Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/include/mash/CommandTaxScreen.h @ 69:33d812a61356

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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67:0e9998148a16 69:33d812a61356
1 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
2 // all rights reserved. Authored by: Brian Ondov, Todd Treangen,
3 // Sergey Koren, and Adam Phillippy
4 //
5 // See the LICENSE.txt file included with this software for license information.
6
7 #ifndef INCLUDED_CommandTaxScreen
8 #define INCLUDED_CommandTaxScreen
9
10 #include "Command.h"
11 #include "Sketch.h"
12 #include <list>
13 #include <string>
14 #include <vector>
15 #include <atomic>
16 #include <unordered_set>
17 #include <unordered_map>
18 #include "MinHashHeap.h"
19 #include "CommandScreen.h"
20
21
22 using std::string;
23 using std::cerr;
24 using std::cout;
25 using std::endl;
26 using std::list;
27 using std::string;
28 using std::unordered_map;
29 using std::unordered_set;
30 using std::vector;
31
32
33 namespace mash {
34
35 using TaxID = uint64_t;
36
37 class CommandTaxScreen : public Command
38 {
39 public:
40
41 CommandTaxScreen();
42
43 int run() const; // override
44
45 private:
46
47 struct Reference
48 {
49 Reference(uint64_t amerCountNew, std::string nameNew, std::string commentNew)
50 : amerCount(amerCountNew), name(nameNew), comment(commentNew) {}
51
52 uint64_t amerCount;
53 std::string name;
54 std::string comment;
55 };
56 };
57
58 } // namespace mash
59
60 #endif