7 * Created by Sarah Westcott on 12/1/08.
8 * Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
13 #include "mothurout.h"
15 /* This class is a representation of the groupfile. It is used by all the shared commands to determine what group a
16 certain sequence belongs to. */
26 bool isValidGroup(string); //return true if string is a valid group
27 string getGroup(string);
28 void setGroup(string, string);
29 vector<string> getNamesOfGroups() {
30 sort(namesOfGroups.begin(), namesOfGroups.end());
32 for (int i = 0; i < namesOfGroups.size(); i++) { groupIndex[namesOfGroups[i]] = i; }
35 void setNamesOfGroups(vector<string> sn) { namesOfGroups = sn; }
36 map<string, int> groupIndex; //groupname, vectorIndex in namesOfGroups. - used by collectdisplays and libshuff commands.
37 int getNumSeqs() { return groupmap.size(); }
38 vector<string> getNamesSeqs();
39 vector<string> getNamesSeqs(vector<string>); //get names of seqs belonging to a group or set of groups
40 int getNumSeqs(string); //return the number of seqs in a given group
43 vector<string> namesOfGroups;
48 map<string, string>::iterator it;
49 void setNamesOfGroups(string);
50 map<string, string> groupmap; //sequence name and groupname
51 map<string, int> seqsPerGroup; //maps groupname to number of seqs in that group