This file is indexed.

/usr/include/gromacs/options/options.h is in libgromacs-dev 5.1.2-1ubuntu1.

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
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 2010,2011,2012,2014, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with GROMACS; if not, see
 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 *
 * If you want to redistribute modifications to GROMACS, please
 * consider that scientific software is very special. Version
 * control is crucial - bugs must be traceable. We will be happy to
 * consider code for inclusion in the official distribution, but
 * derived work must not be called official GROMACS. Details are found
 * in the README & COPYING files - if they are missing, get the
 * official version at http://www.gromacs.org.
 *
 * To help us fund GROMACS development, we humbly ask that you cite
 * the research papers on the package. Check out http://www.gromacs.org.
 */
/*! \file
 * \brief
 * Declares gmx::Options.
 *
 * Together with basicoptions.h, this header forms the part of the public
 * API that most classes will use to provide options.
 *
 * \author Teemu Murtola <teemu.murtola@gmail.com>
 * \inpublicapi
 * \ingroup module_options
 */
#ifndef GMX_OPTIONS_OPTIONS_H
#define GMX_OPTIONS_OPTIONS_H

#include <string>

#include "gromacs/options/abstractoption.h"
#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/gmxassert.h"

namespace gmx
{

template <typename T> class ConstArrayRef;

class AbstractOption;
class OptionsAssigner;
class OptionsIterator;

/*! \brief
 * Base class for option managers.
 *
 * This class is used as a marker for all classes that are used with
 * Options::addManager().  It doesn't provide any methods, but only supports
 * transporting these classes through the Options collection into the
 * individual option implementation classes.
 *
 * The virtual destructor is present to make this class polymorphic, such that
 * `dynamic_cast` can be used when retrieving a manager of a certain type for
 * the individual options.
 *
 * \inlibraryapi
 * \ingroup module_options
 */
class OptionManagerInterface
{
    protected:
        virtual ~OptionManagerInterface();
};

/*! \brief
 * Collection of options.
 *
 * This class provides a standard interface for implementing input options.
 * Standard usage is to write a method that creates an Options that is owned by
 * the object, populates it with supported options, and then returns it:
 * \code
   // <as class attributes>
   using gmx::Options;
   Options      options("common", "Common Options");
   std::string  arg1;
   int          arg2;

   // <populating>
   using gmx::StringOption;
   using gmx::IntegerOption;
   options.addOption(StringOption("arg1").store(&arg1));
   options.addOption(IntegerOption("arg2").store(&arg2));
   return &options;
   \endcode
 * The caller of that method can then use a parser implementation such as
 * CommandLineParser to provide values for the options.
 *
 * Header basicoptions.h provides declarations of several standard
 * option types for use with addOption().  Documentation of those classes
 * also give more examples of how to define options.
 *
 * In order to keep the public interface of this class simple and to reduce
 * build dependencies on objects that simply provide options, functionality
 * to assign values to options is provided by a separate OptionsAssigner class.
 * Similarly, functionality for looping over all options (e.g., for writing out
 * help) is provided by OptionsIterator.
 *
 * \inpublicapi
 * \ingroup module_options
 */
class Options
{
    public:
        /*! \brief
         * Initializes the name and title of an option collection.
         *
         * \param[in] name  Single-word name.
         * \param[in] title Descriptive title.
         *
         * Copies the input strings.
         */
        Options(const char *name, const char *title);
        ~Options();

        //! Returns the short name of the option collection.
        const std::string &name() const;
        //! Returns the title of the option collection.
        const std::string &title() const;
        //! Returns the full description of the option collection.
        const std::string &description() const;

        /*! \brief
         * Sets the full description of the option collection.
         *
         * \param[in] desc  String to set as the description.
         *
         * This overload is mainly useful if the description is very short.
         * Currently this is mostly the case in unit testing.
         */
        void setDescription(const std::string &desc);
        /*! \brief
         * Sets the full description of the option collection from string array.
         *
         * \param[in] descArray  String array to set as the description.
         *
         * All strings in `descArray` are concatenated to form the description.
         * Spaces are inserted between strings if they are missing.
         *
         * Example usage:
         * \code
           const char *const desc[] = {
               "This is the description",
               "for the options"
           };

           gmx::Options options(NULL, NULL);
           options.setDescription(desc);
           \endcode
         *
         * To use this overload, you must also include
         * `gromacs/utility/arrayref.h`.
         */
        void setDescription(const ConstArrayRef<const char *> &descArray);

        /*! \brief
         * Adds an option manager.
         *
         * \param    manager Manager to add.
         * \throws   std::bad_alloc if out of memory.
         *
         * Option managers are used by some types of options that require
         * interaction between different option instances (e.g., selection
         * options), or need to support globally set properties (e.g., a global
         * default file prefix).  Option objects can retrieve the pointer to
         * their manager when they are created, and the caller can alter the
         * behavior of the options through the manager.
         * See the individual managers for details.
         *
         * Caller is responsible for memory management of \p manager.
         * The Options object (and its contained options) only stores a
         * reference to the object.
         *
         * This method cannot be called after adding options or subsections.
         */
        void addManager(OptionManagerInterface *manager);

        /*! \brief
         * Adds an option collection as a subsection of this collection.
         *
         * \param[in] section Subsection to add.
         *
         * The name() field of \p section is used as the name of the
         * subsection.  If an attempt is made to add two different subsections
         * with the same name, this function asserts.
         *
         * \p section should not have any options added at the point this
         * method is called.
         *
         * Only a pointer to the provided object is stored.  The caller is
         * responsible that the object exists for the lifetime of the
         * collection.
         * It is not possible to add the same Options object as a subsection to
         * several different Options.
         * If an attempt is made, the function asserts.
         */
        void addSubSection(Options *section);
        /*! \brief
         * Adds a recognized option to the collection.
         *
         * \param[in] settings Option description.
         * \returns   OptionInfo object for the created option (never NULL).
         * \throws    APIError if invalid option settings are provided.
         *
         * This method provides the internal implementation, but in most cases
         * the templated method is called from user code.
         * See the templated method for more details.
         */
        OptionInfo *addOption(const AbstractOption &settings);
        /*! \brief
         * Adds a recognized option to the collection.
         *
         * \tparam    OptionType Type of the options description object.
         * \param[in] settings   Option description.
         * \returns   OptionInfo object for the created option (never NULL).
         * \throws    APIError if invalid option settings are provided.
         *
         * The return value is a pointer for more convenient use in callers:
         * often callers need to declare the variable that will hold the return
         * value in wider scope than would be achieved by declaring it at the
         * site where addOption() is called.
         * The returned pointer must not be freed.
         *
         * See \link Options class documentation \endlink for example usage.
         *
         * \libinternal
         * \p OptionType::InfoType must specify a type that derives from
         * OptionInfo and matches the type that is returned by
         * AbstractOptionStorage::optionInfo() for the storage object that
         * corresponds to \p OptionType.
         */
        template <class OptionType>
        typename OptionType::InfoType *addOption(const OptionType &settings)
        {
            OptionInfo *info
                = addOption(static_cast<const AbstractOption &>(settings));
            GMX_ASSERT(info->isType<typename OptionType::InfoType>(),
                       "Mismatching option info type declaration and implementation");
            return info->toType<typename OptionType::InfoType>();
        }

        //! Returns true if option \p name is set.
        bool isSet(const char *name) const;
        /*! \brief
         * Notifies the collection that all option values are assigned.
         *
         * \throws InvalidInputError if invalid user input is detected.
         *
         * This function should be called after no more option values are
         * to be assigned.  Values in storage variables are guaranteed to be
         * available only after this call, although in most cases, they are
         * available already during assignment.
         *
         * If invalid option values, e.g., missing required option, is detected
         * at this point, this function throws.  The thrown exception contains
         * information on all errors detected during the call.
         */
        void finish();

    private:
        class Impl;

        PrivateImplPointer<Impl> impl_;

        //! Needed to be able to extend the interface of this object.
        friend class OptionsAssigner;
        //! Needed to be able to extend the interface of this object.
        friend class OptionsIterator;
        //! Needed to be able to extend the interface of this object.
        friend class OptionsModifyingIterator;
};

} // namespace gmx

#endif