net.sf.basedb.core.data
Class ExperimentData

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.ExperimentData

All Implemented Interfaces:

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

public class ExperimentData
extends CommonData
implements DiskConsumableData, RegisteredData, LoggableData

Holds information about an experiment.

Version:

2.0

Author:

Nicklas

See Also:

Experiment, Experiments and analysis overview

Last modified

$Date: 2009-08-20 10:53:16 +0200 (Thu, 20 Aug 2009) $

Hibernate: class

table="`Experiments`" lazy="true"

Field Summary

private String	affiliations
private String	authors
private Set<BioAssaySetData>	bioAssaySets
private long	bytes
private DirectoryData	directory
private DiskUsageData	diskUsage
private Date	entryDate
private Set<AnnotationTypeData>	experimentalFactors
private String	experimentDesign
private String	experimentType
private Set<JobData>	jobs
static int	MAX_ABSTRACT_LENGTH
static int	MAX_AFFILIATIONS_LENGTH
static int	MAX_AUTHORS_LENGTH
static int	MAX_EXPERIMENT_DESIGN_LENGTH
static int	MAX_EXPERIMENT_TYPE_LENGTH
static int	MAX_PUBLICATION_LENGTH
static int	MAX_PUBMEDID_LENGTH
static int	MAX_TITLE_LENGTH
private String	publication
private Date	publicationDate
private String	pubMedId
private Set<RawBioAssayData>	rawBioAssays
private String	rawDataType
private Set<ReporterListData>	reporterLists
private String	theAbstract
private String	title
private Set<TransformationData>	transformations
private VirtualDbData	virtualDb

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

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

ExperimentData()

Method Summary

String	getAbstract() Get the abstract for this experiment.
String	getAffiliations() Get the affiliations for this experiment.
String	getAuthors() Get the authors for this experiment.
(package private) Set<BioAssaySetData>	getBioAssaySets() This is the inverse end.
long	getBytes() The number of bytes the analysed data in this experiment occupies on disk.
DirectoryData	getDirectory() Get the associated DirectoryData item directory where it is recommended for plugins to save files related to the experiment.
DiskUsageData	getDiskUsage() Get the DiskUsageData that this item use.
Date	getEntryDate() Get the date this item was added to the database.
Set<AnnotationTypeData>	getExperimentalFactors() The annotation types which describes the experimental factors for this experiment.
String	getExperimentDesign() Get the experimental design for this experiment.
String	getExperimentType() Get the experimental type for this experiment.
(package private) Set<JobData>	getJobs() This is the inverse end.
String	getPublication() Get the publication for this experiment.
Date	getPublicationDate() Get the publication date for this experiment.
String	getPubMedId() Get the publication for this experiment.
Set<RawBioAssayData>	getRawBioAssays() A set that manages which raw bioassays are available in the experiment.
String	getRawDataType() Get the name of the raw data type used in this experiment.
(package private) Set<ReporterListData>	getReporterLists() This is the inverse end.
String	getTitle() Get the title for this experiment.
(package private) Set<TransformationData>	getTransformations() This is the inverse end.
VirtualDbData	getVirtualDb() Get the virtual database this experiment stores the analyzed data in.
void	setAbstract(String theAbstract)
void	setAffiliations(String affiliations)
void	setAuthors(String authors)
(package private) void	setBioAssaySets(Set<BioAssaySetData> bioAssaySets)
void	setBytes(long bytes)
void	setDirectory(DirectoryData directory)
(package private) void	setDiskUsage(DiskUsageData diskUsage)
void	setEntryDate(Date entryDate)
(package private) void	setExperimentalFactors(Set<AnnotationTypeData> experimentalFactors)
void	setExperimentDesign(String experimentDesign)
void	setExperimentType(String experimentType)
(package private) void	setJobs(Set<JobData> jobs)
void	setPublication(String publication)
void	setPublicationDate(Date publicationDate)
void	setPubMedId(String pubMedId)
(package private) void	setRawBioAssays(Set<RawBioAssayData> rawBioAssays)
void	setRawDataType(String rawDataType)
(package private) void	setReporterLists(Set<ReporterListData> reporterLists)
void	setTitle(String title)
(package private) void	setTransformations(Set<TransformationData> transformations)
void	setVirtualDb(VirtualDbData virtualDb)

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.OwnableData

getOwner, setOwner

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

getId, getVersion

Field Detail

diskUsage

private DiskUsageData diskUsage

entryDate

private Date entryDate

bytes

private long bytes

rawDataType

private String rawDataType

directory

private DirectoryData directory

MAX_AUTHORS_LENGTH

public static final int MAX_AUTHORS_LENGTH

See Also:

Constant Field Values

authors

private String authors

MAX_AFFILIATIONS_LENGTH

public static final int MAX_AFFILIATIONS_LENGTH

See Also:

Constant Field Values

affiliations

private String affiliations

MAX_TITLE_LENGTH

public static final int MAX_TITLE_LENGTH

See Also:

Constant Field Values

title

private String title

MAX_ABSTRACT_LENGTH

public static final int MAX_ABSTRACT_LENGTH

See Also:

Constant Field Values

theAbstract

private String theAbstract

MAX_EXPERIMENT_DESIGN_LENGTH

public static final int MAX_EXPERIMENT_DESIGN_LENGTH

See Also:

Constant Field Values

experimentDesign

private String experimentDesign

MAX_EXPERIMENT_TYPE_LENGTH

public static final int MAX_EXPERIMENT_TYPE_LENGTH

See Also:

