helpString += "The groups parameter allows you to specify which of the groups in your shared or relabund you would like analyzed, or if you provide a design file the groups in your design file. The groups may be entered separated by dashes.\n";
helpString += "The label parameter indicates at what distance your tree relates to the shared or relabund.\n";
helpString += "The indicator command should be used in the following format: indicator(tree=test.tre, shared=test.shared, label=0.03)\n";
- helpString += "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n";
return helpString;
}
catch(exception& e) {
}
m->runParse = true;
+ m->Groups.clear();
+ m->namesOfGroups.clear();
+ m->Treenames.clear();
+ m->names.clear();
vector<string> tempOutNames;
outputTypes["tree"] = tempOutNames;
// reading tree info //
/***************************************************/
string groupfile = "";
+ m->setTreeFile(treefile);
Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
treeMap = new TreeMap();
bool mismatch = false;