string CountGroupsCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The count.groups command counts sequences from a specfic group or set of groups from the following file types: group or shared file.\n";
+ helpString += "The count.groups command counts sequences from a specific group or set of groups from the following file types: group or shared file.\n";
helpString += "The count.groups command parameters are accnos, group, shared and groups. You must provide a group or shared file.\n";
helpString += "The accnos parameter allows you to provide a file containing the list of groups.\n";
helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like. You can separate group names with dashes.\n";
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
sharedfile = validParameter.validFile(parameters, "shared", true);
}
}
- if ((accnosfile == "") && (Groups.size() == 0)) { Groups.push_back("all"); m->Groups = Groups; }
+ if ((accnosfile == "") && (Groups.size() == 0)) { Groups.push_back("all"); m->setGroups(Groups); }
}
}
//make sure groups are valid
//takes care of user setting groupNames that are invalid or setting groups=all
SharedUtil util;
- util.setGroups(Groups, groupMap.namesOfGroups);
+ vector<string> nameGroups = groupMap.getNamesOfGroups();
+ util.setGroups(Groups, nameGroups);
for (int i = 0; i < Groups.size(); i++) {
m->mothurOut(Groups[i] + " contains " + toString(groupMap.getNumSeqs(Groups[i])) + "."); m->mothurOutEndLine();
}
in.close();
- m->Groups = Groups;
+ m->setGroups(Groups);
}
catch(exception& e) {