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#ifndef GROUPMAP_H
#define GROUPMAP_H
/*
* groupmap.h
* Mothur
*
* Created by Sarah Westcott on 12/1/08.
* Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "mothur.h"
#include "mothurout.h"
#include "utils.hpp"
/* This class is a representation of the groupfile. It is used by all the shared commands to determine what group a
certain sequence belongs to. */
class GroupMap {
public:
GroupMap() { m = MothurOut::getInstance(); groupFileName = ""; }
GroupMap(string);
~GroupMap();
int getCopy(GroupMap*);
int readMap();
int readMap(vector<string> groups); //selected groups read in. If groups.size() == 0, all groups are read
int readMap(string, vector<string> groups); //filename, selected groups. selected groups read in. If groups.size() == 0, all groups are read
int readMap(string);
int readDesignMap();
int readDesignMap(string);
int getNumGroups();
bool isValidGroup(string); //return true if string is a valid group
string getGroup(string);
vector<string> getGroups(string); //returns groups represented by the seqs passed in. Think column two from a namefile row (seq1,seq2,seq3,seq4,seq5) -> (group1,group2). seqs1,seq3 are from group1, seq2,seq4,seq5 are from group2.
vector<string> getGroups(vector<string>); //returns groups represented by the seqs passed in. Think column two from a namefile row (seq1,seq2,seq3,seq4,seq5) stored as a vector of names -> (group1,group2). seqs1,seq3 are from group1, seq2,seq4,seq5 are from group2.
int getNumSeqs(string, string); //list of seq names, group. returns number of seqs from group passed represented by the seqs passed in. Think column two from a namefile row (seq1,seq2,seq3,seq4,seq5), group1 -> 2. seqs1,seq3 are from group1, seq2,seq4,seq5 are from group2.
int getNumSeqs(vector<string>, string); //vector of seq names, group. returns number of seqs from group passed represented by the seqs passed in. Think column two from a namefile row (seq1,seq2,seq3,seq4,seq5), group1 -> 2. seqs1,seq3 are from group1, seq2,seq4,seq5 are from group2.
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;
}
void removeGroups(vector<string> groups);
vector<string> getNamesSeqs();
vector<string> getNamesSeqs(string); //get names of seqs belonging to group passed in
vector<string> getNamesSeqs(vector<string>); //get names of seqs belonging to the set of groups passed in
void setNamesOfGroups(vector<string> sn) { namesOfGroups = sn; }
int getNumSeqs() { return (int)groupmap.size(); }
int getNumSeqs(string); //return the number of seqs in a given group
int getNumSeqsSmallestGroup(); //returns size of smallest group
int renameSeq(string, string);
int addSeq(string name, string group);
int print(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.
private:
vector<string> namesOfGroups;
MothurOut* m;
string groupFileName;
int index;
map<string, string>::iterator it;
void setNamesOfGroups(string);
map<string, string> groupmap; //sequence name and groupname
map<string, int> seqsPerGroup; //maps groupname to number of seqs in that group
Utils util;
};
#endif
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