Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/include/mash/CommandTaxScreen.h @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@69 | 1 // Copyright © 2015, Battelle National Biodefense Institute (BNBI); |
| jpayne@69 | 2 // all rights reserved. Authored by: Brian Ondov, Todd Treangen, |
| jpayne@69 | 3 // Sergey Koren, and Adam Phillippy |
| jpayne@69 | 4 // |
| jpayne@69 | 5 // See the LICENSE.txt file included with this software for license information. |
| jpayne@69 | 6 |
| jpayne@69 | 7 #ifndef INCLUDED_CommandTaxScreen |
| jpayne@69 | 8 #define INCLUDED_CommandTaxScreen |
| jpayne@69 | 9 |
| jpayne@69 | 10 #include "Command.h" |
| jpayne@69 | 11 #include "Sketch.h" |
| jpayne@69 | 12 #include <list> |
| jpayne@69 | 13 #include <string> |
| jpayne@69 | 14 #include <vector> |
| jpayne@69 | 15 #include <atomic> |
| jpayne@69 | 16 #include <unordered_set> |
| jpayne@69 | 17 #include <unordered_map> |
| jpayne@69 | 18 #include "MinHashHeap.h" |
| jpayne@69 | 19 #include "CommandScreen.h" |
| jpayne@69 | 20 |
| jpayne@69 | 21 |
| jpayne@69 | 22 using std::string; |
| jpayne@69 | 23 using std::cerr; |
| jpayne@69 | 24 using std::cout; |
| jpayne@69 | 25 using std::endl; |
| jpayne@69 | 26 using std::list; |
| jpayne@69 | 27 using std::string; |
| jpayne@69 | 28 using std::unordered_map; |
| jpayne@69 | 29 using std::unordered_set; |
| jpayne@69 | 30 using std::vector; |
| jpayne@69 | 31 |
| jpayne@69 | 32 |
| jpayne@69 | 33 namespace mash { |
| jpayne@69 | 34 |
| jpayne@69 | 35 using TaxID = uint64_t; |
| jpayne@69 | 36 |
| jpayne@69 | 37 class CommandTaxScreen : public Command |
| jpayne@69 | 38 { |
| jpayne@69 | 39 public: |
| jpayne@69 | 40 |
| jpayne@69 | 41 CommandTaxScreen(); |
| jpayne@69 | 42 |
| jpayne@69 | 43 int run() const; // override |
| jpayne@69 | 44 |
| jpayne@69 | 45 private: |
| jpayne@69 | 46 |
| jpayne@69 | 47 struct Reference |
| jpayne@69 | 48 { |
| jpayne@69 | 49 Reference(uint64_t amerCountNew, std::string nameNew, std::string commentNew) |
| jpayne@69 | 50 : amerCount(amerCountNew), name(nameNew), comment(commentNew) {} |
| jpayne@69 | 51 |
| jpayne@69 | 52 uint64_t amerCount; |
| jpayne@69 | 53 std::string name; |
| jpayne@69 | 54 std::string comment; |
| jpayne@69 | 55 }; |
| jpayne@69 | 56 }; |
| jpayne@69 | 57 |
| jpayne@69 | 58 } // namespace mash |
| jpayne@69 | 59 |
| jpayne@69 | 60 #endif |