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();
private:
bool abort, allLines;
- string taxonomyFileName, label;
+ string taxonomyFileName, label, outputDir, namefile;
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;
map<int, int>::iterator itCurrent;
+
+ int readNamesFile();
};