string getCommandName() { return "unifrac.unweighted"; }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
-
+ string getCitation() { return "Lozupone C, Knight R (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-35. \nhttp://www.mothur.org/wiki/Unifrac.unweighted"; }
+ string getDescription() { return "generic tests that describes whether two or more communities have the same structure"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
- ReadTree* read;
- SharedUtil* util;
FileOutput* output;
vector<Tree*> T; //user trees
TreeMap* tmap;
- Unweighted* unweighted;
string sumFile, allGroups;
vector<string> groupComb; // AB. AC, BC...
int iters, numGroups, numComp, counter, processors, numUniquesInName;
ofstream outSum, out;
ifstream inFile;
- map<string, string> nameMap;
void printUWSummaryFile(int);
void printUnweightedFile();
void createPhylipFile(int);
- int readNamesFile();
-
};