public:
HomovaCommand(string);
HomovaCommand();
- ~HomovaCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ ~HomovaCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "homova"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+ string getHelpString();
+ string getCitation() { return "Stewart CN, Excoffier L (1996). Assessing population genetic structure and variability with RAPD data: Application to Vaccinium macrocarpon (American Cranberry). J Evol Biol 9: 153-71. \nhttp://www.mothur.org/wiki/Homova"; }
+
int execute();
- void help();
+ void help() { m->mothurOut(getHelpString()); }
private:
double runHOMOVA(ofstream& , map<string, vector<int> >, double);
map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
bool abort;
- map<string, vector<string> > outputTypes;
vector<string> outputNames;
string outputDir, inputDir, designFileName, phylipFileName;