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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 "../legacyheaders/types/simple.h"
50 #include "../utility/common.h"
51 #include "../utility/gmxassert.h"
53 #include "dataframe.h"
58 class AbstractAnalysisData;
59 class AnalysisDataFrameHeader;
60 class AnalysisDataFrameRef;
61 class AnalysisDataParallelOptions;
63 class AnalysisDataStorage;
67 class AnalysisDataStorageFrameData;
68 } // namespace internal
70 /*! \libinternal \brief
71 * Allows assigning values for a data frame in AnalysisDataStorage.
73 * This class implements the necessary methods to add new data into the
74 * storage. AnalysisDataStorage::startFrame() returns an object of this type,
75 * which can be used to add one or more point sets to that data frame.
76 * When all data has been added, finishFrame() needs to be called.
79 * \ingroup module_analysisdata
81 class AnalysisDataStorageFrame
84 /*! \brief Frees the frame object.
86 * Should not be called outside AnalysisDataStorage.
88 ~AnalysisDataStorageFrame();
91 * Select data set that all other methods operate on.
93 * \param[in] index Zero-based data set index to select.
95 * With multipoint data, a single point set can only contain values in
97 * With non-multipoint data, arbitrary sequences of selectDataSet() and
98 * setValue() are supported. The full frame is notified to the modules
99 * once it is finished.
103 void selectDataSet(int index);
105 //! Returns number of columns for the frame.
106 int columnCount() const { return columnCount_; }
109 * Sets value for a column.
111 * \param[in] column Zero-based column index.
112 * \param[in] value Value to set for the column.
113 * \param[in] bPresent Present flag to set for the column.
115 * If called multiple times for a column (within one point set for
116 * multipoint data), old values are overwritten.
120 void setValue(int column, real value, bool bPresent = true)
122 GMX_ASSERT(column >= 0 && column < columnCount(),
123 "Invalid column index");
124 values_[currentOffset_ + column].setValue(value, bPresent);
125 bPointSetInProgress_ = true;
128 * Sets value for a column.
130 * \param[in] column Zero-based column index.
131 * \param[in] value Value to set for the column.
132 * \param[in] error Error estimate to set for the column.
133 * \param[in] bPresent Present flag to set for the column.
135 * If called multiple times for a column (within one point set for
136 * multipoint data), old values are overwritten.
140 void setValue(int column, real value, real error, bool bPresent = true)
142 GMX_ASSERT(column >= 0 && column < columnCount(),
143 "Invalid column index");
144 values_[currentOffset_ + column].setValue(value, error, bPresent);
145 bPointSetInProgress_ = true;
148 * Access value for a column.
150 * \param[in] column Zero-based column index.
152 * Should only be called after the column value has been set using
153 * setValue(); assigning a value to \c value(i) does not mark the
158 real &value(int column)
160 GMX_ASSERT(column >= 0 && column < columnCount(),
161 "Invalid column index");
162 return values_[currentOffset_ + column].value();
165 * Access value for a column.
167 * \param[in] column Zero-based column index.
169 * Should only be called after the column value has been set using
174 real value(int column) const
176 GMX_ASSERT(column >= 0 && column < columnCount(),
177 "Invalid column index");
178 return values_[currentOffset_ + column].value();
181 * Mark point set as finished for multipoint data.
183 * Must be called after each point set for multipoint data, including
184 * the last (i.e., no values must be set between the last call to this
185 * method and AnalysisDataStorage::finishFrame()).
186 * Must not be called for non-multipoint data.
188 * After this method has been called, all values appear as not set.
190 * Calls AbstractAnalysisData::notifyPointsAdd(), and throws any
191 * exception this method throws.
193 void finishPointSet();
195 * Finish storing a frame.
197 * Must be called exactly once for each frame returned by startFrame(),
198 * after the corresponding call.
199 * The frame object must not be accessed after the call.
201 * Calls notification methods in AbstractAnalysisData, and throws any
202 * exceptions these methods throw.
209 * Create a new storage frame.
211 * \param[in] data Data object for which the frame is for
212 * (used for data set and column counts).
214 explicit AnalysisDataStorageFrame(const AbstractAnalysisData &data);
216 //! Clear all column values from the frame.
219 //! Implementation data.
220 internal::AnalysisDataStorageFrameData *data_;
221 //! Values for the currently in-progress point set.
222 std::vector<AnalysisDataValue> values_;
224 //! Index of the currently active dataset.
226 //! Offset of the first value in \a values_ for the current data set.
228 //! Number of columns in the current data set.
231 //! Whether any values have been set in the current point set.
232 bool bPointSetInProgress_;
234 //! Needed for access to the constructor.
235 friend class AnalysisDataStorage;
236 //! Needed for managing the frame the object points to.
237 friend class internal::AnalysisDataStorageFrameData;
239 GMX_DISALLOW_COPY_AND_ASSIGN(AnalysisDataStorageFrame);
242 /*! \libinternal \brief
243 * Helper class that implements storage of data.
