#include "command.hpp"
#include "listvector.hpp"
-#include "globaldata.hpp"
+
class RemoveRareCommand : public Command {
RemoveRareCommand(string);
RemoveRareCommand();
~RemoveRareCommand(){}
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+
+ vector<string> setParameters();
+ string getCommandName() { return "remove.rare"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "http://www.mothur.org/wiki/Remove.rare"; }
+ string getDescription() { return "removes rare sequences from a sabund, rabund, shared or list and group file"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
- string sabundfile, rabundfile, sharedfile, groupfile, listfile, outputDir, groups, label;
+ string sabundfile, rabundfile, sharedfile, groupfile, countfile, listfile, outputDir, groups, label;
int nseqs, allLines;
bool abort, byGroup;
vector<string> outputNames, Groups;
set<string> labels;
- map<string, vector<string> > outputTypes;
int processSabund();
int processRabund();
int processList();
int processShared();
- int processLookup(vector<SharedRAbundVector*>&, ofstream&);
+ int processLookup(vector<SharedRAbundVector*>&);
};