This file is indexed.

/usr/include/pbbam/DataSetXsd.h is in libpbbam-dev 0.7.4+ds-1.

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
// 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.
//
// File Description
/// \file DataSetXsd.h
/// \brief Defines the XSD- and namespace-related classes for DataSetXML.
//
// Author: Derek Barnett

#ifndef DATASETXSD_H
#define DATASETXSD_H

#include "pbbam/Config.h"
#include <map>
#include <string>

namespace PacBio {
namespace BAM {

/// \brief The XsdType enum defines the supported XSD namespaces.
///
enum class XsdType
{
    NONE

  , AUTOMATION_CONSTRAINTS
  , BASE_DATA_MODEL
  , COLLECTION_METADATA
  , COMMON_MESSAGES
  , DATA_MODEL
  , DATA_STORE
  , DATASETS
  , DECL_DATA
  , PART_NUMBERS
  , PRIMARY_METRICS
  , REAGENT_KIT
  , RIGHTS_AND_ROLES
  , SAMPLE_INFO
  , SEEDING_DATA
};

/// \brief The NamespaceInfo class provides XML namespace info (prefix & URI).
///
class PBBAM_EXPORT NamespaceInfo
{
public:
    /// \brief Creates an empty entry.
    ///
    /// This constructor only exists for STL container compatibility.
    ///
    NamespaceInfo(void);

    /// \brief Creates a valid info entry.
    NamespaceInfo(const std::string& name,
                  const std::string& uri);

public:
    /// \brief Fetches namespace name (i.e. prefix)
    const std::string& Name(void) const { return name_; }

    /// \brief Fetches namespace URI.
    const std::string& Uri(void) const { return uri_; }

private:
    std::string name_;
    std::string uri_;
};

/// \brief The NamespaceRegistry class provides a per-dataset registry of XML
///        namespace information.
///
/// This is used to format XML output - properly prefixing element labels with
/// namespace as appropriate.
///
class PBBAM_EXPORT NamespaceRegistry
{
public:
    /// \name Constructors & Related Methods
    /// \{

    NamespaceRegistry(void);
    NamespaceRegistry(const NamespaceRegistry& other);
    NamespaceRegistry(NamespaceRegistry&& other);
    NamespaceRegistry& operator=(const NamespaceRegistry& other);
    NamespaceRegistry& operator=(NamespaceRegistry&& other);
    ~NamespaceRegistry(void);

    /// \}

public:
    /// \name Registry Access
    /// \{

    /// \brief Fetches namespace info for the dataset's default XSD type.
    const NamespaceInfo& DefaultNamespace(void) const;

    /// \brief Fetches dataset's default XSD type.
    XsdType DefaultXsd(void) const;

    /// \brief Fetches namespace info for the requested XSD type.
    const NamespaceInfo& Namespace(const XsdType& xsd) const;

    /// \brief Registers namespace info for a particular XSD type.
    void Register(const XsdType& xsd, const NamespaceInfo& namespaceInfo);

    /// \brief Updates dataset's default XSD type.
    void SetDefaultXsd(const XsdType& xsd);

    /// \brief Fetches the XSD type for \p elementLabel.
    XsdType XsdForElement(const std::string& elementLabel) const;

    /// \brief Fetches the XSD type for a particular URI.
    XsdType XsdForUri(const std::string& uri) const;

    /// \}

private:
    std::map<XsdType, NamespaceInfo> data_;
    XsdType defaultXsdType_;
};

} // namespace PacBio
} // namespace BAM

#endif // DATASETXSD_H