#include "sharedlennon.h"
#include "sharedmorisitahorn.h"
#include "sharedbraycurtis.h"
+#include "sharedjackknife.h"
+#include "sharedwhittaker.h"
cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
}else if (globaldata->Estimators[i] == "sharednseqs") {
cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
+
}else if (globaldata->Estimators[i] == "ochiai") {
cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai")));
}else if (globaldata->Estimators[i] == "anderberg") {
//if the users entered no valid calculators don't execute command
if (cDisplays.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;
+ order = input->getSharedOrderVector();
- input = globaldata->ginput;
- SharedList = globaldata->gSharedList;
- order = SharedList->getSharedOrderVector();
- }
set<string> orderList;
//set users groups
}
//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;
- }
- }
-
+ delete order;
+ order = input->getSharedOrderVector();
count++;
}
set<string>::iterator i;