#include <gromacs/analysisdata/abstractdata.h>

Inheritance diagram for gmx::AbstractAnalysisData:

Description

Abstract base class for all objects that provide data.

The public interface includes methods for querying the data (isMultipoint(), dataSetCount(), columnCount(), frameCount(), tryGetDataFrame(), getDataFrame(), requestStorage()) and methods for using modules for processing the data (addModule(), addColumnModule(), applyModule()).

Notice that even for non-const objects, the interface does not provide any means of altering the data. It is only possible to add modules, making it relatively safe to return a non-const pointer of this type pointing to an internal data structure without worrying about possible modifications of the data.

This class also provides protected methods for use in derived classes. The properties returned by isMultipoint(), dataSetCount(), and columnCount() must be set using setMultipoint(), setDataSetCount(), and setColumnCount(). notify*() methods in the AnalysisDataModuleManager returned by moduleManager() must be used to report when data becomes available for modules to process it. There are also three pure virtual methods that need to be implemented to provide access to stored data: one public (frameCount()) and two protected ones (requestStorageInternal() and tryGetDataFrameInternal()).

It is up to subclasses to ensure that the virtual methods and the notifications in AnalysisDataModuleManager are called in a correct sequence (the methods will assert in most incorrect use cases), and that the data provided through the public interface matches that passed to the modules with the notify methods. Helper class AnalysisDataStorage provides a default implementation for storing data (calls to the pure virtual methods can simply be forwarded to appropriate methods in the helper class), and takes care of correctly calling the notification methods when new data is added to the storage. In most cases, it should be used to implement the derived classes.

Currently, it is not possible to continue using the data object if an attached module throws an exception during data processing; it is only safe to destroy such data object.

Todo:: Improve the exception-handling semantics. In most cases, it doesn't make much sense to continue data processing after one module fails, but having the alternative would not hurt.

Public Member Functions
bool	isMultipoint () const
	Whether the data can have multiple points in the same column in the same frame. More...

int	dataSetCount () const
	Returns the number of data sets in the data object. More...

int	columnCount (int dataSet) const
	Returns the number of columns in a data set. More...

int	columnCount () const
	Returns the number of columns in the data. More...

virtual int	frameCount () const =0
	Returns the total number of frames in the data. More...

AnalysisDataFrameRef	tryGetDataFrame (int index) const
	Access stored data. More...

AnalysisDataFrameRef	getDataFrame (int index) const
	Access stored data. More...

bool	requestStorage (int nframes)
	Request storage of frames. More...

void	addModule (const AnalysisDataModulePointer &module)
	Adds a module to process the data. More...

void	addColumnModule (int col, int span, const AnalysisDataModulePointer &module)
	Adds a module that processes only a subset of the columns. More...

void	applyModule (IAnalysisDataModule *module)
	Applies a module to process data that is ready. More...

Protected Member Functions
	AbstractAnalysisData ()
	Initializes a new analysis data object. More...

void	setDataSetCount (int dataSetCount)
	Sets the number of data sets. More...

void	setColumnCount (int dataSet, int columnCount)
	Sets the number of columns for a data set. More...

void	setMultipoint (bool bMultipoint)
	Sets whether the data has multiple points per column in a frame. More...

virtual AnalysisDataFrameRef	tryGetDataFrameInternal (int index) const =0
	Implements access to data frames. More...

virtual bool	requestStorageInternal (int nframes)=0
	Implements storage requests. More...

AnalysisDataModuleManager &	moduleManager ()
	Returns the module manager to use for calling notification methods.

const AnalysisDataModuleManager &	moduleManager () const
	Returns the module manager to use for calling notification methods.

Constructor & Destructor Documentation

gmx::AbstractAnalysisData::AbstractAnalysisData ( )

protected

Initializes a new analysis data object.

Exceptions

std::bad_alloc if out of memory.

Member Function Documentation

void gmx::AbstractAnalysisData::addColumnModule	(	int	col,
		int	span,
		const AnalysisDataModulePointer &	module
	)

Adds a module that processes only a subset of the columns.

Parameters

[in]	col	First column.
[in]	span	Number of columns.
	module	Module to add.

Throws in the same situations as addModule().

