InputData* input;
ValidCalculators* validCalculator;
vector<SharedRAbundVector*> lookup;
- vector<SharedRAbundVector*> lastLookup;
+ string lastLabel;
string format, outputFile, groupNames, filename;
int numGroups;
ofstream out;
float precision, cutoff;
- OptionParser* parser;
- map<string, string> parameters;
- map<string, string>::iterator it;
+
bool abort, allLines;
- set<int> lines; //hold lines to be used
set<string> labels; //holds labels to be used
- string phylipfile, columnfile, namefile, calc, groups, line, label;
+ string phylipfile, columnfile, namefile, calc, groups, label, outputDir;
vector<string> Estimators, Groups; //holds estimators to be used
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.