*/
#include "command.hpp"
-
-//class GlobalData;
class GroupMap;
class AmovaCommand : public Command {
public:
AmovaCommand(string);
AmovaCommand();
- ~AmovaCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ ~AmovaCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "amova"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\nhttp://www.mothur.org/wiki/Amova"; }
+ string getDescription() { return "analysis of molecular variance"; }
+
int execute();
- void help();
+ void help() { m->mothurOut(getHelpString()); }
private:
double runAMOVA(ofstream&, map<string, vector<int> >, double);
double calcSSTotal(map<string, vector<int> >&);
map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
-
bool abort;
- map<string, vector<string> > outputTypes;
- vector<string> outputNames;
+ vector<string> outputNames, Sets;
string outputDir, inputDir, designFileName, phylipFileName;
GroupMap* designMap;