public:
UnifracWeightedCommand(string);
+ UnifracWeightedCommand();
~UnifracWeightedCommand() { if (abort == false) { delete weighted; delete util; } }
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
int num;
linePair(int i, int j) : start(i), num(j) {}
};
- vector<linePair*> lines;
+ vector<linePair> lines;
GlobalData* globaldata;
SharedUtil* util;
vector<double> utreeScores; //user tree unweighted scores
vector<double> WScoreSig; //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
vector<string> groupComb; // AB. AC, BC...
- Tree* randT; //random tree
TreeMap* tmap;
Weighted* weighted;
string sumFile, outputDir;
vector< map<float, float> > rCumul; //map <weighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each c
map<float, float> validScores; //map contains scores from random
- bool abort, phylip, random;
- string groups, itersString;
+ bool abort, phylip, random, includeRoot;
+ string groups, itersString, outputForm;
vector<string> Groups, outputNames; //holds groups to be used
+ map<string, vector<string> > outputTypes;
int processors;
//void removeValidScoresDuplicates();
int findIndex(float, int);
void calculateFreqsCumuls();
- int createProcesses(Tree*, Tree*, vector< vector<string> >, vector<double>&, vector< vector<double> >&);
- int driver(Tree*, Tree*, vector< vector<string> >, int, int, vector<double>&, vector< vector<double> >&);
+ int createProcesses(Tree*, vector< vector<string> >, vector< vector<double> >&);
+ int driver(Tree*, vector< vector<string> >, int, int, vector< vector<double> >&);
};