Cluster* cluster;
HCluster* hcluster;
ListVector* list;
+ CountTable* ct;
ListVector oldList;
RAbundVector rav;
vector<seqDist> overlapMatrix;
double cutoff;
float penalty;
int precision, length, precisionLength;
- bool abort, minWanted, hclusterWanted, merge, hard, large;
+ bool abort, minWanted, hclusterWanted, merge, hard;
void printData(ListVector*);
ListVector* mergeOPFs(map<string, int>, float);
void sortHclusterFiles(string, string);
vector<seqDist> getSeqs(ifstream&);
- void createRabund(CountTable);
+ void createRabund(CountTable*&, ListVector*&, RAbundVector*&);
};