7 * Created by Sarah Westcott on 1/26/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
14 #include "listvector.hpp"
16 /* This class is used by the read.tree command to build the tree container. */
34 void setIndex(string, int); //sequencename, index
35 int getIndex(string); //returns vector index of sequence
36 bool isValidGroup(string); //return true if string is a valid group
37 string getGroup(string);
38 vector<string> namesOfGroups;
39 vector<string> namesOfSeqs;
40 map<string,int> seqsPerGroup; //groupname, number of seqs in that group.
41 map<string, GroupIndex> treemap; //sequence name and <groupname, vector index>
43 void makeSim(GroupMap*); //takes groupmap info and fills treemap for use by tree.shared command.
44 void makeSim(ListVector*); //takes listvector info and fills treemap for use by tree.shared command.
50 map<string, GroupIndex>::iterator it;
51 map<string, int>::iterator it2;
52 void setNamesOfGroups(string);