1 #ifndef PARSELISTCOMMAND_H
2 #define PARSELISTCOMMAND_H
7 * Created by Sarah Westcott on 1/2/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 #include "command.hpp"
13 #include "rabundvector.hpp"
14 #include "sharedlistvector.h"
15 #include "inputdata.h"
20 /* The parselist() command:
21 The parselist command is similar to the shared command.
22 It parses a list file and separates it into groups. It outputs a .list file for each group.
23 The parselist command parameter options are listfile and groupfile.
24 The parselist command should be in the following format: parselist(listfile=yourListFile, groupfile=yourGroupFile).
25 The listfile parameter and groupfile paramater are required. */
29 class ParseListCommand : public Command {
38 GlobalData* globaldata;
42 map<string, ofstream*> filehandles;
43 map<string, SharedListVector*> mapOfLists;
44 SharedListVector* list;
45 map<string, string> listGroups; //maps group name to sequences from that group in a specific OTU
46 map<string, string>::iterator it;
47 map<string, SharedListVector*>::iterator it2;
48 map<string, ofstream*>::iterator it3;
49 void parse(int, SharedListVector*);
50 void process(SharedListVector*);