vector<string> setParameters();
string getCommandName() { return "tree.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getOutputFileNameTag(string, string);
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Tree.shared"; }
string getDescription() { return "generate a tree file that describes the dissimilarity among groups"; }
Tree* createTree(vector< vector<double> >&);
void printSims(ostream&, vector< vector<double> >&);
int makeSimsShared();
- vector< vector<double> > makeSimsDist();
+ vector< vector<double> > makeSimsDist(SparseDistanceMatrix*);
int writeTree(string, Tree*);
int driver(vector<SharedRAbundVector*>, int, int, vector< vector<seqDist> >&);
- ReadMatrix* readMatrix;
- SparseMatrix* matrix;
NameAssignment* nameMap;
ListVector* list;
TreeMap* tmap;