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35 /*! \libinternal \file
37 * Declares gmx::AnalysisDataStorage.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
41 * \ingroup module_analysisdata
43 #ifndef GMX_ANALYSISDATA_DATASTORAGE_H
44 #define GMX_ANALYSISDATA_DATASTORAGE_H
48 #include "../utility/common.h"
49 #include "../utility/gmxassert.h"
50 #include "../utility/real.h"
52 #include "dataframe.h"
57 class AbstractAnalysisData;
58 class AnalysisDataFrameHeader;
59 class AnalysisDataFrameRef;
60 class AnalysisDataModuleManager;
61 class AnalysisDataParallelOptions;
63 class AnalysisDataStorage;
67 class AnalysisDataStorageImpl;
68 class AnalysisDataStorageFrameData;
69 } // namespace internal
71 /*! \libinternal \brief
72 * Allows assigning values for a data frame in AnalysisDataStorage.
74 * This class implements the necessary methods to add new data into the
75 * storage. AnalysisDataStorage::startFrame() returns an object of this type,
76 * which can be used to add one or more point sets to that data frame.
77 * When all data has been added, finishFrame() needs to be called.
80 * \ingroup module_analysisdata
82 class AnalysisDataStorageFrame
85 /*! \brief Frees the frame object.
87 * Should not be called outside AnalysisDataStorage.
89 ~AnalysisDataStorageFrame();
92 * Select data set that all other methods operate on.
94 * \param[in] index Zero-based data set index to select.
96 * With multipoint data, a single point set can only contain values in
98 * With non-multipoint data, arbitrary sequences of selectDataSet() and
99 * setValue() are supported. The full frame is notified to the modules
100 * once it is finished.
104 void selectDataSet(int index);
106 //! Returns number of columns for the frame.
107 int columnCount() const { return columnCount_; }
110 * Sets value for a column.
112 * \param[in] column Zero-based column index.
113 * \param[in] value Value to set for the column.
114 * \param[in] bPresent Present flag to set for the column.
116 * If called multiple times for a column (within one point set for
117 * multipoint data), old values are overwritten.
121 void setValue(int column, real value, bool bPresent = true)
123 GMX_ASSERT(column >= 0 && column < columnCount(),
124 "Invalid column index");
125 values_[currentOffset_ + column].setValue(value, bPresent);
126 bPointSetInProgress_ = true;
129 * Sets value for a column.
131 * \param[in] column Zero-based column index.
132 * \param[in] value Value to set for the column.
133 * \param[in] error Error estimate to set for the column.
134 * \param[in] bPresent Present flag to set for the column.
136 * If called multiple times for a column (within one point set for
137 * multipoint data), old values are overwritten.
141 void setValue(int column, real value, real error, bool bPresent = true)
143 GMX_ASSERT(column >= 0 && column < columnCount(),
144 "Invalid column index");
145 values_[currentOffset_ + column].setValue(value, error, bPresent);
146 bPointSetInProgress_ = true;
149 * Access value for a column.
151 * \param[in] column Zero-based column index.
153 * Should only be called after the column value has been set using
154 * setValue(); assigning a value to \c value(i) does not mark the
159 real &value(int column)
161 GMX_ASSERT(column >= 0 && column < columnCount(),
162 "Invalid column index");
163 return values_[currentOffset_ + column].value();
166 * Access value for a column.
168 * \param[in] column Zero-based column index.
170 * Should only be called after the column value has been set using
175 real value(int column) const
177 GMX_ASSERT(column >= 0 && column < columnCount(),
178 "Invalid column index");
179 return values_[currentOffset_ + column].value();
182 * Mark point set as finished for multipoint data.
184 * Must be called after each point set for multipoint data, including
185 * the last (i.e., no values must be set between the last call to this
186 * method and AnalysisDataStorage::finishFrame()).
187 * Must not be called for non-multipoint data.
189 * After this method has been called, all values appear as not set.
191 * May call AnalysisDataModuleManager::notifyPointsAdd() and
192 * AnalysisDataModuleManager::notifyParallelPointsAdd(), and may throw
193 * any exception these methods throw.
195 void finishPointSet();
197 * Finish storing a frame.
199 * Must be called exactly once for each frame returned by startFrame(),
200 * after the corresponding call.
201 * The frame object must not be accessed after the call.
203 * Calls notification methods in AnalysisDataModuleManager, and may
204 * throw any exceptions these methods throw.
211 * Create a new storage frame.
213 * \param[in] data Data object for which the frame is for
214 * (used for data set and column counts).
216 explicit AnalysisDataStorageFrame(const AbstractAnalysisData &data);
218 //! Clear all column values from the frame.
221 //! Implementation data.
222 internal::AnalysisDataStorageFrameData *data_;
223 //! Values for the currently in-progress point set.
224 std::vector<AnalysisDataValue> values_;
226 //! Index of the currently active dataset.
228 //! Offset of the first value in \a values_ for the current data set.
230 //! Number of columns in the current data set.
233 //! Whether any values have been set in the current point set.
234 bool bPointSetInProgress_;
236 //! Needed for access to the constructor.
237 friend class internal::AnalysisDataStorageImpl;
238 //! Needed for managing the frame the object points to.
239 friend class internal::AnalysisDataStorageFrameData;
241 GMX_DISALLOW_COPY_AND_ASSIGN(AnalysisDataStorageFrame);
244 /*! \libinternal \brief
245 * Helper class that implements storage of data.
247 * This class implements a standard way of storing data to avoid implementing
248 * storage in each class derived from AbstractAnalysisData separately.
