#include <gromacs/analysisdata/arraydata.h>

Inheritance diagram for gmx::AbstractAnalysisArrayData:

Collaboration diagram for gmx::AbstractAnalysisArrayData:

Description

Abstract base class for data objects that present in-memory data.

This class implements a subclass of AbstractAnalysisData that presents an in-memory array through the AbstractAnalysisData interface. Subclasses should initialize the in-memory array through the provided protected member functions. This class provides public accessor methods for read access to the data.

Public accessor methods in this class do not throw, but assert if data is accessed before it is available.

Todo:: Add support for multiple data sets.

Public Member Functions
int	frameCount () const override
	Returns the total number of frames in the data. More...

int	rowCount () const
	Returns the number of rows in the data array. More...

bool	isAllocated () const
	Returns true if values have been allocated.

real	xstart () const
	Returns the x value of the first frame.

real	xstep () const
	Returns the step between frame x values.

real	xvalue (int row) const
	Returns the x value of a row.

const AnalysisDataValue &	value (int row, int col) const
	Returns a given array element.

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...

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
	AbstractAnalysisArrayData ()
	Initializes an empty array data object. More...

void	setColumnCount (int ncols)
	Sets the number of columns in the data array. More...

void	setRowCount (int rowCount)
	Sets the number of rows in the data array. More...

void	allocateValues ()
	Allocates memory for the values. More...

void	setXAxis (real start, real step)
	Sets the values reported as x values for frames. More...

void	setXAxisValue (int row, real value)
	Sets a single value reported as x value for frames. More...

AnalysisDataValue &	value (int row, int col)
	Returns a reference to a given array element.

void	valuesReady ()
	Notifies modules of the data. More...

Static Protected Member Functions
static void	copyContents (const AbstractAnalysisArrayData src, AbstractAnalysisArrayData dest)
	Copies the contents into a new object. More...

Constructor & Destructor Documentation

gmx::AbstractAnalysisArrayData::AbstractAnalysisArrayData ( )

protected

Initializes an empty array data object.

Exceptions

std::bad_alloc if out of memory.

Member Function Documentation

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

inherited

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 )

inherited

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::AbstractAnalysisArrayData::allocateValues ( )

protected

Allocates memory for the values.

Exceptions

std::bad_alloc if memory allocation fails.

setColumnCount() and setRowCount() must have been called.

Strong exception safety guarantee.

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

inherited

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

inherited

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.

Does not throw.

int gmx::AbstractAnalysisData::columnCount ( ) const

inherited

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)

void gmx::AbstractAnalysisArrayData::copyContents	(	const AbstractAnalysisArrayData *	src,
		AbstractAnalysisArrayData *	dest
	)

staticprotected

Copies the contents into a new object.

Parameters

[in]	src	Object to copy data from.
[in,out]	dest	Empty array data object to copy data to.

Exceptions

std::bad_alloc if memory allocation for dest fails.

dest should not have previous contents.

int gmx::AbstractAnalysisData::dataSetCount ( ) const

inherited

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.

Does not throw.

int gmx::AbstractAnalysisArrayData::frameCount ( ) const

inlineoverridevirtual

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.

Implements gmx::AbstractAnalysisData.

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

inherited

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

inherited

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.

Does not throw.

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

inherited

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()

int gmx::AbstractAnalysisArrayData::rowCount ( ) const

inline

Returns the number of rows in the data array.

This function is identical to frameCount(), except that frameCount() returns 0 before valuesReady() has been called.

void gmx::AbstractAnalysisArrayData::setColumnCount ( int ncols )

protected

Sets the number of columns in the data array.

Parameters

[in] ncols Number of columns in the data.

Cannot be called after allocateValues().

See AbstractAnalysisData::setColumnCount() for exception behavior.

void gmx::AbstractAnalysisArrayData::setRowCount ( int rowCount )

protected

Sets the number of rows in the data array.

Parameters

[in] rowCount Number of rows in the data.

Cannot be called after allocateValues().

Does not throw.

void gmx::AbstractAnalysisArrayData::setXAxis	(	real	start,
		real	step
	)

protected

Sets the values reported as x values for frames.

Parameters

[in]	start	x value for the first frame.
[in]	step	Step between x values of successive frames.

Must not be called after valuesReady(). Any values set with setXAxisValue() are overwritten.

Does not throw.

void gmx::AbstractAnalysisArrayData::setXAxisValue	(	int	row,
		real	value
	)

protected

Sets a single value reported as x value for frames.

Parameters

[in]	row	Row/frame for which to set the value.
[in]	value	x value for the frame specified by `row`.

Must not be called after valuesReady().

Does not throw.

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

inherited

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()

void gmx::AbstractAnalysisArrayData::valuesReady ( )

protected

Notifies modules of the data.

Exceptions

unspecified Any exception thrown by attached data modules in data notification methods.

This function should be called once the values in the array have been initialized. The values should not be changed after this function has been called.

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

src/gromacs/analysisdata/arraydata.h
src/gromacs/analysisdata/arraydata.cpp

Description

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Constructor & Destructor Documentation

Member Function Documentation