*/
#include "command.hpp"
+#include "sharedrabundvector.h"
+#include "listvector.hpp"
+
class RemoveLineageCommand : public Command {
private:
set<string> names;
vector<string> outputNames, listOfTaxons;
- string fastafile, namefile, groupfile, alignfile, listfile, countfile, taxfile, outputDir, taxons;
+ string fastafile, namefile, groupfile, alignfile, listfile, countfile, taxfile, outputDir, taxons, sharedfile, constaxonomy, label;
bool abort, dups;
+ vector<SharedRAbundVector*> lookup;
+ ListVector* list;
int readFasta();
int readName();
int readCount();
int readAlign();
int readList();
- int readTax();
+ int readTax();
+ int readShared();
+ int readConsTax();
+ int readConsList();
+ int getShared();
+ int getListVector();
vector< map<string, float> > getTaxons(string);
};