public:
MGClusterCommand(string);
+ MGClusterCommand();
~MGClusterCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
ListVector* list;
ListVector oldList;
vector<seqDist> overlapMatrix;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
string blastfile, method, namefile, overlapFile, distFile, outputDir;
ofstream sabundFile, rabundFile, listFile;
- float cutoff, penalty;
+ double cutoff;
+ float penalty;
int precision, length, precisionLength;
- bool abort, minWanted, hclusterWanted, merge;
+ bool abort, minWanted, hclusterWanted, merge, hard;
void printData(ListVector*);
ListVector* mergeOPFs(map<string, int>, float);