public:
PhylotypeCommand(string);
PhylotypeCommand();
- ~PhylotypeCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~PhylotypeCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "phylotype"; }
+ string getCommandCategory() { return "Clustering"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
+ string getDescription() { return "cluster your sequences into OTUs based on their classifications"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
bool abort, allLines;
- string taxonomyFileName, label, outputDir, namefile;
+ string taxonomyFileName, label, outputDir, namefile, countfile;
set<string> labels; //holds labels to be used
int cutoff;
map<string, string> namemap;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
map<int, int> currentNodes;
map<int, int> parentNodes;