249 * To use this class in a class derived from AbstractAnalysisData, a member
250 * variable of this type should be declared and the pure virtual methods
251 * forwarded to frameCount(), tryGetDataFrame() and requestStorage().
252 * Storage properties should be set up, and then startDataStorage() or
253 * startParallelDataStorage() called.
254 * New frames can then be added using startFrame(), currentFrame() and
255 * finishFrame() methods. When all frames are ready, finishDataStorage() must
256 * be called. These methods (and AnalysisDataStorageFrame::finishPointSet())
257 * take the responsibility of calling all the notification methods in
258 * AnalysisDataModuleManager,
261 * Proper multi-threaded implementation.
264 * \ingroup module_analysisdata
266 class AnalysisDataStorage
269 //! Constructs a storage object.
270 AnalysisDataStorage();
271 ~AnalysisDataStorage();
274 * Returns the number of ready frames.
276 * This method is designed such that calls to
277 * AbstractAnalysisData::frameCount() can be directly forwarded to this
278 * method. See that method for more documentation.
280 * If this method returns N, this means that the first N frames have
283 * \see AbstractAnalysisData::frameCount()
285 int frameCount() const;
287 * Implements access to data frames.
289 * This method is designed such that calls to
290 * AbstractAnalysisData::tryGetDataFrameInternal() can be directly
291 * forwarded to this method. See that method for more documentation.
293 * A valid reference for a frame will be returned after finishFrame()
294 * has been called for that frame.
296 * \see AbstractAnalysisData::tryGetDataFrameInternal()
298 AnalysisDataFrameRef tryGetDataFrame(int index) const;
300 * Implements storage requests.
302 * This method is designed such that calls to
303 * AbstractAnalysisData::requestStorageInternal() can be directly
304 * forwarded to this method. See that method for more documentation.
306 * \see AbstractAnalysisData::requestStorageInternal()
308 bool requestStorage(int nframes);
311 * Start storing data.
313 * \param[in] data AbstractAnalysisData object containing this
315 * \param modules Module manager for \p data.
316 * \exception std::bad_alloc if storage allocation fails.
318 * Typically called as \c startDataStorage(this, &moduleManager())
319 * from a member of \p data when the data is ready to be started.
320 * The storage object will take responsibility of calling all
321 * module notification methods in AnalysisDataModuleManager using
324 * Lifetime of \p data and \p modules must exceed the lifetime of the
326 * (typically, the storage object will be a member in \p data).
328 * Calls AnalysisDataModuleManager::notifyDataStart(), and throws any
329 * exceptions this method throws.
331 void startDataStorage(AbstractAnalysisData *data,
332 AnalysisDataModuleManager *modules);
334 * Start storing data in parallel.
336 * \param[in] data AbstractAnalysisData object containing this
338 * \param[in] options Parallelization options to use.
339 * \param modules Module manager for \p data.
340 * \exception std::bad_alloc if storage allocation fails.
342 * Should be called instead of startDataStorage() if the data will be
343 * produced in parallel. Works as startDataStorage(), but additionally
344 * initializes the storage and the attached modules to prepare for
345 * out-of-order data frames.
347 * Calls AnalysisDataModuleManager::notifyParallelDataStart(), and
348 * throws any exceptions this method throws.
350 void startParallelDataStorage(
351 AbstractAnalysisData *data,
352 AnalysisDataModuleManager *modules,
353 const AnalysisDataParallelOptions &options);
355 * Starts storing a new frame.
357 * \param[in] header Header for the new frame.
358 * \retval Frame object corresponding to the started frame.
359 * \exception std::bad_alloc if storage reallocation fails
360 * (only possible if storage of all frames has been requested).
361 * \exception APIError if frame is too far in the future.
363 * The returned object will be valid until the corresponding
364 * finishFrame() call.
366 * Must be called exactly once for each frame index.
368 * Currently, the implementation only works if the new frame is not too
370 * If \c i is the index of the last frame such that all frames from
371 * 0, ..., \c i have been finished, then \p header().index() should be
372 * at most \c 2*parallelizationFactor-1 larger than \c i, where
373 * parallelizationFactor is the parallelization factor passed to
374 * setParallelOptions().
375 * Throws APIError if this constraint is violated.
377 * Calls AnalysisDataModuleManager::notifyFrameStart() (in certain
378 * cases) and AnalysisDataModuleManager::notifyParallelFrameStart(),
379 * and throws any exceptions these methods throw.
381 AnalysisDataStorageFrame &startFrame(const AnalysisDataFrameHeader &header);
383 * Convenience method to start storing a new frame.
385 * Identical to \c startFrame(AnalysisDataFrameHeader(index, x, dx));
387 AnalysisDataStorageFrame &startFrame(int index, real x, real dx);
389 * Obtain a frame object for an in-progress frame.
391 * \param[in] index Frame index.
392 * \retval Frame object corresponding to \p index.
394 * startFrame() should have been called for the frame with index
395 * \p index, and finishFrame() should not yet have been called.
396 * Returns the same object as returned by the original startFrame()
397 * call for the same index.
401 AnalysisDataStorageFrame ¤tFrame(int index);
403 * Convenience method for finishing a data frame.
405 * \param[in] index Frame index.
407 * Identical to \c currentFrame(index).finishFrame().
409 * \see AnalysisDataStorageFrame::finishFrame()
411 void finishFrame(int index);
413 * Finishes storing data.
415 * Calls AnalysisDataModuleManager::notifyDataFinish(), and throws any
416 * exceptions this method throws.
418 void finishDataStorage();
421 typedef internal::AnalysisDataStorageImpl Impl;
423 PrivateImplPointer<Impl> impl_;