Package annotation

Class DataAnnotationType<TDataAnnotation extends DataAnnotation<?>>

java.lang.Object

annotation.DataAnnotationType<TDataAnnotation>

Direct Known Subclasses:

BaseClassificationAnnotationType, BearingAnnotationType, BearingLocAnnotationType, BFAnnotationType, ClickClassificationType, DLAnnotationType, DummyAnnotationType, MatchedClickAnnotationType, SNRAnnotationType, SPLAnnotationType, StringAnnotationType, TimestampAnnotationType, TMAnnotationType, UserFormAnnotationType, WavAnnotationType

public abstract class DataAnnotationType<TDataAnnotation extends DataAnnotation<?>>
extends Object

Something that can tell us a little more about a type of DataAnnotation, such as how to store and display and edit the data in that annotation.

This base type is intended for annotations which are genuinely annotations of existing data units. Stand alone annotations, which create their own dataunit should base upon SoloAnnotationType

Author:

Doug Gillespie

See Also:

• invalid reference

  SoloAnnotationType

Field Summary

Fields

Modifier and Type	Field	Description
static final int	SHORTIDCODELENGTH

Constructor Summary

Constructors

Constructor	Description
DataAnnotationType()

Method Summary

Modifier and Type	Method	Description
TDataAnnotation	autoAnnotate(PamDataUnit pamDataUnit)	Automatically annotate the data unit with this annotation.
abstract boolean	canAnnotate(Class dataUnitType)	Find out whether or not a particular type of data can be annotated
boolean	canAutoAnnotate()
abstract Class	getAnnotationClass()
abstract String	getAnnotationName()
AnnotationOptions	getAnnotationOptions()
AnnotationBinaryHandler<TDataAnnotation>	getBinaryHandler()	Get an optional AnnotationBinaryHandler which can be used to add the annotation information for binary files and also read data back from them.
DataBlockSpeciesManager	getDataBlockSpeciesManager()	Annotations may have a species manager.
protected AnnotationDataSelCreator	getDataSelectCreator(String selectorName, boolean allowScores)
DataSelector	getDataSelector(PamDataBlock pamDataBlock, String selectorName, boolean allowScores, String selectorType)	Get a data selector specific to this annotation, which will merge seamlessly into a master data selector combining data unit specific and annotation selections
AnnotationDialogPanel	getDialogPanel()	Get a dialog component that can be incorporated into a larger dialog.
AnnotationSettingsPanel	getSettingsPanel()
String	getShortIdCode()	A short identifying code which MUST be unique to the data annotation and MUST be four characters long.
SQLLoggingAddon	getSQLLoggingAddon()	Get an SQLLogging add on.
SymbolModifier	getSymbolModifier(PamSymbolChooser symbolChooser)	Some annotations may be able to set the type of symbol.
PamDataBlock	getTargetDataBlock()
AnnotationXMLWriter<TDataAnnotation>	getXMLWriter()	Get something that can write an annotation as XML
boolean	hasSettingsPanel()
boolean	isAnnotating(PamDataBlock pamDataBlock)	Is this type annotating a particular datablock.
void	setAnnotationOptions(AnnotationOptions annotationOptions)
void	setTargetDataBlock(PamDataBlock targetDataBlock)
String	toString()
String	toString(TDataAnnotation dataAnnotation)	Get the annotation as a string for use in tables, tool tips, etc.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

SHORTIDCODELENGTH

public static final int SHORTIDCODELENGTH

See Also:

• Constant Field Values

Constructor Details

DataAnnotationType

public DataAnnotationType()

Method Details

getAnnotationName

public abstract String getAnnotationName()

toString

public String toString(TDataAnnotation dataAnnotation)

Get the annotation as a string for use in tables, tool tips, etc.

Parameters:

dataAnnotation - Data Annotation

Returns:

String representation of the data

getAnnotationClass

public abstract Class getAnnotationClass()

Returns:

Class type for the annotations

canAnnotate

public abstract boolean canAnnotate(Class dataUnitType)

Find out whether or not a particular type of data can be annotated

Parameters:

dataUnitType - Class of a type of data unit. Can be null in which case annotation can be stand alone.

Returns:

true if the data unit Class can be annotated.

canAutoAnnotate

public boolean canAutoAnnotate()

Returns:

True if annotation can be automatic (i.e. calculated rather than input by user).

autoAnnotate

public TDataAnnotation autoAnnotate(PamDataUnit pamDataUnit)

Automatically annotate the data unit with this annotation.

Parameters:

pamDataUnit - data unit to annotate

Returns:

the annotation (though this should have already been added to the data unit).

getSQLLoggingAddon

public SQLLoggingAddon getSQLLoggingAddon()

Get an SQLLogging add on. For stand alone annotations, this will be used to generate a stand alone database table. For annotations of existing data this will be used to add additional columns to the existing data tables.

Returns:

An SQLLoggingAddon or null if SQL logging unavailable for this type of annotation.

getXMLWriter

public AnnotationXMLWriter<TDataAnnotation> getXMLWriter()

Get something that can write an annotation as XML

Returns:

getBinaryHandler

public AnnotationBinaryHandler<TDataAnnotation> getBinaryHandler()

Get an optional AnnotationBinaryHandler which can be used to add the annotation information for binary files and also read data back from them.

Returns:

handler for binary data i/o.

getDialogPanel

public AnnotationDialogPanel getDialogPanel()

Get a dialog component that can be incorporated into a larger dialog.

Note that this is for setting the data for a specific annotation, NOT the dialog for setting options controlling how the annotation type works.

Returns:

a dialog panel (contains a component = a few other functions).

getSettingsPanel

public AnnotationSettingsPanel getSettingsPanel()

hasSettingsPanel

public boolean hasSettingsPanel()

getAnnotationOptions

public AnnotationOptions getAnnotationOptions()

Returns:

the annotationOptions

setAnnotationOptions

public void setAnnotationOptions(AnnotationOptions annotationOptions)

Parameters:

annotationOptions - the annotationOptions to set

getShortIdCode

public String getShortIdCode()

A short identifying code which MUST be unique to the data annotation and MUST be four characters long. Classes can override this with something even more cryptic so long as it remains unique.

Returns:

a four character id string.

getSymbolModifier

public SymbolModifier getSymbolModifier(PamSymbolChooser symbolChooser)

Some annotations may be able to set the type of symbol. This will be accessed from a datablocks SymbolManager

Returns:

toString

public String toString()

Overrides:

toString in class Object

getDataSelectCreator

protected AnnotationDataSelCreator getDataSelectCreator(String selectorName,
 boolean allowScores)

getDataSelector

public DataSelector getDataSelector(PamDataBlock pamDataBlock,
 String selectorName,
 boolean allowScores,
 String selectorType)

Get a data selector specific to this annotation, which will merge seamlessly into a master data selector combining data unit specific and annotation selections

Parameters:

pamDataBlock -

selectorName -

allowScores -

Returns:

data selector

isAnnotating

public boolean isAnnotating(PamDataBlock pamDataBlock)

Is this type annotating a particular datablock.

Parameters:

pamDataBlock -

Returns:

getTargetDataBlock

public PamDataBlock getTargetDataBlock()

Returns:

the targetDataBlock

setTargetDataBlock

public void setTargetDataBlock(PamDataBlock targetDataBlock)

Parameters:

targetDataBlock - the targetDataBlock to set

getDataBlockSpeciesManager

public DataBlockSpeciesManager getDataBlockSpeciesManager()

Annotations may have a species manager. Most won't.

Returns: