
out2.close();
}else {
printSharedData(lookup, out, printHeaders); //prints info to the .shared file
}
delete lookup;
delete SharedList;
}
if (!pickedGroups) { out.close(); }
if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
if (m->getControl_pressed()) {
if (!pickedGroups) { util.mothurRemove(filename); }
return 0;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "SharedCommand", "createSharedFromListGroup");
exit(1);
}
}
int SharedCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//getting output filename
filename = listfile;
if (outputDir == "") { outputDir += m->hasPath(filename); }
filename = outputDir + m->getRootName(m->getSimpleName(filename));
filename = filename + "shared";
outputTypes["shared"].push_back(filename);
m->openOutputFile(filename, out);
pickedGroups = false;
//if hte user has not specified any groups then use them all
if (Groups.size() == 0) {
Groups = groupMap->getNamesOfGroups(); m->setGroups(Groups);
}else { pickedGroups = true; }
//fill filehandles with neccessary ofstreams
int i;
ofstream* temp;
for (i=0; i<Groups.size(); i++) {
temp = new ofstream;
filehandles[Groups[i]] = temp;
}
//set fileroot
fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
//clears file before we start to write to it below
for (int i=0; i<Groups.size(); i++) {
m->mothurRemove((fileroot + Groups[i] + ".rabund"));
outputNames.push_back((fileroot + Groups[i] + ".rabund"));
outputTypes["rabund"].push_back((fileroot + Groups[i] + ".rabund"));
}
//lookup.clear();
string errorOff = "no error";
//errorOff = "";
//if user provided an order file containing the order the shared file should be in read it
if (ordergroupfile != "") { readOrderFile(); }
input = new InputData(listfile, "shared");
SharedList = input->getSharedListVector();
string lastLabel = SharedList->getLabel();
vector<SharedRAbundVector*> lookup;
if (m->control_pressed) {
delete input; delete SharedList; delete groupMap;
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
//sanity check
int error = ListGroupSameSeqs();
if ((!pickedGroups) && (SharedList->getNumSeqs() != groupMap->getNumSeqs())) { //if the user has not specified any groups and their files don't match exit with error
m->mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine();
out.close();
m->mothurRemove(filename); //remove blank shared file you made
createMisMatchFile();
//delete memory
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
delete it3->second;
}
delete input; delete SharedList; delete groupMap;
return 0;
}
if (error == 1) { m->control_pressed = true; }
//if user has specified groups make new groupfile for them
if (pickedGroups) { //make new group file
string groups = "";
if (m->getNumGroups() < 4) {
for (int i = 0; i < m->getNumGroups(); i++) {
groups += (m->getGroups())[i] + ".";
}
}else { groups = "merge"; }
string newGroupFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + groups + "groups";
outputTypes["group"].push_back(newGroupFile);
outputNames.push_back(newGroupFile);
ofstream outGroups;
m->openOutputFile(newGroupFile, outGroups);
vector<string> names = groupMap->getNamesSeqs();
string groupName;
for (int i = 0; i < names.size(); i++) {
groupName = groupMap->getGroup(names[i]);
if (isValidGroup(groupName, m->getGroups())) {
outGroups << names[i] << '\t' << groupName << endl;
}
}
outGroups.close();
}
//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;
while((SharedList != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) {
delete input; delete SharedList; delete groupMap;
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
if(allLines == 1 || labels.count(SharedList->getLabel()) == 1){
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
if (pickedGroups) { //check for otus with no seqs in them
eliminateZeroOTUS(lookup);
}
if (m->control_pressed) {
delete input; delete SharedList; delete groupMap;
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
processedLabels.insert(SharedList->getLabel());
userLabels.erase(SharedList->getLabel());
}
if ((m->anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = SharedList->getLabel();
delete SharedList;
SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
if (pickedGroups) { //check for otus with no seqs in them
eliminateZeroOTUS(lookup);
}
if (m->control_pressed) {
delete input; delete SharedList; delete groupMap;
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
processedLabels.insert(SharedList->getLabel());
userLabels.erase(SharedList->getLabel());
//restore real lastlabel to save below
SharedList->setLabel(saveLabel);
}
lastLabel = SharedList->getLabel();
delete SharedList;
SharedList = input->getSharedListVector(); //get new list vector to process
}
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
if (processedLabels.count(lastLabel) != 1) {
needToRun = true;
}
}
//run last label if you need to
if (needToRun == true) {
if (SharedList != NULL) { delete SharedList; }
SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
if (pickedGroups) { //check for otus with no seqs in them
eliminateZeroOTUS(lookup);
}
if (m->control_pressed) {
delete input; delete groupMap;
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
delete SharedList;
}
out.close();
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
delete it3->second;
}
delete input; delete groupMap;
if (m->control_pressed) {
m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
//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("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->mothurOut(filename); m->mothurOutEndLine();
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "SharedCommand", "execute");
exit(1);
}
}
