#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.

The x axis defaults to one with uniform spacing between values, which caters to a typical case of e.g. a time series equally spaced in time across a series of trajectory frames. However, non-uniform cases are supported via setXAxisValue(), which can be useful when handling other kinds of data.

Todo:: Add support for multiple data sets.

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

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

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

real	xstep () const
	Returns the step between frame x values when the x axis is uniform.

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

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

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

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

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

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

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

AnalysisDataFrameRef	getDataFrame (size_t 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 (size_t col, size_t 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 (size_t ncols)
	Sets the number of columns in the data array. More...

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

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

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

Protected Member Functions inherited from gmx::AbstractAnalysisData
	AbstractAnalysisData ()
	Initializes a new analysis data object. More...

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

void	setColumnCount (size_t dataSet, size_t 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...

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.

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::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::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.

size_t 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.

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.

Implements gmx::AbstractAnalysisData.

size_t 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 ( size_t 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 ( size_t 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().

Cannot be called after setXAxisValues() made a non-uniform X axis unless ncols equals the largest such X-axis value previously set.

Does not throw.

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

protected

Sets the values reported as x values for frames.

Afterwards, the X axis is uniform.

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	(	size_t	row,
		real	value
	)

protected

Sets a single value reported as x value for frames.

Afterwards, the X axis is non-uniform. Can be used to adjust the values of an X axis created with setXAxis().

The row count is never changed, and might need to be managed explicitly with setRowCount() if needed.

Parameters

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

When the row count is already set, row must be in range.

Must not be called after valuesReady().

Does not throw.

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:

api/legacy/include/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