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added sort.seqs command. puts sequences from a fasta, name, group, quality or taxono...
[mothur.git] / sortseqscommand.h
1 #ifndef Mothur_sortseqscommand_h
2 #define Mothur_sortseqscommand_h
3
4
5 //
6 //  sortseqscommand.h
7 //  Mothur
8 //
9 //  Created by Sarah Westcott on 2/3/12.
10 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
11 //
12
13
14
15 #include "command.hpp"
16
17 class SortSeqsCommand : public Command {
18         
19 public:
20         
21     SortSeqsCommand(string);    
22     SortSeqsCommand();
23     ~SortSeqsCommand(){}
24         
25     vector<string> setParameters();
26     string getCommandName()                     { return "sort.seqs";                           }
27     string getCommandCategory()         { return "Sequence Processing";         }
28     string getHelpString();     
29     string getCitation() { return "http://www.mothur.org/wiki/Sort.seqs"; }
30     string getDescription()             { return "puts sequences from a fasta, name, group, quality or taxonomy file in the same order"; }
31     
32     int execute(); 
33     void help() { m->mothurOut(getHelpString()); }      
34         
35         
36 private:
37     map<string, int> names;
38     string accnosfile, fastafile, namefile, groupfile, taxfile, qualfile, outputDir;
39     bool abort, large;
40     vector<string> outputNames;
41     
42     int readFasta();
43     int readName();
44     int readGroup();
45     int readAccnos();
46     int readTax();
47     int readQual();
48     
49 };
50
51 #endif
52
53