helpString += "The phylo.diversity command should be in the following format: phylo.diversity(groups=yourGroups, rarefy=yourRarefy, iters=yourIters).\n";
helpString += "Example phylo.diversity(groups=A-B-C, rarefy=T, iters=500).\n";
helpString += "The phylo.diversity command output two files: .phylo.diversity and if rarefy=T, .rarefaction.\n";
- helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
return helpString;
}
catch(exception& e) {
}
m->runParse = true;
+ m->Groups.clear();
+ m->namesOfGroups.clear();
+ m->Treenames.clear();
+ m->names.clear();
//check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ m->setTreeFile(treefile);
+
//read in group map info.
tmap = new TreeMap(groupfile);
tmap->readMap();