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 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 GetSAbundCommand::processList(ofstream& out){
try {
CountTable ct;
ct.readTable(countfile, 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);
SAbundVector sabund = rabund->getSAbundVector();
sabund.print(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);
SAbundVector sabund = rabund->getSAbundVector();
sabund.print(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);
SAbundVector sabund = rabund->getSAbundVector();
sabund.print(out);
delete rabund;
delete list;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSAbundCommand", "processList");
exit(1);
}
}