void setReleaseDate(string r) { releaseDate = r; }
string getVersion() { return version; }
void setVersion(string r) { version = r; }
- vector<string> Groups;
+
+ void addGroup(string g) { Groups.push_back(g); }
+ void setGroups(vector<string>& g) { sort(g.begin(), g.end()); Groups = g; }
+ void clearGroups() { Groups.clear(); }
+ int getNumGroups() { return Groups.size(); }
+ vector<string> getGroups() { sort(Groups.begin(), Groups.end()); return Groups; }
+ void addAllGroup(string g) { namesOfGroups.push_back(g); }
+ void setAllGroups(vector<string>& g) { sort(g.begin(), g.end()); namesOfGroups = g; }
+ void clearAllGroups() { namesOfGroups.clear(); }
+ int getNumAllGroups() { return namesOfGroups.size(); }
+
+ vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
vector<string> Treenames;
map<string, string> names;
- vector<string> namesOfGroups;
vector<string> binLabelsInFile;
vector<string> currentBinLabels;
string saveNextLabel, argv, sharedHeaderMode;
string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
-
+ vector<string> Groups;
+ vector<string> namesOfGroups;
ofstream out;
int mem_usage(double&, double&);