net.sf.basedb.util.export.spotdata
Class AnnotationAssayField

java.lang.Object
  net.sf.basedb.util.export.spotdata.AnnotationAssayField

All Implemented Interfaces:

AssayField, ExportableField

public class AnnotationAssayField
extends Object
implements AssayField

Assay field implementation that exports the annotations of a bioassay. Before it can be used an AnnotationType must be configured. One instance of this class is considered to be equal to another if they are configured with the same annotation type and title.

Version:

2.12

Author:

Nicklas

Last modified

$Date: 2010-08-03 11:11:54 +0200 (Tue, 03 Aug 2010) $

Field Summary

private AnnotationType	at
private Formatter<?>	formatter
private SnapshotManager	snapshotManager
private String	title

Constructor Summary

AnnotationAssayField()
Create a new annotation field.

Method Summary

boolean	equals(Object obj) An assay field is equal to another assay field if it uses the same annotation type and has the same title.
AnnotationType	getAnnotationType() Get the configured annotation type.
Collection<?>	getAssayValue(DbControl dc, BioAssay ba) Return all annotation values that are related to the specified bioassay, or null if not configured.
Formatter<?>	getFormatter() Get a formatter that converts the values in this field to strings.
String	getTitle() Returns the name of the configured annotation type, or the empty string if not configured.
Type	getType() Return the value type of the annotation type, or null if not configured.
int	hashCode()
boolean	isAnnotation() A boolean flag indicating if the field is an annotation or not.
void	setAnnotationType(AnnotationType at) Set the annotation type of the annotations that should be exported in this field.
void	setFormatter(Formatter<?> formatter) Set a formatter to use for formatting the exported values.
void	setSnapshotManager(SnapshotManager snapshotManager) Set the snapshot manager that should be used to load annotation values.
void	setTitle(String title) Set a custom title for the assay field.
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

at

private AnnotationType at

title

private String title

formatter

private Formatter<?> formatter

snapshotManager

private SnapshotManager snapshotManager

Constructor Detail

AnnotationAssayField

public AnnotationAssayField()

Create a new annotation field. Call setAnnotationType(AnnotationType) before use.

Method Detail

getTitle

public String getTitle()

Returns the name of the configured annotation type, or the empty string if not configured.

Specified by:

getTitle in interface ExportableField

getAssayValue

public Collection<?> getAssayValue(DbControl dc,
                                   BioAssay ba)

Return all annotation values that are related to the specified bioassay, or null if not configured.

Specified by:

getAssayValue in interface AssayField

Parameters:

dc - The DbControl that is used for database access

ba - The bioassay to get the value(s) from

Returns:

A collection with one or more values, or null or an empty collection if there is no value for the given bioassay

getType

public Type getType()

Return the value type of the annotation type, or null if not configured.

Specified by:

getType in interface ExportableField

Returns:

A type object or null if not known

Since:

2.15

getFormatter

public Formatter<?> getFormatter()

Description copied from interface: ExportableField

Get a formatter that converts the values in this field to strings.

Specified by:

getFormatter in interface ExportableField

Returns:

A formatter or null to use default formatting (normally this means calling the toString() method).

isAnnotation

public boolean isAnnotation()

Description copied from interface: AssayField

A boolean flag indicating if the field is an annotation or not.

Specified by:

isAnnotation in interface AssayField

Returns:

Always TRUE

equals

public boolean equals(Object obj)

An assay field is equal to another assay field if it uses the same annotation type and has the same title.

Overrides:

equals in class Object

Since:

2.15

hashCode

public int hashCode()

Overrides:

hashCode in class Object

Since:

2.15

toString

public String toString()

Overrides:

toString in class Object

Since:

2.15

setAnnotationType

public void setAnnotationType(AnnotationType at)

Set the annotation type of the annotations that should be exported in this field.

getAnnotationType

public AnnotationType getAnnotationType()

Get the configured annotation type.

setFormatter

public void setFormatter(Formatter<?> formatter)

Set a formatter to use for formatting the exported values.

setSnapshotManager

public void setSnapshotManager(SnapshotManager snapshotManager)

Set the snapshot manager that should be used to load annotation values.

Since:

2.14

setTitle

public void setTitle(String title)

Set a custom title for the assay field.

Parameters:

title - The custom title or null to use the name of the annotation type