net.sf.basedb.core.data
Class ArrayDesignData

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.AnnotatedData
                      net.sf.basedb.core.data.ArrayDesignData

All Implemented Interfaces:

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

public class ArrayDesignData
extends AnnotatedData
implements FileStoreEnabledData, RegisteredData

This class holds information about an arrayDesign

Version:

2.0

Author:

enell

See Also:

ArrayDesign, Array LIMS - arrays overview

Last modified

$Date: 2009-04-06 14:52:39 +0200 (Mon, 06 Apr 2009) $

Hibernate: class

table="`ArrayDesigns`" lazy="true"

Field Summary

private boolean	affyChip
private Set<ArrayBatchData>	arrayBatches
private Set<ArrayDesignBlockData>	arrayDesignBlocks
private int	dbFeatures
private Date	entryDate
private int	featureIdentificationMethod
private int	fileFeatures
private FileSetData	fileSet
private boolean	hasFeatures
private JobData	job
private int	numArrays
private Set<ArrayDesignPlateData>	plates
private PlatformData	platform
private PlatformVariantData	variant

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

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

ArrayDesignData()

Method Summary

(package private) Set<ArrayBatchData>	getArrayBatches() This is the inverse end.
(package private) Set<ArrayDesignBlockData>	getArrayDesignBlocks() This is the inverse end.
Date	getEntryDate() Get the date this item was added to the database.
int	getFeatureIdentificationMethod() The method to use for identiying features. 1 = COORDINATES, 2 = POSITION, 3 = FEATURE_ID
FileSetData	getFileSet() Get the file set attached to this item.
boolean	getHasFeatures() If the array design has features or not.
JobData	getJob() Get the job that was used to import features to this array desing
int	getNumArrays() The number of arrays on a single slide.
int	getNumDbFeatures() The number of features on this array design that are stored in the database.
int	getNumFileFeatures() The number of features on this array design that are stored inside files.
Set<ArrayDesignPlateData>	getPlates() The plates this design is made from.
PlatformData	getPlatform() Get the platform this raw bioassay uses
PlatformVariantData	getVariant() Get the platform variant this raw bioassay uses, or null.
boolean	isAffyChip() Deprecated. Has been replaced by platform
void	setAffyChip(boolean affyChip) Deprecated. Has been replaced by platform
(package private) void	setArrayBatches(Set<ArrayBatchData> arrayBatches)
(package private) void	setArrayDesignBlocks(Set<ArrayDesignBlockData> arrayDesignBlocks)
void	setEntryDate(Date entryDate)
void	setFeatureIdentificationMethod(int featureIdentificationMethod)
void	setFileSet(FileSetData fileSet) Attach a file set to the item.
void	setHasFeatures(boolean hasFeatures)
void	setJob(JobData job)
void	setNumArrays(int numArrays)
void	setNumDbFeatures(int dbFeatures)
void	setNumFileFeatures(int fileFeatures)
(package private) void	setPlates(Set<ArrayDesignPlateData> plates)
void	setPlatform(PlatformData platform)
void	setVariant(PlatformVariantData variant)

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

getAnnotationSet, setAnnotationSet

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

fileSet

private FileSetData fileSet

entryDate

private Date entryDate

platform

private PlatformData platform

variant

private PlatformVariantData variant

job

private JobData job

numArrays

private int numArrays

affyChip

private boolean affyChip

hasFeatures

private boolean hasFeatures

dbFeatures

private int dbFeatures

fileFeatures

private int fileFeatures

featureIdentificationMethod

private int featureIdentificationMethod

arrayDesignBlocks

private Set<ArrayDesignBlockData> arrayDesignBlocks

plates

private Set<ArrayDesignPlateData> plates

arrayBatches

private Set<ArrayBatchData> arrayBatches

Constructor Detail

ArrayDesignData

public ArrayDesignData()

Method Detail

getFileSet

public FileSetData getFileSet()

Description copied from interface: FileStoreEnabledData

Get the file set attached to this item.

