#include "command.hpp"
#include "readtree.h"
#include "treemap.h"
-#include "globaldata.hpp"
#include "sharedrabundvector.h"
#include "sharedrabundfloatvector.h"
#include "inputdata.h"
public:
IndicatorCommand(string);
IndicatorCommand();
- ~IndicatorCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ ~IndicatorCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "indicator"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+ string getHelpString();
+ string getCitation() { return "Dufrene M, Legendre P (1997). Species assemblages and indicator species: The need for a flexible asymmetrical approach. Ecol Monogr 67: 345-66.\n McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Indicator"; }
+
int execute();
- void help();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
ReadTree* read;
TreeMap* treeMap;
GroupMap* designMap;
string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir, designfile;
bool abort;
vector<string> outputNames, Groups;
- map<string, vector<string> > outputTypes;
vector<SharedRAbundVector*> lookup;
vector<SharedRAbundFloatVector*> lookupFloat;