245 * This class implements a standard way of storing data to avoid implementing
246 * storage in each class derived from AbstractAnalysisData separately.
247 * To use this class in a class derived from AbstractAnalysisData, a member
248 * variable of this type should be declared and the data storage methods
249 * forwarded to tryGetDataFrame() and requestStorage() in that object.
250 * Storage properties should be set up, and then startDataStorage() called
251 * after calling AbstractAnalysisData::notifyDataStart().
252 * New frames can then be added using startFrame(), currentFrame() and
253 * finishFrame() methods. These methods (and
254 * AnalysisDataStorageFrame::finishPointSet()) take the responsibility of
255 * calling AbstractAnalysisData::notifyFrameStart(),
256 * AbstractAnalysisData::notifyPointsAdd() and
257 * AbstractAnalysisData::notifyFrameFinish() appropriately.
260 * Proper multi-threaded implementation.
263 * \ingroup module_analysisdata
265 class AnalysisDataStorage
268 //! Constructs a storage object.
269 AnalysisDataStorage();
270 ~AnalysisDataStorage();
273 * Set parallelization options for the storage.
275 * \param[in] opt Parallization options to use.
277 * If this method is not called, the storage is set up for serial
282 void setParallelOptions(const AnalysisDataParallelOptions &opt);
285 * Implements access to data frames.
287 * This method is designed such that calls to
288 * AbstractAnalysisData::tryGetDataFrameInternal() can be directly
289 * forwarded to this method. See that method for more documentation.
291 * A valid reference for a frame will be returned after finishFrame()
292 * has been called for that frame.
294 * \see AbstractAnalysisData::tryGetDataFrameInternal()
296 AnalysisDataFrameRef tryGetDataFrame(int index) const;
298 * Implements storage requests.
300 * This method is designed such that calls to
301 * AbstractAnalysisData::requestStorageInternal() can be directly
302 * forwarded to this method. See that method for more documentation.
304 * \see AbstractAnalysisData::requestStorageInternal()
306 bool requestStorage(int nframes);
309 * Start storing data.
311 * \param data AbstractAnalysisData object containing this storage.
312 * \exception std::bad_alloc if storage allocation fails.
314 * Lifetime of \p data must exceed the lifetime of the storage object
315 * (typically, the storage object will be a member in \p data).
316 * The storage object will take responsibility of calling
317 * AbstractAnalysisData::notifyFrameStart(),
318 * AbstractAnalysisData::notifyPointsAdd() and
319 * AbstractAnalysisData::notifyFrameFinish() for \p data appropriately.
321 * AbstractAnalysisData::notifyDataStart() must have been called for
322 * \p data, because that may trigger storage requests from attached
325 void startDataStorage(AbstractAnalysisData *data);
327 * Starts storing a new frame.
329 * \param[in] header Header for the new frame.
330 * \retval Frame object corresponding to the started frame.
331 * \exception std::bad_alloc if storage reallocation fails
332 * (only possible if storage of all frames has been requested).
333 * \exception APIError if frame is too far in the future.
335 * The returned object will be valid until the corresponding
336 * finishFrame() call.
338 * Must be called exactly once for each frame index.
340 * Currently, the implementation only works if the new frame is not too
342 * If \c i is the index of the last frame such that all frames from
343 * 0, ..., \c i have been finished, then \p header().index() should be
344 * at most \c 2*parallelizationFactor-1 larger than \c i, where
345 * parallelizationFactor is the parallelization factor passed to
346 * setParallelOptions().
347 * Throws APIError if this constraint is violated.
349 * Calls AbstractAnalysisData::notifyDataStarted() in certain cases,
350 * and throws any exceptions this method throws.
352 AnalysisDataStorageFrame &startFrame(const AnalysisDataFrameHeader &header);
354 * Convenience method to start storing a new frame.
356 * Identical to \c startFrame(AnalysisDataFrameHeader(index, x, dx));
358 AnalysisDataStorageFrame &startFrame(int index, real x, real dx);
360 * Obtain a frame object for an in-progress frame.
362 * \param[in] index Frame index.
363 * \retval Frame object corresponding to \p index.
365 * startFrame() should have been called for the frame with index
366 * \p index, and finishFrame() should not yet have been called.
367 * Returns the same object as returned by the original startFrame()
368 * call for the same index.
372 AnalysisDataStorageFrame ¤tFrame(int index);
374 * Convenience method for finishing a data frame.
376 * \param[in] index Frame index.
378 * Identical to \c currentFrame(index).finishFrame().
380 * \see AnalysisDataStorageFrame::finishFrame()
382 void finishFrame(int index);
387 PrivateImplPointer<Impl> impl_;
389 //! Needed because the frame needs to access the implementation class.
390 friend class internal::AnalysisDataStorageFrameData;