#include <gromacs/analysisdata/modules/lifetime.h>

Inheritance diagram for gmx::AnalysisDataLifetimeModule:

Collaboration diagram for gmx::AnalysisDataLifetimeModule:

Description

Data module for computing lifetime histograms for columns in input data.

The input data set is treated as a boolean array: each value that is present (AnalysisDataValue::isPresent() returns true) and is >0 is treated as present, other values are treated as absent. For each input data set, analyzes the columns to identify the intervals where a column is continuously present. Produces a histogram from the lengths of these intervals. Input data should have frames with evenly spaced x values.

Output data contains one column for each data set in the input data. This column gives the lifetime histogram for the corresponding data set. x axis in the output is spaced the same as in the input data, and extends as long as required to cover all the histograms. Histograms are padded with zeros as required to be of the same length. setCumulative() can be used to alter the handling of subintervals in the output histogram.

The output data becomes available only after the input data has been finished.

Classes
class	Impl
	Private implementation class for AnalysisDataLifetimeModule. More...

Public Member Functions
void	setCumulative (bool bCumulative)
	Sets a cumulative histogram mode. More...

virtual int	flags () const
	Returns properties supported by the module. More...

virtual void	dataStarted (AbstractAnalysisData *data)
	Called (once) when the data has been set up properly. More...

virtual void	frameStarted (const AnalysisDataFrameHeader &header)
	Called at the start of each data frame. More...

virtual void	pointsAdded (const AnalysisDataPointSetRef &points)
	Called one or more times during each data frame. More...

virtual void	frameFinished (const AnalysisDataFrameHeader &header)
	Called when a data frame is finished. More...

virtual void	dataFinished ()
	Called (once) when no more data is available. More...

Public Member Functions inherited from gmx::AbstractAnalysisArrayData
virtual int	frameCount () const
	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.

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...

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 (AnalysisDataModulePointer module)
	Adds a module to process the data. More...

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

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

Additional Inherited Members
Public Types inherited from gmx::AnalysisDataModuleInterface
enum	Flag { efAllowMultipoint = 1<<0, efOnlyMultipoint = 1<<1, efAllowMulticolumn = 1<<2, efAllowMissing = 1<<3, efAllowMultipleDataSets = 1<<4 }
	Possible flags for flags(). More...

Protected Member Functions inherited from gmx::AbstractAnalysisArrayData
	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...

Protected Member Functions inherited from gmx::AbstractAnalysisData
	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...

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 inherited from gmx::AbstractAnalysisArrayData
static void	copyContents (const AbstractAnalysisArrayData src, AbstractAnalysisArrayData dest)
	Copies the contents into a new object. More...

Member Function Documentation

void gmx::AnalysisDataLifetimeModule::dataFinished ( )

virtual

Called (once) when no more data is available.

Exceptions

unspecified Can throw any exception required by the implementing class to report errors.

Implements gmx::AnalysisDataModuleSerial.

void gmx::AnalysisDataLifetimeModule::dataStarted ( AbstractAnalysisData * data )

virtual

Called (once) when the data has been set up properly.

Parameters

[in] data Data object to which the module is added.

Exceptions

APIError	if the provided data is not compatible.
unspecified	Can throw any exception required by the implementing class to report errors.

When the data is ready, either this method or parallelDataStarted() is called, depending on the nature of the input data. If this method is called, the input data will always present the frames in sequential order.

The data to which the module is attached is passed as an argument to provide access to properties of the data for initialization and/or validation. The module can also call AbstractAnalysisData::requestStorage() if needed.

This is the only place where the module gets access to the data; if properties of the data are required later, the module should store them internally. It is guaranteed that the data properties (column count, whether it's multipoint) do not change once this method has been called.

Notice that data will be a proxy object if the module is added as a column module, not the data object for which AbstractAnalysisData::addColumnModule() was called.

Implements gmx::AnalysisDataModuleSerial.

int gmx::AnalysisDataLifetimeModule::flags ( ) const

virtual

Returns properties supported by the module.

The return value of this method should not change after the module has been added to a data (this responsibility can, and in most cases must, be delegated to the user of the module).

The purpose of this method is to remove the need for common checks for data compatibility in the classes that implement the interface. Instead, AbstractAnalysisData performs these checks based on the flags provided.

Does not throw.

Implements gmx::AnalysisDataModuleSerial.

void gmx::AnalysisDataLifetimeModule::frameFinished ( const AnalysisDataFrameHeader & header )

virtual

Called when a data frame is finished.

Parameters

[in] header Header information for the frame that is ending.

Exceptions

unspecified Can throw any exception required by the implementing class to report errors.

Implements gmx::AnalysisDataModuleSerial.

void gmx::AnalysisDataLifetimeModule::frameStarted ( const AnalysisDataFrameHeader & frame )

virtual

Called at the start of each data frame.

Parameters

[in] frame Header information for the frame that is starting.

Exceptions

unspecified Can throw any exception required by the implementing class to report errors.

Implements gmx::AnalysisDataModuleSerial.

void gmx::AnalysisDataLifetimeModule::pointsAdded ( const AnalysisDataPointSetRef & points )

virtual

Called one or more times during each data frame.

Parameters

[in] points Set of points added (also provides access to frame-level data).

Exceptions

APIError	if the provided data is not compatible.
unspecified	Can throw any exception required by the implementing class to report errors.

Can be called once or multiple times for a frame. For all data objects currently implemented in the library (and all objects that will use AnalysisDataStorage for internal implementation), it is called exactly once for each frame if the data is not multipoint, but currently this restriction is not enforced.

Implements gmx::AnalysisDataModuleSerial.

void gmx::AnalysisDataLifetimeModule::setCumulative ( bool bCumulative )

Sets a cumulative histogram mode.

Parameters

[in] bCumulative If true, all subintervals of a long interval are also explicitly added into the histogram.

Does not throw.

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

src/gromacs/analysisdata/modules/lifetime.h
src/gromacs/analysisdata/modules/lifetime.cpp

Description

Classes

Public Member Functions

Additional Inherited Members

Member Function Documentation