#include "listvector.hpp"
#include "sequence.hpp"
#include "groupmap.h"
-#include "globaldata.hpp"
//**********************************************************************************************************************
class GetSharedOTUCommand : public Command {
GetSharedOTUCommand(string);
GetSharedOTUCommand();
- ~GetSharedOTUCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~GetSharedOTUCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "get.sharedseqs"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getRequiredCommand() { return "none"; }
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Get.sharedseqs"; }
+ string getDescription() { return "identifies sequences that are either unique or shared by specific groups"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+
private:
-
- GlobalData* globaldata;
ListVector* list;
GroupMap* groupMap;
set<string> labels;
- string fastafile, label, groups, listfile, groupfile, output, userGroups, outputDir;
+ string fastafile, label, groups, listfile, groupfile, output, userGroups, outputDir, format;
bool abort, allLines, unique;
vector<string> Groups;
map<string, string> groupFinder;
map<string, string>::iterator it;
vector<Sequence> seqs;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
int process(ListVector*);