class UnifracWeightedCommand : public Command {
public:
- UnifracWeightedCommand(string);
- ~UnifracWeightedCommand() { delete weighted; delete util; }
+ UnifracWeightedCommand(string);
+ ~UnifracWeightedCommand() { if (abort == false) { delete weighted; delete util; } }
int execute();
void help();
private:
+ struct linePair {
+ int start;
+ int num;
+ linePair(int i, int j) : start(i), num(j) {}
+ };
+ vector<linePair*> lines;
+
GlobalData* globaldata;
SharedUtil* util;
FileOutput* output;
Tree* randT; //random tree
TreeMap* tmap;
Weighted* weighted;
- string sumFile;
+ string sumFile, outputDir;
int iters, numGroups, numComp, counter;
EstOutput userData; //weighted score info for user tree
EstOutput randomData; //weighted score info for random trees
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;
+ bool abort, phylip, random;
string groups, itersString;
- vector<string> Groups; //holds groups to be used
+ vector<string> Groups, outputNames; //holds groups to be used
+ int processors;
ofstream outSum;
void printWSummaryFile();
void printWeightedFile();
+ void createPhylipFile();
//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> >&);
};