/usr/include/mash/CommandScreen.h is in libmash-dev 2.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 | // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
// 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_CommandScreen
#define INCLUDED_CommandScreen
#include "Command.h"
#include "Sketch.h"
#include <list>
#include <string>
#include <vector>
#include <atomic>
#include <unordered_set>
#include <unordered_map>
#include "MinHashHeap.h"
namespace mash {
typedef std::unordered_map< uint64_t, std::unordered_set<uint64_t> > HashTable;
static const std::unordered_map< std::string, char > codons =
{
{"AAA", 'K'},
{"AAC", 'N'},
{"AAG", 'K'},
{"AAT", 'N'},
{"ACA", 'T'},
{"ACC", 'T'},
{"ACG", 'T'},
{"ACT", 'T'},
{"AGA", 'R'},
{"AGC", 'S'},
{"AGG", 'R'},
{"AGT", 'S'},
{"ATA", 'I'},
{"ATC", 'I'},
{"ATG", 'M'},
{"ATT", 'I'},
{"CAA", 'Q'},
{"CAC", 'H'},
{"CAG", 'Q'},
{"CAT", 'H'},
{"CCA", 'P'},
{"CCC", 'P'},
{"CCG", 'P'},
{"CCT", 'P'},
{"CGA", 'R'},
{"CGC", 'R'},
{"CGG", 'R'},
{"CGT", 'R'},
{"CTA", 'L'},
{"CTC", 'L'},
{"CTG", 'L'},
{"CTT", 'L'},
{"GAA", 'E'},
{"GAC", 'D'},
{"GAG", 'E'},
{"GAT", 'D'},
{"GCA", 'A'},
{"GCC", 'A'},
{"GCG", 'A'},
{"GCT", 'A'},
{"GGA", 'G'},
{"GGC", 'G'},
{"GGG", 'G'},
{"GGT", 'G'},
{"GTA", 'V'},
{"GTC", 'V'},
{"GTG", 'V'},
{"GTT", 'V'},
{"TAA", '*'},
{"TAC", 'Y'},
{"TAG", '*'},
{"TAT", 'Y'},
{"TCA", 'S'},
{"TCC", 'S'},
{"TCG", 'S'},
{"TCT", 'S'},
{"TGA", '*'},
{"TGC", 'C'},
{"TGG", 'W'},
{"TGT", 'C'},
{"TTA", 'L'},
{"TTC", 'F'},
{"TTG", 'L'},
{"TTT", 'F'}
};
class CommandScreen : public Command
{
public:
struct HashInput
{
HashInput(std::unordered_map<uint64_t, std::atomic<uint32_t> > & hashCountsNew, MinHashHeap * minHashHeapNew, char * seqNew, uint64_t lengthNew, const Sketch::Parameters & parametersNew, bool transNew)
:
hashCounts(hashCountsNew),
minHashHeap(minHashHeapNew),
seq(seqNew),
length(lengthNew),
parameters(parametersNew),
trans(transNew)
{}
~HashInput()
{
if ( seq != 0 )
{
delete [] seq;
}
}
std::string fileName;
char * seq;
uint64_t length;
bool trans;
Sketch::Parameters parameters;
std::unordered_map<uint64_t, std::atomic<uint32_t> > & hashCounts;
MinHashHeap * minHashHeap;
};
struct HashOutput
{
HashOutput(MinHashHeap * minHashHeapNew)
:
minHashHeap(minHashHeapNew)
{}
MinHashHeap * minHashHeap;
};
CommandScreen();
int run() const; // override
private:
struct Reference
{
Reference(uint64_t amerCountNew, std::string nameNew, std::string commentNew)
: amerCount(amerCountNew), name(nameNew), comment(commentNew) {}
uint64_t amerCount;
std::string name;
std::string comment;
};
};
char aaFromCodon(const char * codon);
double estimateIdentity(uint64_t common, uint64_t denom, int kmerSize, double kmerSpace);
CommandScreen::HashOutput * hashSequence(CommandScreen::HashInput * input);
double pValueWithin(uint64_t x, uint64_t setSize, double kmerSpace, uint64_t sketchSize);
void translate(const char * src, char * dst, uint64_t len);
void useThreadOutput(CommandScreen::HashOutput * output, std::unordered_set<MinHashHeap *> & minHashHeaps);
} // namespace mash
#endif
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