TreeMap() { m = MothurOut::getInstance(); }
TreeMap(string);
~TreeMap();
- void readMap();
+ int readMap();
int getNumGroups();
int getNumSeqs();
void setIndex(string, int); //sequencename, index
void removeSeq(string); //removes a sequence, this is to accomadate trees that do not contain all the seqs in your groupfile
string getGroup(string);
void addSeq(string, string);
- vector<string> namesOfGroups;
+ void addGroup(string s) { setNamesOfGroups(s); }
+ vector<string> getNamesOfGroups() {
+ sort(namesOfGroups.begin(), namesOfGroups.end());
+ return namesOfGroups;
+ }
vector<string> namesOfSeqs;
map<string,int> seqsPerGroup; //groupname, number of seqs in that group.
map<string, GroupIndex> treemap; //sequence name and <groupname, vector index>
void print(ostream&);
- void makeSim(GroupMap*); //takes groupmap info and fills treemap for use by tree.shared command.
+ void makeSim(vector<string>); //takes groupmap info and fills treemap for use by tree.shared command.
void makeSim(ListVector*); //takes listvector info and fills treemap for use by tree.shared command.
private:
+ vector<string> namesOfGroups;
ifstream fileHandle;
string groupFileName;
int numGroups;