#include "command.hpp"
#include "inputdata.h"
-#include "readotu.h"
#include "sharedrabundvector.h"
-class GlobalData;
-
class NormalizeSharedCommand : public Command {
public:
NormalizeSharedCommand(string);
- ~NormalizeSharedCommand();
- int execute();
- void help();
+ NormalizeSharedCommand();
+ ~NormalizeSharedCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "normalize.shared"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "http://www.mothur.org/wiki/Normalize.shared"; }
+ string getDescription() { return "normalize samples in a shared or relabund file"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- GlobalData* globaldata;
- ReadOTUFile* read;
InputData* input;
vector<SharedRAbundVector*> lookup;
+ vector<SharedRAbundFloatVector*> lookupFloat;
- bool abort, allLines, pickedGroups;
+ bool abort, allLines, pickedGroups, makeRelabund;
set<string> labels; //holds labels to be used
- string groups, label, outputDir, method;
+ string groups, label, outputDir, method, sharedfile, relabundfile, format, inputfile;
int norm;
- vector<string> Groups;
-
- int normalize(vector<SharedRAbundVector*>&, ofstream&);
- int eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup);
+ vector<string> Groups, outputNames;
+
+ int normalize(vector<SharedRAbundVector*>&);
+ int normalize(vector<SharedRAbundFloatVector*>&);
+ int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+ int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
};