/usr/include/gromacs/analysisdata/datamodule.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 | /*
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014, 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::AnalysisDataModuleInterface and related convenience classes.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \inlibraryapi
* \ingroup module_analysisdata
*/
#ifndef GMX_ANALYSISDATA_DATAMODULE_H
#define GMX_ANALYSISDATA_DATAMODULE_H
namespace gmx
{
class AbstractAnalysisData;
class AnalysisDataFrameHeader;
class AnalysisDataParallelOptions;
class AnalysisDataPointSetRef;
/*! \brief
* Interface for a module that gets notified whenever data is added.
*
* The interface provides one method (flags()) that describes features of
* data objects the module supports. Only most common features are included
* in the flags; custom checks can be implemented in the dataStarted() and/or
* parallelDataStarted() methods (see below).
* All other methods in the interface are callbacks that are called by the
* data object to which the module is attached to describe the data.
* See \ref module_analysisdata for an overview of the notifications the
* modules receive, and \ref page_analysisdata for overview of the terminology.
*
* Concrete modules typically do not directly derive from this interface, but
* from either AnalysisDataModuleSerial or AnalysisDataModuleParallel.
* Both these classes implement one of dataStarted()/parallelDataStarted() by
* forwarding the calls to the other method of this pair. This allows the
* module to only implement the initialization once, without needing to worry
* how to correctly handle both cases.
*
* Currently, if the module throws an exception, it requires the analysis tool
* to terminate, since AbstractAnalysisData will be left in a state where it
* is not possible to continue processing. See a related todo item in
* AbstractAnalysisData.
*
* \inlibraryapi
* \ingroup module_analysisdata
*/
class AnalysisDataModuleInterface
{
public:
/*! \brief
* Possible flags for flags().
*/
enum Flag
{
//! The module can process multipoint data.
efAllowMultipoint = 1<<0,
//! The module does not make sense for non-multipoint data.
efOnlyMultipoint = 1<<1,
//! The module can process data with more than one column.
efAllowMulticolumn = 1<<2,
//! The module can process data with missing points.
efAllowMissing = 1<<3,
//! The module can process data with multiple data sets.
efAllowMultipleDataSets = 1<<4
};
virtual ~AnalysisDataModuleInterface() {};
/*! \brief
* Returns properties supported by the module.
*
* The return value of this method should not change after the module
* has been added to a data (this responsibility can, and in most cases
* must, be delegated to the user of the module).
*
* The purpose of this method is to remove the need for common checks
* for data compatibility in the classes that implement the interface.
* Instead, AbstractAnalysisData performs these checks based on the
* flags provided.
*
* Does not throw.
*/
virtual int flags() const = 0;
/*! \brief
* Called (once) when the data has been set up properly.
*
* \param[in] data Data object to which the module is added.
* \throws APIError if the provided data is not compatible.
* \throws unspecified Can throw any exception required by the
* implementing class to report errors.
*
* When the data is ready, either this method or parallelDataStarted()
* is called, depending on the nature of the input data. If this
* method is called, the input data will always present the frames in
* sequential order.
*
* The data to which the module is attached is passed as an argument
* to provide access to properties of the data for initialization
* and/or validation. The module can also call
* AbstractAnalysisData::requestStorage() if needed.
*
* This is the only place where the module gets access to the data;
* if properties of the data are required later, the module should
* store them internally. It is guaranteed that the data properties
* (column count, whether it's multipoint) do not change once this
* method has been called.
*
* Notice that \p data will be a proxy object if the module is added as
* a column module, not the data object for which
* AbstractAnalysisData::addColumnModule() was called.
*/
virtual void dataStarted(AbstractAnalysisData *data) = 0;
/*! \brief
* Called (once) for parallel data when the data has been set up.
*
* \param[in] data Data object to which the module is added.
* \param[in] options Parallelization properties of the input data.
* \returns true if the module can process the input in
* non-sequential order.
* \throws APIError if the provided data is not compatible.
* \throws unspecified Can throw any exception required by the
* implementing class to report errors.
*
* This method is called instead of dataStarted() if the input data has
* the capability to present data in non-sequential order.
* If the method returns true, then the module accepts this and frame
* notification methods may be called in that non-sequential order.
* If the method returns false, then the frame notification methods are
* called in sequential order, as if dataStarted() had been called.
*
* See dataStarted() for general information on initializing the data.
