+ void setGroup(string, string);
+ vector<string> getNamesOfGroups() {
+ sort(namesOfGroups.begin(), namesOfGroups.end());
+ groupIndex.clear();
+ for (int i = 0; i < namesOfGroups.size(); i++) { groupIndex[namesOfGroups[i]] = i; }
+ return namesOfGroups;
+ }
+ vector<string> getNamesSeqs();
+ void setNamesOfGroups(vector<string> sn) { namesOfGroups = sn; }
+ int getNumSeqs() { return groupmap.size(); }
+ vector<string> getNamesSeqs(vector<string>); //get names of seqs belonging to a group or set of groups
+ int getNumSeqs(string); //return the number of seqs in a given group
+ int getCopy(GroupMap*);
+ int renameSeq(string, string);
+ int print(ofstream&);
+ int print(ofstream&, vector<string>); //print certain groups
+
+
+ map<string, int> groupIndex; //groupname, vectorIndex in namesOfGroups. - used by collectdisplays and libshuff commands.
+