fileNameRoot = getRootName(globaldata->inputFileName);
format = globaldata->getFormat();
validCalculator = new ValidCalculators();
- util = new SharedUtil();
int i;
for (i=0; i<globaldata->Estimators.size(); i++) {
//**********************************************************************************************************************
RareFactSharedCommand::~RareFactSharedCommand(){
- delete order;
delete input;
delete rCurve;
delete read;
- delete util;
}
//**********************************************************************************************************************
//if the users entered no valid calculators don't execute command
if (rDisplays.size() == 0) { return 0; }
- if (format == "sharedfile") {
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
+ read = new ReadOTUFile(globaldata->inputFileName);
+ read->read(&*globaldata);
- input = globaldata->ginput;
- order = input->getSharedOrderVector();
- }else {
- //you are using a list and a groupfile
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
+ input = globaldata->ginput;
+ lookup = input->getSharedRAbundVectors();
- input = globaldata->ginput;
- SharedList = globaldata->gSharedList;
- order = SharedList->getSharedOrderVector();
+ if (lookup.size() < 2) {
+ cout << "I cannot run the command without at least 2 valid groups.";
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ return 0;
}
+
- //set users groups
- util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "rarefact");
+ while(lookup[0] != NULL){
- while(order != NULL){
-
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
//create collectors curve
- rCurve = new Rarefact(order, rDisplays);
+ rCurve = new Rarefact(lookup, rDisplays);
convert(globaldata->getFreq(), freq);
convert(globaldata->getIters(), nIters);
rCurve->getSharedCurve(freq, nIters);
delete rCurve;
- cout << order->getLabel() << '\t' << count << endl;
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
}
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
//get next line to process
- if (format == "sharedfile") {
- order = input->getSharedOrderVector();
- }else {
- //you are using a list and a groupfile
- SharedList = input->getSharedListVector(); //get new list vector to process
- if (SharedList != NULL) {
- order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
- }else {
- break;
- }
- }
-
+ lookup = input->getSharedRAbundVectors();
count++;
}