net.sf.basedb.core.data
Class AnnotationTypeData

java.lang.Object
  net.sf.basedb.core.data.BasicData
      net.sf.basedb.core.data.OwnedData
          net.sf.basedb.core.data.SharedData
              net.sf.basedb.core.data.CommonData
                  net.sf.basedb.core.data.AnnotationTypeData

All Implemented Interfaces:

IdentifiableData, LoggableData, NameableData, OwnableData, RegisteredData, RemovableData, ShareableData

public class AnnotationTypeData
extends CommonData
implements RegisteredData, LoggableData

This class holds information about an annotation type.

Version:

2.0

Author:

Nicklas

See Also:

AnnotationType, Annotations overview

Last modified

$Date: 2010-04-20 10:02:16 +0200 (Tue, 20 Apr 2010) $

Hibernate: class

table="`AnnotationTypes`" lazy="false"

Field Summary

private Set<AnnotationData>	annotations
private Set<AnnotationTypeCategoryData>	categories
private UnitData	defaultUnit
private String	defaultValue
private Date	entryDate
private ParameterValueData<?>	enumerationValues
private Set<ExperimentData>	experiments
private String	externalId
private int	height
private boolean	isEnumeration
private boolean	isProtocolParameter
private Set<Integer>	itemTypes
static int	MAX_DEFAULT_VALUE_LENGTH
static int	MAX_EXTERNAL_ID_LENGTH The maximum length of the external id that can be stored in the database.
static int	MAX_OPTION_LENGTH
private int	multiplicity
private Map<String,String>	options
private Set<ProtocolData>	protocols
private QuantityData	quantity
private boolean	requiredForMiame
private Set<UnitData>	usableUnits
private int	valueType
private int	width

Fields inherited from interface net.sf.basedb.core.data.NameableData

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

AnnotationTypeData()

Method Summary

(package private) Set<AnnotationData>	getAnnotations() This is the inverse end.
Set<AnnotationTypeCategoryData>	getCategories() Get the set that manages the categories of this annotation type.
UnitData	getDefaultUnit() Get the unit used to store annotation values for this type.
String	getDefaultValue() The default value of new annotations.
Date	getEntryDate() Get the date this item was added to the database.
ParameterValueData<?>	getEnumerationValues() The allowed values if this is an enumeration.
(package private) Set<ExperimentData>	getExperiments() This is the inverse end.
String	getExternalId() Get the external id for the biomaterial
int	getHeight() The recommended height (lines) to display input fields for this annotation in client applications.
Set<Integer>	getItemTypes() The item code for all items this annotation type can be applied to.
int	getMultiplicity() How many values are allowed for this annotations of this type. 0 = no limit
Map<String,String>	getOptions() Additional options depending on the value type.
(package private) Set<ProtocolData>	getProtocols() This is the inverse end.
QuantityData	getQuantity() Get the quantity this annotation type uses.
Set<UnitData>	getUsableUnits() The units that it makes sense to use with this annotation type.
int	getValueType() The code for the value type.
int	getWidth() The recommended width (characters) to display input fields for this annotation in client applications.
boolean	isEnumeration() If this annotation type defines a list of allowed values or not.
boolean	isProtocolParameter() If this annotation type is intended to be used as a protocol parameter or as a regular annotation.
boolean	isRequiredForMiame() If an annotation of this type must be present for an annotatable item to be compliant with MIAME.
(package private) void	setAnnotations(Set<AnnotationData> annotations)
(package private) void	setCategories(Set<AnnotationTypeCategoryData> categories)
void	setDefaultUnit(UnitData defaultUnit)
void	setDefaultValue(String defaultValue)
void	setEntryDate(Date entryDate)
void	setEnumeration(boolean isEnumeration)
void	setEnumerationValues(ParameterValueData<?> enumerationValues)
(package private) void	setExperiments(Set<ExperimentData> experiments)
void	setExternalId(String externalId)
void	setHeight(int height)
(package private) void	setItemTypes(Set<Integer> itemTypes)
void	setMultiplicity(int multiplicity)
(package private) void	setOptions(Map<String,String> options)
void	setProtocolParameter(boolean isProtocolParameter)
(package private) void	setProtocols(Set<ProtocolData> protocols)
void	setQuantity(QuantityData quantity)
void	setRequiredForMiame(boolean requiredForMiame)
(package private) void	setUsableUnits(Set<UnitData> usableUnits)
void	setValueType(int valueType)
void	setWidth(int width)

