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gmx::AbstractAnalysisData Class Referenceabstract

#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 (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 (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...
 
AnalysisDataModuleManagermoduleManager ()
 Returns the module manager to use for calling notification methods.
 
const AnalysisDataModuleManagermoduleManager () 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_allocif out of memory.

Member Function Documentation

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

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

Parameters
[in]colFirst column.
[in]spanNumber of columns.
moduleModule 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 ( AnalysisDataModulePointer  module)

Adds a module to process the data.

Parameters
moduleModule to add.
Exceptions
std::bad_allocif out of memory.
APIErrorif
  • module is not compatible with the data object
  • data has already been added to the data object and everything is not available through getDataFrame().
unspecifiedAny 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
moduleModule to apply.
Exceptions
APIErrorin same situations as addModule().
unspecifiedAny 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]dataSetZero-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::AnalysisDataFrameAverageModule, gmx::AnalysisData, and gmx::AbstractAnalysisArrayData.

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

Access stored data.

Parameters
[in]indexZero-based frame index to access.
Returns
Frame reference to frame index.
Exceptions
APIErrorif 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]nframesRequest 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]nframesRequest 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]dataSetZero-based index of the data set.
[in]columnCountNumber of columns in dataSet (must be > 0).
Exceptions
APIErrorif 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]dataSetCountNumber of data sets (must be > 0).
Exceptions
std::bad_allocif out of memory.
APIErrorif 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]bMultipointWhether multiple points per column are possible.
Exceptions
APIErrorif 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]indexZero-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]indexZero-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: