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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/include/mash/CommandTriangle.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_CommandTriangle
8 #define INCLUDED_CommandTriangle
9
10 #include "Command.h"
11 #include "CommandDistance.h"
12 #include "Sketch.h"
13
14 namespace mash {
15
16 class CommandTriangle : public Command
17 {
18 public:
19
20 struct TriangleInput
21 {
22 TriangleInput(const Sketch & sketchNew, uint64_t indexNew, const Sketch::Parameters & parametersNew, double maxDistanceNew, double maxPValueNew)
23 :
24 sketch(sketchNew),
25 index(indexNew),
26 parameters(parametersNew),
27 maxDistance(maxDistanceNew),
28 maxPValue(maxPValueNew)
29 {}
30
31 const Sketch & sketch;
32 uint64_t index;
33 const Sketch::Parameters & parameters;
34 double maxDistance;
35 double maxPValue;
36 };
37
38 struct TriangleOutput
39 {
40 TriangleOutput(const Sketch & sketchNew, uint64_t indexNew)
41 :
42 sketch(sketchNew),
43 index(indexNew)
44 {
45 pairs = new CommandDistance::CompareOutput::PairOutput[index];
46 }
47
48 ~TriangleOutput()
49 {
50 delete [] pairs;
51 }
52
53 const Sketch & sketch;
54 uint64_t index;
55
56 CommandDistance::CompareOutput::PairOutput * pairs;
57 };
58
59 CommandTriangle();
60
61 int run() const; // override
62
63 private:
64
65 double pValueMax;
66 bool comment;
67
68 void writeOutput(TriangleOutput * output, bool comment, bool edge, double & pValuePeakToSet) const;
69 };
70
71 CommandTriangle::TriangleOutput * compare(CommandTriangle::TriangleInput * input);
72
73 } // namespace mash
74
75 #endif