#include "collectcommand.h"
#include "ace.h"
#include "sobs.h"
+#include "nseqs.h"
#include "chao1.h"
#include "bootstrap.h"
#include "simpson.h"
#include "npshannon.h"
#include "shannon.h"
#include "jackknife.h"
+#include "geom.h"
+#include "qstat.h"
+#include "logsd.h"
+#include "bergerparker.h"
+#include "bstick.h"
//**********************************************************************************************************************
-
-
CollectCommand::CollectCommand(){
try {
globaldata = GlobalData::getInstance();
fileNameRoot = getRootName(globaldata->inputFileName);
int i;
validCalculator = new ValidCalculators();
-
for (i=0; i<globaldata->Estimators.size(); i++) {
if (validCalculator->isValidCalculator("single", globaldata->Estimators[i]) == true) {
if (globaldata->Estimators[i] == "sobs") {
cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
}else if (globaldata->Estimators[i] == "chao") {
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] == "ace") {
- cDisplays.push_back(new CollectDisplay(new Ace(), new ThreeColumnFile(fileNameRoot+"ace")));
+ convert(globaldata->getAbund(), abund);
+ cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
}else if (globaldata->Estimators[i] == "jack") {
cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
}else if (globaldata->Estimators[i] == "shannon") {
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] == "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] == "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")));
}
}
}
order = globaldata->gorder;
input = globaldata->ginput;
-
+ set<string> orderList;
+
while(order != NULL){
+ orderList.insert(order->getLabel());
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
-
cCurve = new Collect(order, cDisplays);
convert(globaldata->getFreq(), freq);
cCurve->getCurve(freq);
cout << order->getLabel() << '\t' << count << endl;
}
-
order = (input->getOrderVector());
count++;
-
}
-
+ set<string>::iterator i;
+ for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
+ if(orderList.count(*i) == 0)
+ cout << "'" << *i << "'" << " is not a valid label.\n";
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
return 0;
}