Methods inherited from class net.sf.basedb.core.data.CommonData

getDescription, getName, isRemoved, setDescription, setName, setRemoved

Methods inherited from class net.sf.basedb.core.data.SharedData

getItemKey, getProjectKey, setItemKey, setProjectKey

Methods inherited from class net.sf.basedb.core.data.OwnedData

getOwner, setOwner

Methods inherited from class net.sf.basedb.core.data.BasicData

equals, getId, getVersion, hashCode, setId, setVersion, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.sf.basedb.core.data.IdentifiableData

getId, getVersion

Methods inherited from interface net.sf.basedb.core.data.OwnableData

getOwner, setOwner

Field Detail

entryDate

private Date entryDate

quantity

private QuantityData quantity

defaultUnit

private UnitData defaultUnit

usableUnits

private Set<UnitData> usableUnits

MAX_EXTERNAL_ID_LENGTH

public static final int MAX_EXTERNAL_ID_LENGTH

The maximum length of the external id that can be stored in the database.

Since:

2.2

See Also:

setExternalId(String), Constant Field Values

externalId

private String externalId

multiplicity

private int multiplicity

requiredForMiame

private boolean requiredForMiame

isEnumeration

private boolean isEnumeration

height

private int height

width

private int width

defaultValue

private String defaultValue

MAX_DEFAULT_VALUE_LENGTH

public static final int MAX_DEFAULT_VALUE_LENGTH

See Also:

Constant Field Values

valueType

private int valueType

itemTypes

private Set<Integer> itemTypes

MAX_OPTION_LENGTH

public static final int MAX_OPTION_LENGTH

See Also:

Constant Field Values

options

private Map<String,String> options

enumerationValues

private ParameterValueData<?> enumerationValues

experiments

private Set<ExperimentData> experiments

annotations

private Set<AnnotationData> annotations

isProtocolParameter

private boolean isProtocolParameter

protocols

private Set<ProtocolData> protocols

categories

private Set<AnnotationTypeCategoryData> categories

Constructor Detail

AnnotationTypeData

public AnnotationTypeData()

Method Detail

getEntryDate

public Date getEntryDate()

Description copied from interface: RegisteredData

Get the date this item was added to the database. The value is generated at creation time and can't be modified later.

Specified by:

getEntryDate in interface RegisteredData

setEntryDate

public void setEntryDate(Date entryDate)

getQuantity

public QuantityData getQuantity()

Get the quantity this annotation type uses. Can't be changed after creation.

Since:

2.9

Hibernate: many-to-one

column="`quantity_id`" not-null="false" outer-join="false"

setQuantity

public void setQuantity(QuantityData quantity)

Since:

2.9

getDefaultUnit

public UnitData getDefaultUnit()

Get the unit used to store annotation values for this type. NOTE! If the unit changes to another unit with a different reference factor all annotation values must be recalculated. NOTE! This value is always null if the quantity is null.

Since:

2.9

Hibernate: many-to-one

column="`default_unit_id`" not-null="false" outer-join="false"

setDefaultUnit

public void setDefaultUnit(UnitData defaultUnit)

Since:

2.9

getUsableUnits

public Set<UnitData> getUsableUnits()

The units that it makes sense to use with this annotation type. If empty, any unit for the given quantity can be used.

Since:

2.9

Hibernate: set

table="`AnnotationTypeUnits`" lazy="true"

Hibernate: collection-key

column="`annotationtype_id`"

Hibernate: collection-many-to-many

column="`unit_id`" class="net.sf.basedb.core.data.UnitData"

setUsableUnits

void setUsableUnits(Set<UnitData> usableUnits)

Since:

2.9

getExternalId

public String getExternalId()

Get the external id for the biomaterial

Since:

2.2

Hibernate: property

column="`external_id`" type="string" length="255" not-null="false"

setExternalId

public void setExternalId(String externalId)

getMultiplicity

public int getMultiplicity()

How many values are allowed for this annotations of this type. 0 = no limit

Hibernate: property

column="`multiplicity`" type="int" not-null="true"

setMultiplicity

public void setMultiplicity(int multiplicity)

isRequiredForMiame

public boolean isRequiredForMiame()

If an annotation of this type must be present for an annotatable item to be compliant with MIAME.

