public:
UnifracUnweightedCommand(string);
- ~UnifracUnweightedCommand() { delete unweighted; delete util; }
+ UnifracUnweightedCommand();
+ ~UnifracUnweightedCommand() { globaldata->Groups.clear(); if (abort == false) { delete unweighted; delete util; } }
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
Unweighted* unweighted;
string sumFile, allGroups;
vector<string> groupComb; // AB. AC, BC...
- int iters, numGroups, numComp, counter;
+ int iters, numGroups, numComp, counter, processors;
EstOutput userData; //unweighted score info for user tree
EstOutput randomData; //unweighted score info for random trees
vector< vector<float> > utreeScores; //scores for users trees for each comb.
vector< map<float, float> > rscoreFreq; //map <unweighted score, number of random trees with that score.> -vector entry for each combination.
vector< map<float, float> > rCumul; //map <unweighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each combination.
- bool abort;
- string groups, itersString;
- vector<string> Groups; //holds groups to be used
+ bool abort, phylip, random, includeRoot;
+ string groups, itersString, outputDir, outputForm;
+ vector<string> Groups, outputNames; //holds groups to be used
+ map<string, vector<string> > outputTypes;
ofstream outSum, out;
ifstream inFile;
void printUWSummaryFile(int);
void printUnweightedFile();
+ void createPhylipFile(int);
};
-
-
-#endif
\ No newline at end of file
+#endif