void clear();
void refresh();
string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, cutoff, format;
- string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary, randomtree, abund, sorted, trump, soft, filter, scale, ends, processors, size;
- string templatefile, search, ksize, align, match, mismatch, gapopen, gapextend;
+ string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary, randomtree, abund, sorted, trump, soft, filter, scale, countends, processors, size;
+ string candidatefile, search, ksize, align, match, mismatch, gapopen, gapextend;
string commandName, optionText;
bool errorFree;