Currently, all data sets are filtered using the same column mask.

Todo:: This method doesn't currently work in all cases with multipoint data or with multiple data sets. In particular, if the added module requests storage and uses getDataFrame(), it will behave unpredictably (most likely asserts).

Todo:: Generalize this method to multiple data sets (e.g., for adding modules that only process a single data set).

See Also: addModule()

void gmx::AbstractAnalysisData::addModule ( const AnalysisDataModulePointer & module )

Adds a module to process the data.

Parameters

module Module to add.

Exceptions

std::bad_alloc	if out of memory.
APIError	if `module` is not compatible with the data object data has already been added to the data object and everything is not available through getDataFrame().
unspecified	Any exception thrown by `module` in its notification methods (if data has been added).

If data has already been added to the data, the new module immediately processes all existing data. APIError is thrown if all data is not available through getDataFrame().

The caller can keep a copy of the module pointer if it requires later access to the module.

If the method throws, the state of the data object is not changed. The state of the data module is indeterminate.

void gmx::AbstractAnalysisData::applyModule ( IAnalysisDataModule * module )

Applies a module to process data that is ready.

Parameters

module Module to apply.

Exceptions

APIError	in same situations as addModule().
unspecified	Any exception thrown by `module` in its notification methods.

This function works as addModule(), except that it does not keep a reference to module within the data object after it returns. Also, it can only be called after the data is ready, and only if getDataFrame() gives access to all of the data. It is provided for additional flexibility in postprocessing in-memory data.

Todo:: Currently, this method may not work correctly if module requests storage (addModule() has the same problem if called after data is started).

int gmx::AbstractAnalysisData::columnCount ( int dataSet ) const

Returns the number of columns in a data set.

Parameters

[in] dataSet Zero-based index of the data set to query.

Returns: The number of columns in the data.

If the number of columns is not yet known, returns 0. The returned value does not change after modules have been notified of data start, but may change multiple times before that, depending on the actual data class. Derived classes should set the number of columns with setColumnCount(), within the above limitations.

Does not throw.

int gmx::AbstractAnalysisData::columnCount ( ) const

Returns the number of columns in the data.

Returns: The number of columns in the data.

This is a convenience method for data objects with a single data set. Can only be called if dataSetCount() == 1.

Does not throw.

See Also: columnCount(int)

int gmx::AbstractAnalysisData::dataSetCount ( ) const

Returns the number of data sets in the data object.

Returns: The number of data sets in the data.

If the number is not yet known, returns 0. The returned value does not change after modules have been notified of data start, but may change multiple times before that, depending on the actual data class. Derived classes should set the number of columns with setDataSetCount(), within the above limitations.

Does not throw.

virtual int gmx::AbstractAnalysisData::frameCount ( ) const

pure virtual

Returns the total number of frames in the data.

Returns: The total number of frames in the data.

This function returns the number of frames that the object has produced. If requestStorage() has been successfully called, tryGetDataframe() or getDataFrame() can be used to access some or all of these frames.

Does not throw.

Derived classes should implement this to return the number of frames. The frame count should not be incremented before tryGetDataFrameInternal() can return the new frame. The frame count must be incremented before AnalysisDataModuleManager::notifyFrameFinish() is called.

Implemented in gmx::AnalysisDataWeightedHistogramModule, gmx::AnalysisDataSimpleHistogramModule, gmx::AnalysisData, gmx::AnalysisDataFrameAverageModule, and gmx::AbstractAnalysisArrayData.

AnalysisDataFrameRef gmx::AbstractAnalysisData::getDataFrame ( int index ) const

Access stored data.

Parameters

[in] index Zero-based frame index to access.

Returns: Frame reference to frame index.

Exceptions

APIError if the requested frame is not accessible.

If the data is not certainly available, use tryGetDataFrame().

See Also: requestStorage(); tryGetDataFrame()

bool gmx::AbstractAnalysisData::isMultipoint ( ) const

Whether the data can have multiple points in the same column in the same frame.

Returns: true if multiple points in the same column are allowed within a single frame.

This kind of data can appear in many histogramming applications (e.g., RDFs), where each trajectory frame has several data points (possibly a different number for each frame). The current interface doesn't support storing such data, but this should rarely be necessary.

