set<string> labels; //holds labels to be used
map<string, int> nameToIndex; //maps sequence name to index in sparsematrix
vector<string> outputNames;
+ map<string, string> outputNameFiles;
float cutoff;
int precision;
vector<SeqMap> seqVec; // contains maps with sequence index and distance
void readNamesFile();
int process(ListVector*);
SeqMap getMap(int);
- string findRep(int, string&, ListVector*, int&); // returns the name of the "representative" sequence of given bin,
- // fills a string containing the groups in that bin if a groupfile is given,
- // and returns the number of sequences in the given bin
+ string findRep(int, ListVector*); // returns the name of the "representative" sequence of given bin
+ int processNames(string, string);
+
};