#include "logsd.h"
#include "bergerparker.h"
#include "bstick.h"
+#include "goodscoverage.h"
-//**********************************************************************************************************************
+#include "coverage.h"
+//**********************************************************************************************************************
CollectCommand::CollectCommand(){
try {
globaldata = GlobalData::getInstance();
cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
}else if (globaldata->Estimators[i] == "nseqs") {
cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
+ }else if (globaldata->Estimators[i] == "coverage") {
+ cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
}else if (globaldata->Estimators[i] == "ace") {
convert(globaldata->getAbund(), abund);
cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
}else if (globaldata->Estimators[i] == "bootstrap") {
cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
- }else if (globaldata->Estimators[i] == "geom") {
- cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geom")));
+ }else if (globaldata->Estimators[i] == "geometric") {
+ cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
}else if (globaldata->Estimators[i] == "qstat") {
cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
- }else if (globaldata->Estimators[i] == "logsd") {
- cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logsd")));
+ }else if (globaldata->Estimators[i] == "logseries") {
+ cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
}else if (globaldata->Estimators[i] == "bergerparker") {
cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
}else if (globaldata->Estimators[i] == "bstick") {
- cDisplays.push_back(new CollectDisplay(new BStick(), new OneColumnFile(fileNameRoot+"bstick")));
+ cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
+ }else if (globaldata->Estimators[i] == "goodscoverage") {
+ cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
}
}
}
//if the users entered no valid calculators don't execute command
if (cDisplays.size() == 0) { return 0; }
- read = new ReadPhilFile(globaldata->inputFileName);
+ read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
order = globaldata->gorder;
cout << order->getLabel() << '\t' << count << endl;
}
+
+ delete order;
order = (input->getOrderVector());
count++;
}