/usr/include/pbdata/reads/ScanData.hpp is in libpbdata-dev 0~20151014+gitbe5d1bf-2.
This file is owned by root:root, with mode 0o644.
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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 | // Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
//
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted (subject to the limitations in the
// disclaimer below) provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
//
// * Neither the name of Pacific Biosciences nor the names of its
// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
// SUCH DAMAGE.
// Author: Mark Chaisson
#ifndef DATASTRUCTURES_READS_SCAN_DATA_H_
#define DATASTRUCTURES_READS_SCAN_DATA_H_
#include <string>
#include <map>
#include "Enumerations.h"
#include "PacBioDefs.h"
class HDFScanDataReader;
class HDFScanDataWriter;
class ScanData {
friend class HDFScanDataReader;
friend class HDFScanDataWriter;
public:
// Convert base map from a map<char, size_t> to a string.
// e.g., {{'A', 2}, {'C', 1}, {'T', 0}, {'G', 3}} --> TCAG
static std::string BaseMapToStr(const std::map<char, size_t> & baseMap);
// Convert base map from a string to a map<char, size_t>.
// e.g., TCAG --> {{'A', 2}, {'C', 1}, {'T', 0}, {'G', 3}}
static std::map<char, size_t> StrToBaseMap(const std::string & baseMapStr);
// A baseMap must contain maps from bases (e.g., ACGT) to indices (e.g., 0, 1, 2, 3).
static bool IsValidBaseMap(const std::map<char, size_t> & baseMap);
public:
PlatformId platformId;
float frameRate;
unsigned int numFrames;
std::string movieName, runCode;
std::string whenStarted;
std::map<char, size_t> baseMap;
ScanData();
std::string GetMovieName();
ScanData & PlatformID(const PlatformId & id);
ScanData & FrameRate(const float & rate);
ScanData & NumFrames(const unsigned int & num);
ScanData & MovieName(const std::string & name);
ScanData & RunCode(const std::string & code);
ScanData & WhenStarted(const std::string & when);
ScanData & BaseMap(const std::map<char, size_t> & bmp);
ScanData & BaseMap(const std::string & baseMapStr);
ScanData & SequencingKit(const std::string sequencingKit);
ScanData & BindingKit(const std::string bindingKit);
PlatformId PlatformID(void) const;
float FrameRate(void) const;
unsigned int NumFrames(void) const;
std::string MovieName(void) const;
std::string RunCode(void) const;
std::string WhenStarted(void) const;
std::map<char, size_t> BaseMap(void) const;
std::string BaseMapStr(void) const;
std::string SequencingKit(void) const;
std::string BindingKit(void) const;
private:
std::string sequencingKit_;
std::string bindingKit_;
};
#endif
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