vector<string> setParameters();
string getCommandName() { return "phylo.diversity"; }
string getCommandCategory() { return "Hypothesis Testing"; }
vector<string> setParameters();
string getCommandName() { return "phylo.diversity"; }
string getCommandCategory() { return "Hypothesis Testing"; }
string getCitation() { return "Faith DP (1994). Phylogenetic pattern and the quantification of organismal biodiversity. Philos Trans R Soc Lond B Biol Sci 345: 45-58. \nhttp://www.mothur.org/wiki/Phylo.diversity"; }
string getDescription() { return "phylo.diversity"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string getCitation() { return "Faith DP (1994). Phylogenetic pattern and the quantification of organismal biodiversity. Philos Trans R Soc Lond B Biol Sci 345: 45-58. \nhttp://www.mothur.org/wiki/Phylo.diversity"; }
string getDescription() { return "phylo.diversity"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
float freq;
int iters, processors, numUniquesInName;
bool abort, rarefy, summary, collect, scale;
float freq;
int iters, processors, numUniquesInName;
bool abort, rarefy, summary, collect, scale;
- string groups, outputDir, treefile, groupfile, namefile;
+ string groups, outputDir, treefile, groupfile, namefile, countfile;
vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
map<string, int> getRootForGroups(Tree* t);
vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
map<string, int> getRootForGroups(Tree* t);