//**********************************************************************************************************************
GetRelAbundCommand::GetRelAbundCommand(){
try {
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["relabund"] = tempOutNames;
}
GetRelAbundCommand::GetRelAbundCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
int GetRelAbundCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "relabund";
ofstream out;
int GetRelAbundCommand::getRelAbundance(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
try {
- if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
-
for (int i = 0; i < thisLookUp.size(); i++) {
out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t' << thisLookUp[i]->getNumBins() << '\t';
}
}
//**********************************************************************************************************************
-int GetRelAbundCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
- try {
-
- vector<SharedRAbundVector*> newLookup;
- for (int i = 0; i < thislookup.size(); i++) {
- SharedRAbundVector* temp = new SharedRAbundVector();
- temp->setLabel(thislookup[i]->getLabel());
- temp->setGroup(thislookup[i]->getGroup());
- newLookup.push_back(temp);
- }
-
- //for each bin
- for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
- if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
-
- //look at each sharedRabund and make sure they are not all zero
- bool allZero = true;
- for (int j = 0; j < thislookup.size(); j++) {
- if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
- }
-
- //if they are not all zero add this bin
- if (!allZero) {
- for (int j = 0; j < thislookup.size(); j++) {
- newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
- }
- }
- }
-
- for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
-
- thislookup = newLookup;
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "GetRelAbundCommand", "eliminateZeroOTUS");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************