public:
PhyloDiversityCommand(string);
+ PhyloDiversityCommand();
~PhyloDiversityCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
bool abort, rarefy, summary, collect, scale;
string groups, outputDir;
vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
+ map<string, vector<string> > outputTypes;
void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);
void printSumData(map< string, vector<float> >&, ofstream&, int);
- float calcBranchLength(Tree*, int, map< string, set<int> >&);
+ vector<float> calcBranchLength(Tree*, int, map< string, set<int> >&);
int driver(Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&, bool);
int createProcesses(vector<int>&, Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&);