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.
15 #include "command.hpp"
16 #include "rabundvector.hpp"
17 #include "sharedlistvector.h"
18 #include "inputdata.h"
20 #include "readmatrix.hpp"
23 /* The parselist() command:
24 The parselist command is similar to the shared command.
25 It parses a list file and separates it into groups. It outputs a .list file for each group.
26 The parselist command parameter options are listfile and groupfile.
27 The parselist command should be in the following format: parselist(listfile=yourListFile, groupfile=yourGroupFile).
28 The listfile parameter and groupfile paramater are required. */
32 class ParseListCommand : public Command {
40 GlobalData* globaldata;
44 map<string, ofstream*> filehandles;
45 map<string, SharedListVector*> groupOfLists;
46 SharedListVector* list;
47 map<string, string> listGroups; //maps group name to sequences from that group in a specific OTU
48 map<string, string>::iterator it;
49 map<string, SharedListVector*>::iterator it2;
50 map<string, ofstream*>::iterator it3;