using namespace std;
-#include <string>
-#include <map>
#include "utilities.hpp"
#include "sparsematrix.hpp"
#include "progress.hpp"
#include "listvector.hpp"
#include "rabundvector.hpp"
-#include <exception>
-
#include "readmatrix.hpp"
//you have two inputs because in the next if statement if you only have one then it moves ahead in the same file.
//So when you run the collect or summary commands you miss a line.
input = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund.
- inputSabund = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund.
+ inputSabund = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund or shared.
}else {//there is an orderfile
input = new InputData(philFile, globaldata->getOrderFile(), globaldata->getFormat());
}
sabund = inputSabund->getSAbundVector();
globaldata->sabund = sabund; //saving to be used by summary command.
}else if (globaldata->getFormat() == "shared") {
- SharedList = input->getSharedListVector(); //you are reading for parselist command, or shared commands.
+ SharedList = input->getSharedListVector(); //you are reading for collect.shared, rarefaction.shared, summary.shared, parselist command, or shared commands.
globaldata->gSharedList = SharedList;
}
}