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

Inheritance diagram for gmx::AbstractPlotModule:

Collaboration diagram for gmx::AbstractPlotModule:

Description

Abstract data module for writing data into a file.

Implements features common to all plotting modules. Subclasses implement features specific to certain applications (AnalysisDataPlotModule implements straightforward plotting).

By default, the data is written into an xvgr file, according to the options read from the AnalysisDataPlotSettings object given to the constructor. For non-xvgr data, it's possible to skip all headers by calling setPlainOutput().

A single output line corresponds to a single frame. In most cases with multipoint data, setPlainOutput() should be called since the output does not make sense as an xvgr file, but this is not enforced.

Multipoint data and multiple data sets are both supported, in which case all the points are written to the output, in the order in which they are added to the data.

Public Member Functions
void	setSettings (const AnalysisDataPlotSettings &settings)
	Set common settings for the plotting.

void	setFileName (const std::string &filename)
	Set the output file name. More...

void	setPlainOutput (bool bPlain)
	Set plain output. More...

void	setErrorsAsSeparateColumn (bool bSeparate)
	Plot errors as a separate output column after each value column.

void	setOmitX (bool bOmitX)
	Omit the X coordinates from the output. More...

void	setTitle (const char *title)
	Set plot title.

void	setTitle (const std::string &title)
	Set plot title. More...

void	setSubtitle (const char *subtitle)
	Set plot subtitle.

void	setSubtitle (const std::string &subtitle)
	Set plot subtitle. More...

void	setXLabel (const char *label)
	Set X axis label.

void	setXAxisIsTime ()
	Treat X axis as time. More...

void	setYLabel (const char *label)
	Set Y axis label.

void	setLegend (int nsets, const char const setname)
	Add legend from an array of strings. More...

void	appendLegend (const char *setname)
	Add a legend string for the next data set. More...

void	appendLegend (const std::string &setname)
	Add a legend string for the next data set. More...

void	setXFormat (int width, int precision, char format= 'f')
	Set field width and precision for X value output.

void	setYFormat (int width, int precision, char format= 'f')
	Set field width and precision for Y value output.

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=0
	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...

Protected Member Functions
	AbstractPlotModule (const AnalysisDataPlotSettings &settings)
	Creates AbstractPlotModule and assign common settings.

bool	isFileOpen () const
	Whether an output file has been opened.

void	writeValue (const AnalysisDataValue &value) const
	Appends a single value to the current output line. 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...

Member Function Documentation

void gmx::AbstractPlotModule::appendLegend ( const char * setname )

Add a legend string for the next data set.

Multiple calls to setLegend() and/or appendLegend() are added together.

void gmx::AbstractPlotModule::appendLegend ( const std::string & setname )

Add a legend string for the next data set.

Multiple calls to setLegend() and/or appendLegend() are added together.

void gmx::AbstractPlotModule::dataFinished ( )

overridevirtual

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::AbstractPlotModule::dataStarted ( AbstractAnalysisData * data )

overridevirtual

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::AbstractPlotModule::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::AbstractPlotModule::frameFinished ( const AnalysisDataFrameHeader & header )

overridevirtual

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::AbstractPlotModule::frameStarted ( const AnalysisDataFrameHeader & frame )

overridevirtual

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::AbstractPlotModule::pointsAdded ( const AnalysisDataPointSetRef & points )

overridepure 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.

Implemented in gmx::AnalysisDataVectorPlotModule, and gmx::AnalysisDataPlotModule.

void gmx::AbstractPlotModule::setFileName ( const std::string & filename )

Set the output file name.

If no file name is set (or if filename is empty), no output occurs.

void gmx::AbstractPlotModule::setLegend	(	int	nsets,
		const char const	setname
	)

Add legend from an array of strings.

Multiple calls to setLegend() and/or appendLegend() are added together.

void gmx::AbstractPlotModule::setOmitX ( bool bOmitX )

Omit the X coordinates from the output.

This method only makes sense when combined with setPlainOutput().

void gmx::AbstractPlotModule::setPlainOutput ( bool bPlain )

Set plain output.

If bPlain is true, no xvgr headers are written to the file. In this case, only setOmitX(), setXFormat(), and setYFormat() methods have any effect on the output.

void gmx::AbstractPlotModule::setSubtitle ( const std::string & subtitle )

Set plot subtitle.

void gmx::AbstractPlotModule::setTitle ( const std::string & title )

Set plot title.

void gmx::AbstractPlotModule::setXAxisIsTime ( )

Treat X axis as time.

Sets the label for the axis accordingly and also scales output to take into account the correct time unit.

void gmx::AbstractPlotModule::writeValue ( const AnalysisDataValue & value ) const

protected

Appends a single value to the current output line.

Parameters

[in] value Value to append.

Should be used from pointsAdded() implementations in derived classes to write out individual y values to the output.

Must not be called if isFileOpen() returns false.

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

api/legacy/include/gromacs/analysisdata/modules/plot.h
src/gromacs/analysisdata/modules/plot.cpp

Description

Public Member Functions

Protected Member Functions

Additional Inherited Members

Member Function Documentation