RAbundVector ListVector::getRAbundVector() {
try {
RAbundVector rav;
for(int i=0; i<data.size(); i++) {
int binSize = m->getNumNames(data[i]);
rav.push_back(binSize);
}
// This was here before to output data in a nice format, but it screws up the name mapping steps
// sort(rav.rbegin(), rav.rend());
//
// for(int i=data.size()-1;i>=0;i--){
// if(rav.get(i) == 0){ rav.pop_back(); }
// else{
// break;
// }
// }
rav.setLabel(label);
return rav;
}
catch(exception& e) {
m->errorOut(e, "ListVector", "getRAbundVector");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> RareFactCommand::parseSharedFile(string filename, map<string, set<int> >& label2Ends) {
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);
//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();
label2Ends[lookup[i]->getLabel()].insert(rav.getNumSeqs());
}
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;
m->clearGroups();
return filenames;
}
catch(exception& e) {
m->errorOut(e, "RareFactCommand", "parseSharedFile");
exit(1);
}
}
TEST(Test_Container_SharedRabundVector, GetRabundVector) {
vector<int> abunds(10, 10);
SharedRAbundVector temp(abunds);
EXPECT_EQ(temp.getNumBins(), 10);
EXPECT_EQ(temp.getNumSeqs(), 100);
EXPECT_EQ(temp.getMaxRank(), 10);
RAbundVector rabund = temp.getRAbundVector();
EXPECT_EQ(rabund.getNumBins(), 10);
EXPECT_EQ(rabund.getNumSeqs(), 100);
EXPECT_EQ(rabund.getMaxRank(), 10);
}
int Rarefact::driver(RarefactionCurveData* rcd, int increment, int nIters = 1000){
try {
for(int iter=0;iter<nIters;iter++){
for(int i=0;i<displays.size();i++){
displays[i]->init(label);
}
RAbundVector* lookup = new RAbundVector(order->getNumBins());
SAbundVector* rank = new SAbundVector(order->getMaxRank()+1);
random_shuffle(order->begin(), order->end());
for(int i=0;i<numSeqs;i++){
if (m->control_pressed) { delete lookup; delete rank; delete rcd; return 0; }
int binNumber = order->get(i);
int abundance = lookup->get(binNumber);
rank->set(abundance, rank->get(abundance)-1);
abundance++;
lookup->set(binNumber, abundance);
rank->set(abundance, rank->get(abundance)+1);
if((i == 0) || ((i+1) % increment == 0) || (ends.count(i+1) != 0)){
rcd->updateRankData(rank);
}
}
if((numSeqs % increment != 0) || (ends.count(numSeqs) != 0)){
rcd->updateRankData(rank);
}
for(int i=0;i<displays.size();i++){
displays[i]->reset();
}
delete lookup;
delete rank;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "Rarefact", "driver");
exit(1);
}
}
SAbundVector SharedSAbundVector::getSAbundVector(){
try {
RAbundVector rav;
SAbundVector sav;
rav = getRAbundVector();
sav = rav.getSAbundVector();
return sav;
}
catch(exception& e) {
m->errorOut(e, "SharedSAbundVector", "getSAbundVector");
exit(1);
}
}
int Collect::getCurve(float percentFreq = 0.01){
try {
RAbundVector* lookup = new RAbundVector(order->getNumBins());
SAbundVector* rank = new SAbundVector(order->getMaxRank()+1);
CollectorsCurveData* ccd = new CollectorsCurveData();
//sets displays label
for(int i=0;i<displays.size();i++){ displays[i]->init(label); }
ccd->registerDisplays(displays);
//convert freq percentage to number
int increment = 1;
if (percentFreq < 1.0) { increment = numSeqs * percentFreq; }
else { increment = percentFreq; }
for(int i=0;i<numSeqs;i++){
if (m->getControl_pressed()) { delete lookup; delete rank; delete ccd; return 1; }
int binNumber = order->get(i);
int abundance = lookup->get(binNumber);
rank->set(abundance, rank->get(abundance)-1);
abundance++;
lookup->set(binNumber, abundance);
rank->set(abundance, rank->get(abundance)+1); //increment rank(abundance)
if((i == 0) || (i+1) % increment == 0){ ccd->updateRankData(rank); }
}
if(numSeqs % increment != 0){ ccd->updateRankData(rank); }
for(int i=0;i<displays.size();i++){ displays[i]->reset(); }
delete lookup; delete rank; delete ccd;
return 0;
}
catch(exception& e) {
m->errorOut(e, "Collect", "getCurve");
exit(1);
}
}
RAbundVector SAbundVector::getRAbundVector(){
try {
RAbundVector rav;
for(int i=1;i < data.size();i++){
for(int j=0;j<data[i];j++){
rav.push_back(i);
}
}
sort(rav.rbegin(), rav.rend());
rav.setLabel(label);
return rav;
}
catch(exception& e) {
m->errorOut(e, "SAbundVector", "getRAbundVector");
exit(1);
}
}
RAbundVector Geom::getRAbundVector(SAbundVector* rank){
vector <int> rData;
int mr = 1;
int nb = 0;
int ns = 0;
for(int i = rank->size()-1; i > 0; i--) {
int cur = rank->get(i);
if(mr == 1 && cur > 0)
mr = i;
nb += cur;
ns += i*cur;
for(int j = 0; j < cur; j++)
rData.push_back(i);
}
RAbundVector rav = RAbundVector(rData, mr, nb, ns);
rav.setLabel(rank->getLabel());
return rav;
}
//**********************************************************************************************************************
vector<string> SummaryCommand::parseSharedFile(string filename) {
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);
}
}
//**********************************************************************************************************************
int SummaryCommand::process(SAbundVector*& sabund, ofstream& outputFileHandle, ofstream& outAve) {
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);
}
}
//**********************************************************************************************************************
int GetRAbundCommand::processList(ofstream& out){
try {
CountTable ct;
ct.readTable(countfile, false, false);
InputData input(inputfile, format);
ListVector* list = input.getListVector();
string lastLabel = list->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;
if (m->control_pressed) { delete list; return 0; }
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if(allLines == 1 || labels.count(list->getLabel()) == 1){
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { delete list; return 0; }
RAbundVector* rabund = new RAbundVector();
createRabund(ct, list, rabund);
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
delete rabund;
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
}
if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
delete list;
list = input.getListVector(lastLabel);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { delete list; return 0; }
RAbundVector* rabund = new RAbundVector();
createRabund(ct, list, rabund);
