ReadMatrix* readMatrix;
FormatMatrix* formatMatrix;
NameAssignment* nameMap;
- string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format;
+ string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir, groups;
ofstream out;
ifstream in, inNames, inRow;
bool abort, allLines, groupError, large;
set<string> labels; //holds labels to be used
map<string, int> nameToIndex; //maps sequence name to index in sparsematrix
+ vector<string> outputNames, Groups;
+ 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(vector<string>); // returns the name of the "representative" sequence of given bin or subset of a bin, for groups
+ int processNames(string, string);
+
};