The returned value does not change after modules have been notified of data start. Derived classes can change the type by calling setMultipoint() subject to the above restriction. If this is not done, the function always returns false.

Does not throw.

bool gmx::AbstractAnalysisData::requestStorage ( int nframes )

Request storage of frames.

Parameters

[in] nframes Request storing at least nframes previous frames (-1 = request storing all). Must be >= -1.

Returns: true if the request could be satisfied.

If called multiple times, the largest request is honored.

Does not throw. Failure to honor the request is indicated through the return value.

See Also: getDataFrame(); tryGetDataFrame()

virtual bool gmx::AbstractAnalysisData::requestStorageInternal ( int nframes )

protectedpure virtual

Implements storage requests.

Parameters

[in] nframes Request storing at least nframes previous frames (-1 = request storing all). Will be either -1 or >0.

Returns: true if the request could be satisfied.

Must not throw. Failure to access a frame with the given index is indicated through the return value.

Derived classes should be prepared for any number of calls to this method before notifyDataStart() is called (and during that call).

This method is called internally by requestStorage().

See Also: AnalysisDataStorage

void gmx::AbstractAnalysisData::setColumnCount	(	int	dataSet,
		int	columnCount
	)

protected

Sets the number of columns for a data set.

Parameters

[in]	dataSet	Zero-based index of the data set.
[in]	columnCount	Number of columns in `dataSet` (must be > 0).

Exceptions

APIError if modules have been added that are not compatible with the new column count.

Must be called at least once for each data set before AnalysisDataModuleManager::notifyDataStart(). Can be called only before AnalysisDataModuleManager::notifyDataStart(). Multiple calls are allowed before that point; the last call takes effect.

Strong exception safety.

See Also: columnCount()

void gmx::AbstractAnalysisData::setDataSetCount ( int dataSetCount )

protected

Sets the number of data sets.

Parameters

[in] dataSetCount Number of data sets (must be > 0).

Exceptions

std::bad_alloc	if out of memory.
APIError	if modules have been added that are not compatible with the new data set count.

It not called, the data object has a single data set. Can be called only before AnalysisDataModuleManager::notifyDataStart(). Multiple calls are allowed before that point; the last call takes effect.

Strong exception safety.

See Also: dataSetCount()

void gmx::AbstractAnalysisData::setMultipoint ( bool bMultipoint )

protected

Sets whether the data has multiple points per column in a frame.

Parameters

[in] bMultipoint Whether multiple points per column are possible.

Exceptions

APIError if modules have been added that are not compatible with the new setting.

If not called, only a single point per column is allowed. Can be called only before AnalysisDataModuleManager::notifyDataStart(). Multiple calls are allowed before that point; the last call takes effect.

Strong exception safety.

See Also: isMultipoint()

AnalysisDataFrameRef gmx::AbstractAnalysisData::tryGetDataFrame ( int index ) const

Access stored data.

Parameters

[in] index Zero-based frame index to access.

Returns: Frame reference to frame index, or an invalid reference if no such frame is available.

Does not throw. Failure to access a frame with the given index is indicated through the return value. Negative index is allowed, and will always result in an invalid reference being returned.

See Also: requestStorage(); getDataFrame()

virtual AnalysisDataFrameRef gmx::AbstractAnalysisData::tryGetDataFrameInternal ( int index ) const

protectedpure virtual

Implements access to data frames.

Parameters

[in] index Zero-based frame index to access.

Returns: Frame reference to frame index, or an invalid reference if no such frame is available.

Must not throw. Failure to access a frame with the given index is indicated through the return value.

Code in derived classes can assume that index is non-negative and less than frameCount().

Derived classes can choose to return an invalid reference if requestStorageInternal() has not been called at all, or if the frame is too old (compared to the value given to requestStorageInternal()).

This method is called internally by tryGetDataFrame() and getDataFrame().

See Also: AnalysisDataStorage

The documentation for this class was generated from the following files:

api/legacy/include/gromacs/analysisdata/abstractdata.h
src/gromacs/analysisdata/abstractdata.cpp

Description

Public Member Functions

Protected Member Functions

Constructor & Destructor Documentation

Member Function Documentation