public:
OtuHierarchyCommand(string);
OtuHierarchyCommand();
- ~OtuHierarchyCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~OtuHierarchyCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "otu.hierarchy"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Otu.hierarchy"; }
+ string getDescription() { return "relates OTUs at different distances"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
bool abort;
set<string> labels; //holds labels to be used
string label, listFile, outputDir, output;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
vector<ListVector> getListVectors();