#include "rarefactsharedcommand.h"
#include "sharedsobs.h"
+#include "sharednseqs.h"
//**********************************************************************************************************************
fileNameRoot = getRootName(globaldata->inputFileName);
format = globaldata->getFormat();
validCalculator = new ValidCalculators();
+ util = new SharedUtil();
int i;
for (i=0; i<globaldata->Estimators.size(); i++) {
if (validCalculator->isValidCalculator("sharedrarefaction", globaldata->Estimators[i]) == true) {
if (globaldata->Estimators[i] == "sharedobserved") {
rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
+ }else if (globaldata->Estimators[i] == "sharednseqs") {
+ rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
}
+
}
}
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 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;
- SharedList = globaldata->gSharedList;
- order = SharedList->getSharedOrderVector();
- }
+ input = globaldata->ginput;
+ order = input->getSharedOrderVector();
+
+ //set users groups
+ util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "rarefact");
while(order != NULL){
}
//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++;
}
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
+
+ //reset groups parameter
+ globaldata->Groups.clear(); globaldata->setGroups("");
+
return 0;
}
catch(exception& e) {