Hibernate: property

column="`required_for_miame`" type="boolean" not-null="true"

setRequiredForMiame

public void setRequiredForMiame(boolean requiredForMiame)

isEnumeration

public boolean isEnumeration()

If this annotation type defines a list of allowed values or not.

Hibernate: property

column="`is_enumeration`" type="boolean" not-null="true"

setEnumeration

public void setEnumeration(boolean isEnumeration)

getHeight

public int getHeight()

The recommended height (lines) to display input fields for this annotation in client applications.

Hibernate: property

column="`height`" type="int" not-null="true"

setHeight

public void setHeight(int height)

getWidth

public int getWidth()

The recommended width (characters) to display input fields for this annotation in client applications.

Hibernate: property

column="`width`" type="int" not-null="true"

setWidth

public void setWidth(int width)

getDefaultValue

public String getDefaultValue()

The default value of new annotations.

Hibernate: property

column="`default_value`" type="string" length="255" not-null="false"

setDefaultValue

public void setDefaultValue(String defaultValue)

getValueType

public int getValueType()

The code for the value type.

Hibernate: property

column="`value_type`" type="int" not-null="true" update="false"

setValueType

public void setValueType(int valueType)

getItemTypes

public Set<Integer> getItemTypes()

The item code for all items this annotation type can be applied to.

Hibernate: set

table="`AnnotationTypeItems`" lazy="true"

Hibernate: collection-key

column="`annotationtype_id`"

Hibernate: collection-element

column="`item_type`" type="int"

setItemTypes

void setItemTypes(Set<Integer> itemTypes)

getOptions

public Map<String,String> getOptions()

Additional options depending on the value type.

Hibernate: map

table="`AnnotationTypeOptions`" lazy="true"

Hibernate: collection-key

column="`annotationtype_id`"

Hibernate: collection-index

column="`name`" type="string" length="255" not-null="true"

Hibernate: collection-element

column="`value`" type="string" length="255" not-null="true"

setOptions

void setOptions(Map<String,String> options)

getEnumerationValues

public ParameterValueData<?> getEnumerationValues()

The allowed values if this is an enumeration.

Hibernate: many-to-one

column="`enumerationvalues_id`" not-null="false" cascade="all" unique="true"

setEnumerationValues

public void setEnumerationValues(ParameterValueData<?> enumerationValues)

getExperiments

Set<ExperimentData> getExperiments()

This is the inverse end.

See Also:

ExperimentData.getExperimentalFactors()

Hibernate: set

table="`ExperimentalFactors`" lazy="true" inverse="true"

Hibernate: collection-key

column="`annotationtype_id`"

Hibernate: collection-many-to-many

column="`experiment_id`" class="net.sf.basedb.core.data.ExperimentData"

setExperiments

void setExperiments(Set<ExperimentData> experiments)

getAnnotations

Set<AnnotationData> getAnnotations()

This is the inverse end.

Since:

2.15

See Also:

AnnotationData.getAnnotationType()

Hibernate: set

lazy="true" inverse="true"

Hibernate: collection-key

column="`annotationtype_id`"

Hibernate: collection-one-to-many

column="`annotation_id`" class="net.sf.basedb.core.data.AnnotationData"

setAnnotations

void setAnnotations(Set<AnnotationData> annotations)

isProtocolParameter

public boolean isProtocolParameter()

If this annotation type is intended to be used as a protocol parameter or as a regular annotation.

Since:

2.2

Hibernate: property

column="`is_parameter`" type="boolean" not-null="true"

setProtocolParameter

public void setProtocolParameter(boolean isProtocolParameter)

getProtocols

Set<ProtocolData> getProtocols()

This is the inverse end.

Since:

2.2

See Also:

ProtocolData.getParameters()

Hibernate: set

table="`ProtocolParameters`" lazy="true" inverse="true"

Hibernate: collection-key

column="`annotationtype_id`"

Hibernate: collection-many-to-many

column="`protocol_id`" class="net.sf.basedb.core.data.ProtocolData"

setProtocols

void setProtocols(Set<ProtocolData> protocols)

getCategories

public Set<AnnotationTypeCategoryData> getCategories()

Get the set that manages the categories of this annotation type.

Hibernate: set

table="`CategorisedAnnotationTypes`" lazy="true"

Hibernate: collection-key

column="`annotationtype_id`"

Hibernate: collection-many-to-many

column="`category_id`" class="net.sf.basedb.core.data.AnnotationTypeCategoryData"

setCategories

void setCategories(Set<AnnotationTypeCategoryData> categories)