#include "listvector.hpp"
#include "sequence.hpp"
#include "groupmap.h"
+#include "sharedrabundvector.h"
+#include "inputdata.h"
//**********************************************************************************************************************
class GetSharedOTUCommand : public Command {
string getCommandName() { return "get.sharedseqs"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getRequiredCommand() { return "none"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.sharedseqs"; }
string getDescription() { return "identifies sequences that are either unique or shared by specific groups"; }
GroupMap* groupMap;
set<string> labels;
- string fastafile, label, groups, listfile, groupfile, output, userGroups, outputDir, format;
+ string fastafile, label, groups, listfile, groupfile, sharedfile, output, userGroups, outputDir, format;
bool abort, allLines, unique;
vector<string> Groups;
map<string, string> groupFinder;
vector<string> outputNames;
int process(ListVector*);
+ int process(vector<SharedRAbundVector*>&);
+ int runShared();
};
//**********************************************************************************************************************