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
delete rabund;
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
//restore real lastlabel to save below
list->setLabel(saveLabel);
}
lastLabel = list->getLabel();
delete list;
list = input.getListVector();
}
//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 (list != NULL) { delete list; }
list = input.getListVector(lastLabel);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { delete list; return 0; }
RAbundVector* rabund = new RAbundVector();
createRabund(ct, list, rabund);
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
delete rabund;
delete list;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetRAbundCommand", "processList");
exit(1);
}
}
int GetRAbundCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
filename = getOutputFileName("rabund", variables);
m->openOutputFile(filename, out);
if (countfile != "") {
processList(out);
}else {
InputData input(inputfile, format);
RAbundVector* rabund = input.getRAbundVector();
string lastLabel = rabund->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;
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete rabund; return 0; }
while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete rabund; return 0; }
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());
}
if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = rabund->getLabel();
delete rabund;
rabund = input.getRAbundVector(lastLabel);
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete rabund; return 0; }
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());
//restore real lastlabel to save below
rabund->setLabel(saveLabel);
}
lastLabel = rabund->getLabel();
delete rabund;
rabund = input.getRAbundVector();
}
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
//run last label if you need to
if (needToRun == true) {
if (rabund != NULL) { delete rabund; }
rabund = input.getRAbundVector(lastLabel);
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete rabund; return 0; }
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
delete rabund;
}
}
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["rabund"].push_back(filename);
m->mothurOutEndLine();
out.close();
//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); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetRAbundCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
int RemoveRareCommand::processRabund(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(rabundfile); }
string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + "pick" + m->getExtension(rabundfile);
outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
InputData input(rabundfile, "rabund");
RAbundVector* rabund = input.getRAbundVector();
string lastLabel = rabund->getLabel();
set<string> processedLabels;
set<string> userLabels = labels;
while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) { delete rabund; out.close(); return 0; }
if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());
RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());
for (int i = 0; i < rabund->getNumBins(); i++) {
if (rabund->get(i) > nseqs) {
newRabund.push_back(rabund->get(i));
}
}
if (newRabund.getNumBins() > 0) { newRabund.print(out); }
}
if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = rabund->getLabel();
delete rabund;
rabund = input.getRAbundVector(lastLabel);
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());
RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());
for (int i = 0; i < rabund->getNumBins(); i++) {
if (rabund->get(i) > nseqs) {
newRabund.push_back(rabund->get(i));
}
}
if (newRabund.getNumBins() > 0) { newRabund.print(out); }
//restore real lastlabel to save below
rabund->setLabel(saveLabel);
}
lastLabel = rabund->getLabel();
delete rabund;
rabund = input.getRAbundVector();
}
if (m->control_pressed) { out.close(); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
//run last label if you need to
if (needToRun == true) {
if (rabund != NULL) { delete rabund; }
rabund = input.getRAbundVector(lastLabel);
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());
for (int i = 0; i < rabund->getNumBins(); i++) {
if (rabund->get(i) > nseqs) {
newRabund.push_back(rabund->get(i));
}
}
if (newRabund.getNumBins() > 0) { newRabund.print(out); }
delete rabund;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveRareCommand", "processRabund");
exit(1);
}
}
//**********************************************************************************************************************
void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
try {
if (order.size() == 0) { //user has not specified an order so do aplabetically
sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
m->clearGroups();
vector<string> Groups;
//initialize bin values
for (int i = 0; i < thislookup.size(); i++) {
out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
thislookup[i]->print(out);
Groups.push_back(thislookup[i]->getGroup());
RAbundVector rav = thislookup[i]->getRAbundVector();
m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
rav.print(*(filehandles[thislookup[i]->getGroup()]));
(*(filehandles[thislookup[i]->getGroup()])).close();
}
m->setGroups(Groups);
}else{
//create a map from groupName to each sharedrabund
map<string, SharedRAbundVector*> myMap;
map<string, SharedRAbundVector*>::iterator myIt;
for (int i = 0; i < thislookup.size(); i++) {
myMap[thislookup[i]->getGroup()] = thislookup[i];
}
m->clearGroups();
vector<string> Groups;
//loop through ordered list and print the rabund
for (int i = 0; i < order.size(); i++) {
myIt = myMap.find(order[i]);
if(myIt != myMap.end()) { //we found it
out << (myIt->second)->getLabel() << '\t' << (myIt->second)->getGroup() << '\t';
(myIt->second)->print(out);
Groups.push_back((myIt->second)->getGroup());
RAbundVector rav = (myIt->second)->getRAbundVector();
m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
rav.print(*(filehandles[(myIt->second)->getGroup()]));
(*(filehandles[(myIt->second)->getGroup()])).close();
}else{
m->mothurOut("Can't find shared info for " + order[i] + ", skipping."); m->mothurOutEndLine();
}
}
m->setGroups(Groups);
}
}
catch(exception& e) {
m->errorOut(e, "SharedCommand", "printSharedData");
exit(1);
}
}