vector<linePair*> lines;
vector<string> fastaFileNames;
vector<string> namefileNames;
- map<string, int> nameMap;
- map<string, int>::iterator itNames;
+ vector<string> groupfileNames;
+ map<string, vector<string> > nameMap;
+ map<string, vector<string> >::iterator itNames;
Classify* classify;
- string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir;
+ string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
int processors, kmerSize, numWanted, cutoff, iters;
float match, misMatch, gapOpen, gapExtend;
bool abort, probs;