#include "sharedthetayc.h"
#include "sharedthetan.h"
#include "sharedkstest.h"
-#include "sharedbdiversity.h"
+#include "whittaker.h"
#include "sharednseqs.h"
#include "sharedochiai.h"
#include "sharedanderbergs.h"
#include "sharedlennon.h"
#include "sharedmorisitahorn.h"
#include "sharedbraycurtis.h"
+#include "sharedjackknife.h"
+#include "sharedwhittaker.h"
cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
}else if (globaldata->Estimators[i] == "jabund") {
cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund")));
- }else if (globaldata->Estimators[i] == "sorensonabund") {
+ }else if (globaldata->Estimators[i] == "sorabund") {
cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund")));
}else if (globaldata->Estimators[i] == "jclass") {
cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass")));
cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan")));
}else if (globaldata->Estimators[i] == "kstest") {
cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest")));
- }else if (globaldata->Estimators[i] == "bdiversity") {
- cDisplays.push_back(new CollectDisplay(new BDiversity(), new SharedOneColumnFile(fileNameRoot+"bdiversity")));
+ }else if (globaldata->Estimators[i] == "whittaker") {
+ 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 ReadPhilFile(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 ReadPhilFile(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
util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
while(order != NULL){
+
orderList.insert(order->getLabel());
+
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+
//create collectors curve
cCurve = new Collect(order, cDisplays);
convert(globaldata->getFreq(), freq);
}
//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;
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]; }
//reset groups parameter