Specified by:

getFileSet in interface FileStoreEnabledData

Returns:

A FileSetData object or null if no files are attached

setFileSet

public void setFileSet(FileSetData fileSet)

Description copied from interface: FileStoreEnabledData

Attach a file set to the item. Null is allowed to unlink it.

Specified by:

setFileSet in interface FileStoreEnabledData

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)

getPlatform

public PlatformData getPlatform()

Get the platform this raw bioassay uses

Since:

2.5

Hibernate: column

name="`platform_id`" not-null="true"

Hibernate: many-to-one

outer-join="false"

setPlatform

public void setPlatform(PlatformData platform)

getVariant

public PlatformVariantData getVariant()

Get the platform variant this raw bioassay uses, or null.

Since:

2.5

Hibernate: column

name="`variant_id`"

Hibernate: many-to-one

outer-join="false"

setVariant

public void setVariant(PlatformVariantData variant)

getJob

public JobData getJob()

Get the job that was used to import features to this array desing

Since:

2.7

Hibernate: many-to-one

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

setJob

public void setJob(JobData job)

Since:

2.7

getNumArrays

public int getNumArrays()

The number of arrays on a single slide.

Since:

2.6

Hibernate: property

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

setNumArrays

public void setNumArrays(int numArrays)

isAffyChip

public boolean isAffyChip()

Deprecated. Has been replaced by platform

Check if this design is an Affymetrix chip.

Hibernate: property

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

setAffyChip

public void setAffyChip(boolean affyChip)

Deprecated. Has been replaced by platform

getHasFeatures

public boolean getHasFeatures()

If the array design has features or not.

Hibernate: property

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

setHasFeatures

public void setHasFeatures(boolean hasFeatures)

getNumDbFeatures

public int getNumDbFeatures()

The number of features on this array design that are stored in the database.

Since:

2.5

Hibernate: property

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

setNumDbFeatures

public void setNumDbFeatures(int dbFeatures)

getNumFileFeatures

public int getNumFileFeatures()

The number of features on this array design that are stored inside files.

Since:

2.5

Hibernate: property

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

setNumFileFeatures

public void setNumFileFeatures(int fileFeatures)

getFeatureIdentificationMethod

public int getFeatureIdentificationMethod()

The method to use for identiying features. 1 = COORDINATES, 2 = POSITION, 3 = FEATURE_ID

Since:

2.6

Hibernate: property

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

setFeatureIdentificationMethod

public void setFeatureIdentificationMethod(int featureIdentificationMethod)

getArrayDesignBlocks

Set<ArrayDesignBlockData> getArrayDesignBlocks()

This is the inverse end.

See Also:

ArrayDesignBlockData.getArrayDesign()

Hibernate: set

lazy="true" inverse="true" cascade="delete"

Hibernate: collection-key

column="`arraydesign_id`"

Hibernate: collection-one-to-many

class="net.sf.basedb.core.data.ArrayDesignBlockData"

setArrayDesignBlocks

void setArrayDesignBlocks(Set<ArrayDesignBlockData> arrayDesignBlocks)

getPlates

public Set<ArrayDesignPlateData> getPlates()

The plates this design is made from.

Hibernate: set

lazy="true" inverse="true" cascade="all-delete-orphan"

Hibernate: collection-key

column="`arraydesign_id`"

Hibernate: collection-one-to-many

class="net.sf.basedb.core.data.ArrayDesignPlateData"

setPlates

void setPlates(Set<ArrayDesignPlateData> plates)

getArrayBatches

Set<ArrayBatchData> getArrayBatches()

This is the inverse end.

See Also:

ArrayBatchData.getArrayDesign()

Hibernate: set

lazy="true" inverse="true"

Hibernate: collection-key

column="`arraydesign_id`"

Hibernate: collection-one-to-many

class="net.sf.basedb.core.data.ArrayBatchData"

setArrayBatches

void setArrayBatches(Set<ArrayBatchData> arrayBatches)