#include "inputdata.h"
#include "groupmap.h"
#include "sharedcommand.h"
-#include "parselistcommand.h"
/* The read.otu must be run before you execute a collect.single, rarefaction.single, summary.single,
collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund
private:
GlobalData* globaldata;
- ReadOTUFile* read;
+ //ReadOTUFile* read;
InputData* input;
Command* shared;
- Command* parselist;
GroupMap* groupMap;
string filename, listfile, orderfile, sharedfile, line, label, groupfile, sabundfile, rabundfile, format;
- OptionParser* parser;
- map<string, string> parameters;
- map<string, string>::iterator it;
+
bool abort, allLines;
set<int> lines; //hold lines to be used
set<string> labels; //holds labels to be used