/usr/include/mash/CommandContain.h is in libmash-dev 1.1.1-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
// Sergey Koren, and Adam Phillippy
//
// See the LICENSE.txt file included with this software for license information.
#ifndef INCLUDED_CommandContain
#define INCLUDED_CommandContain
#include "Command.h"
#include "Sketch.h"
class CommandContain : public Command
{
public:
struct ContainInput
{
ContainInput(const Sketch & sketchRefNew, const Sketch & sketchQueryNew, uint64_t indexRefNew, uint64_t indexQueryNew, uint64_t pairCountNew, const Sketch::Parameters & parametersNew)
:
sketchRef(sketchRefNew),
sketchQuery(sketchQueryNew),
indexRef(indexRefNew),
indexQuery(indexQueryNew),
pairCount(pairCountNew),
parameters(parametersNew)
{}
const Sketch & sketchRef;
const Sketch & sketchQuery;
uint64_t indexRef;
uint64_t indexQuery;
uint64_t pairCount;
std::string nameRef;
const Sketch::Parameters & parameters;
};
struct ContainOutput
{
ContainOutput(const Sketch & sketchRefNew, const Sketch & sketchQueryNew, uint64_t indexRefNew, uint64_t indexQueryNew, uint64_t pairCountNew)
:
sketchRef(sketchRefNew),
sketchQuery(sketchQueryNew),
indexRef(indexRefNew),
indexQuery(indexQueryNew),
pairCount(pairCountNew)
{
pairs = new PairOutput[pairCount];
}
~ContainOutput()
{
delete [] pairs;
}
struct PairOutput
{
double score;
double error;
};
const Sketch & sketchRef;
const Sketch & sketchQuery;
uint64_t indexRef;
uint64_t indexQuery;
uint64_t pairCount;
PairOutput * pairs;
};
CommandContain();
int run() const; // override
private:
void writeOutput(ContainOutput * output, float error) const;
};
CommandContain::ContainOutput * contain(CommandContain::ContainInput * data);
double containSketches(const HashList & hashesSortedRef, const HashList & hashesSortedQuery, double & errorToSet);
#endif
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