public:
AnosimCommand(string);
AnosimCommand();
- ~AnosimCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ ~AnosimCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "anosim"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+ string getHelpString();
+ string getCitation() { return "Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143.\nhttp://www.mothur.org/wiki/Anosim"; }
+ string getDescription() { return "analysis of similarity"; }
+
int execute();
- void help();
+ void help() { m->mothurOut(getHelpString()); }
private:
bool abort;
GroupMap* designMap;
- map<string, vector<string> > outputTypes;
string outputDir, inputDir, designFileName, phylipFileName;
vector<vector<double> > convertToRanks(vector<vector<double> >);