HCluster* hcluster;
ListVector* list;
ListVector oldList;
- vector<DistNode> overlapMatrix;
- DistNode next;
-
+ vector<seqDist> overlapMatrix;
- string blastfile, method, namefile, overlapFile, distFile;
+ string blastfile, method, namefile, overlapFile, distFile, outputDir;
ofstream sabundFile, rabundFile, listFile;
float cutoff, penalty;
int precision, length, precisionLength;
- bool abort, minWanted, hclusterWanted, exitedBreak, merge;
+ bool abort, minWanted, hclusterWanted, merge;
void printData(ListVector*);
ListVector* mergeOPFs(map<string, int>, float);
void sortHclusterFiles(string, string);
- vector<DistNode> getSeqs(ifstream&);
+ vector<seqDist> getSeqs(ifstream&);
};