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gmx::internal::BasicAverageHistogramModule Class Reference
+ Inheritance diagram for gmx::internal::BasicAverageHistogramModule:
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Description

Implements average histogram module that averages per-frame histograms.

This class is used for accumulating average histograms in per-frame histogram modules (those that use BasicHistogramImpl as their implementation class). There are two columns, first for the average and second for standard deviation.

Public Member Functions

 BasicAverageHistogramModule (const AnalysisHistogramSettings &settings)
 Creates an average histogram module with defined bin parameters.
 
int flags () const override
 Returns properties supported by the module. More...
 
void dataStarted (AbstractAnalysisData *data) override
 Called (once) when the data has been set up properly. More...
 
void frameStarted (const AnalysisDataFrameHeader &header) override
 Called at the start of each data frame. More...
 
void pointsAdded (const AnalysisDataPointSetRef &points) override
 Called one or more times during each data frame. More...
 
void frameFinished (const AnalysisDataFrameHeader &header) override
 Called when a data frame is finished. More...
 
void dataFinished () override
 Called (once) when no more data is available. More...
 
- Public Member Functions inherited from gmx::AbstractAverageHistogram
const AnalysisHistogramSettingssettings () const
 Returns bin properties for the histogram.
 
AverageHistogramPointer resampleDoubleBinWidth (bool bIntegerBins) const
 Creates a copy of the histogram with double the bin width. More...
 
AverageHistogramPointer clone () const
 Creates a deep copy of the histogram. More...
 
void normalizeProbability ()
 Normalizes the histogram such that the integral over it is one.
 
void makeCumulative ()
 Makes the histograms cumulative by summing up each bin to all bins after it. More...
 
void scaleSingle (int index, real factor)
 Scales a single histogram by a uniform scaling factor.
 
void scaleAll (real factor)
 Scales all histograms by a uniform scaling factor.
 
void scaleAllByVector (const real factor[])
 Scales the value of each bin by a different scaling factor.
 
void done ()
 Notifies attached modules of the histogram data. More...
 
- Public Member Functions inherited from gmx::AbstractAnalysisArrayData
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 AnalysisDataValuevalue (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 (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...
 

Additional Inherited Members

- Public Types inherited from gmx::IAnalysisDataModule
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::AbstractAverageHistogram
 AbstractAverageHistogram ()
 Creates a histogram module with undefined bins. More...
 
 AbstractAverageHistogram (const AnalysisHistogramSettings &settings)
 Creates a histogram module with defined bin parameters.
 
void init (const AnalysisHistogramSettings &settings)
 (Re)initializes the histogram from settings.
 
- 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...
 
AnalysisDataValuevalue (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...
 
AnalysisDataModuleManagermoduleManager ()
 Returns the module manager to use for calling notification methods.
 
const AnalysisDataModuleManagermoduleManager () 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::internal::BasicAverageHistogramModule::dataFinished ( )
overridevirtual

Called (once) when no more data is available.

Exceptions
unspecifiedCan throw any exception required by the implementing class to report errors.

Implements gmx::AnalysisDataModuleSerial.

void gmx::internal::BasicAverageHistogramModule::dataStarted ( AbstractAnalysisData data)
overridevirtual

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

Parameters
[in]dataData object to which the module is added.
Exceptions
APIErrorif the provided data is not compatible.
unspecifiedCan 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::internal::BasicAverageHistogramModule::flags ( ) const
overridevirtual

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::internal::BasicAverageHistogramModule::frameFinished ( const AnalysisDataFrameHeader header)
overridevirtual

Called when a data frame is finished.

Parameters
[in]headerHeader information for the frame that is ending.
Exceptions
unspecifiedCan throw any exception required by the implementing class to report errors.

Implements gmx::AnalysisDataModuleSerial.

void gmx::internal::BasicAverageHistogramModule::frameStarted ( const AnalysisDataFrameHeader frame)
overridevirtual

Called at the start of each data frame.

Parameters
[in]frameHeader information for the frame that is starting.
Exceptions
unspecifiedCan throw any exception required by the implementing class to report errors.

Implements gmx::AnalysisDataModuleSerial.

void gmx::internal::BasicAverageHistogramModule::pointsAdded ( const AnalysisDataPointSetRef points)
overridevirtual

Called one or more times during each data frame.

Parameters
[in]pointsSet of points added (also provides access to frame-level data).
Exceptions
APIErrorif the provided data is not compatible.
unspecifiedCan 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.


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