* That applies to this method as well, with the exception that calling
* AbstractAnalysisData::requestStorage() is currently not very well
* supported (or rather, accessing the requested storage doesn't work).
*/
virtual bool parallelDataStarted(
AbstractAnalysisData *data,
const AnalysisDataParallelOptions &options) = 0;
/*! \brief
* Called at the start of each data frame.
*
* \param[in] frame Header information for the frame that is starting.
* \throws unspecified Can throw any exception required by the
* implementing class to report errors.
*/
virtual void frameStarted(const AnalysisDataFrameHeader &frame) = 0;
/*! \brief
* Called one or more times during each data frame.
*
* \param[in] points Set of points added (also provides access to
* frame-level data).
* \throws APIError if the provided data is not compatible.
* \throws unspecified Can throw any exception required by the
* implementing class to report errors.
*
* Can be called once or multiple times for a frame. For all data
* objects currently implemented in the library (and all objects that
* will use AnalysisDataStorage for internal implementation), it is
* called exactly once for each frame if the data is not multipoint,
* but currently this restriction is not enforced.
*/
virtual void pointsAdded(const AnalysisDataPointSetRef &points) = 0;
/*! \brief
* Called when a data frame is finished.
*
* \param[in] header Header information for the frame that is ending.
* \throws unspecified Can throw any exception required by the
* implementing class to report errors.
*/
virtual void frameFinished(const AnalysisDataFrameHeader &header) = 0;
/*! \brief
* Called in sequential order for each frame after they are finished.
*
* \param[in] frameIndex Index of the next finished frame.
* \throws unspecified Can throw any exception required by the
* implementing class to report errors.
*
* This method is called after frameFinished(), but with an additional
* constraint that it is always called in serial and with an increasing
* \p frameIndex. Parallel data modules need this to serialize their
* data for downsteam serial modules; AnalysisDataModuleSerial provides
* an empty implementation, as there frameFinished() can be used for
* the same purpose.
*/
virtual void frameFinishedSerial(int frameIndex) = 0;
/*! \brief
* Called (once) when no more data is available.
*
* \throws unspecified Can throw any exception required by the
* implementing class to report errors.
*/
virtual void dataFinished() = 0;
};
/*! \brief
* Convenience base class for serial analysis data modules.
*
* Implements the parallelDataStarted() method such that initialization is
* always forwarded to dataStarted(), and the module always behaves as serial
* (parallelDataStarted() returns false).
*
* \inlibraryapi
* \ingroup module_analysisdata
*/
class AnalysisDataModuleSerial : public AnalysisDataModuleInterface
{
public:
virtual ~AnalysisDataModuleSerial() {}
virtual int flags() const = 0;
virtual void dataStarted(AbstractAnalysisData *data) = 0;
virtual void frameStarted(const AnalysisDataFrameHeader &frame) = 0;
virtual void pointsAdded(const AnalysisDataPointSetRef &points) = 0;
virtual void frameFinished(const AnalysisDataFrameHeader &header) = 0;
virtual void dataFinished() = 0;
private:
virtual bool parallelDataStarted(
AbstractAnalysisData *data,
const AnalysisDataParallelOptions &options);
virtual void frameFinishedSerial(int /*frameIndex*/) {}
};
/*! \brief
* Convenience base class for parallel analysis data modules.
*
* Implements the dataStarted() method such that initialization is always done
* in parallelDataStarted(). dataStarted() calls are forwarded to
* parallelDataStarted() using a dummy serial AnalysisDataParallelOptions.
*
* \inlibraryapi
* \ingroup module_analysisdata
*/
class AnalysisDataModuleParallel : public AnalysisDataModuleInterface
{
public:
virtual ~AnalysisDataModuleParallel() {}
virtual int flags() const = 0;
virtual bool parallelDataStarted(
AbstractAnalysisData *data,
const AnalysisDataParallelOptions &options) = 0;
virtual void frameStarted(const AnalysisDataFrameHeader &frame) = 0;
virtual void pointsAdded(const AnalysisDataPointSetRef &points) = 0;
virtual void frameFinished(const AnalysisDataFrameHeader &header) = 0;
virtual void frameFinishedSerial(int index) = 0;
virtual void dataFinished() = 0;
private:
virtual void dataStarted(AbstractAnalysisData *data);
};
} // namespace gmx
#endif
|