Constant Field Values

experimentType

private String experimentType

MAX_PUBLICATION_LENGTH

public static final int MAX_PUBLICATION_LENGTH

See Also:

Constant Field Values

publication

private String publication

MAX_PUBMEDID_LENGTH

public static final int MAX_PUBMEDID_LENGTH

See Also:

Constant Field Values

pubMedId

private String pubMedId

publicationDate

private Date publicationDate

virtualDb

private VirtualDbData virtualDb

rawBioAssays

private Set<RawBioAssayData> rawBioAssays

bioAssaySets

private Set<BioAssaySetData> bioAssaySets

transformations

private Set<TransformationData> transformations

jobs

private Set<JobData> jobs

experimentalFactors

private Set<AnnotationTypeData> experimentalFactors

reporterLists

private Set<ReporterListData> reporterLists

Constructor Detail

ExperimentData

public ExperimentData()

Method Detail

getDiskUsage

public DiskUsageData getDiskUsage()

Description copied from interface: DiskConsumableData

Get the DiskUsageData that this item use.

Specified by:

getDiskUsage in interface DiskConsumableData

setDiskUsage

void setDiskUsage(DiskUsageData diskUsage)

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)

getBytes

public long getBytes()

The number of bytes the analysed data in this experiment occupies on disk. Updates to this column are done through SQL statements and not through this object.

Hibernate: property

column="`bytes`" type="long" not-null="true" update="false"

setBytes

public void setBytes(long bytes)

getRawDataType

public String getRawDataType()

Get the name of the raw data type used in this experiment.

Hibernate: property

column="`rawdatatype`" type="string" length="255" not-null="true" update="false"

setRawDataType

public void setRawDataType(String rawDataType)

getDirectory

public DirectoryData getDirectory()

Get the associated DirectoryData item directory where it is recommended for plugins to save files related to the experiment.

Hibernate: column

name="`directory_id`" not-null="false"

Hibernate: many-to-one

outer-join="false"

setDirectory

public void setDirectory(DirectoryData directory)

getAuthors

public String getAuthors()

Get the authors for this experiment.

Hibernate: property

column="`authors`" type="text" not-null="false"

setAuthors

public void setAuthors(String authors)

getAffiliations

public String getAffiliations()

Get the affiliations for this experiment.

Hibernate: property

column="`affiliations`" type="text" not-null="false"

setAffiliations

public void setAffiliations(String affiliations)

getTitle

public String getTitle()

Get the title for this experiment.

Hibernate: property

column="`title`" type="text" not-null="false"

setTitle

public void setTitle(String title)

getAbstract

public String getAbstract()

Get the abstract for this experiment.

Hibernate: property

column="`abstract`" type="text" not-null="false"

setAbstract

public void setAbstract(String theAbstract)

getExperimentDesign

public String getExperimentDesign()

Get the experimental design for this experiment.

Hibernate: property

column="`experiment_design`" type="text" not-null="false"

setExperimentDesign

public void setExperimentDesign(String experimentDesign)

getExperimentType

public String getExperimentType()

Get the experimental type for this experiment.

Hibernate: property

column="`experiment_type`" type="text" not-null="false"

setExperimentType

public void setExperimentType(String experimentType)

getPublication

public String getPublication()

Get the publication for this experiment.

Hibernate: property

column="`publication`" type="text" not-null="false"

setPublication

public void setPublication(String publication)

getPubMedId

public String getPubMedId()

Get the publication for this experiment.

Hibernate: property

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

setPubMedId

public void setPubMedId(String pubMedId)

getPublicationDate

public Date getPublicationDate()

Get the publication date for this experiment.

Hibernate: property

column="`publication_date`" type="date" not-null="false"

setPublicationDate

public void setPublicationDate(Date publicationDate)

getVirtualDb

public VirtualDbData getVirtualDb()

Get the virtual database this experiment stores the analyzed data in.

Hibernate: many-to-one

column="`virtualdb_id`" not-null="true" unique="true" outer-join="false" update="false" cascade="save-update"

setVirtualDb

public void setVirtualDb(VirtualDbData virtualDb)

getRawBioAssays

public Set<RawBioAssayData> getRawBioAssays()

A set that manages which raw bioassays are available in the experiment.

Hibernate: set

table="`ExperimentRawBioAssays`" lazy="true"

Hibernate: collection-key

column="`experiment_id`"

Hibernate: collection-many-to-many

column="`rawbioassay_id`" class="net.sf.basedb.core.data.RawBioAssayData"

setRawBioAssays

void setRawBioAssays(Set<RawBioAssayData> rawBioAssays)

getBioAssaySets

Set<BioAssaySetData> getBioAssaySets()

This is the inverse end.

See Also:

BioAssaySetData.getExperiment()

Hibernate: set

lazy="true" inverse="true"

Hibernate: collection-key

column="`experiment_id`"

Hibernate: collection-one-to-many

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

setBioAssaySets

void setBioAssaySets(Set<BioAssaySetData> bioAssaySets)

getTransformations

Set<TransformationData> getTransformations()

This is the inverse end.

See Also:

TransformationData.getExperiment()

Hibernate: set

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

Hibernate: collection-key

column="`experiment_id`"

Hibernate: collection-one-to-many

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

setTransformations

void setTransformations(Set<TransformationData> transformations)

getJobs

Set<JobData> getJobs()

This is the inverse end.

Since:

2.4

See Also:

JobData.getExperiment()

Hibernate: set

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

Hibernate: collection-key

column="`experiment_id`"

Hibernate: collection-one-to-many

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

setJobs

void setJobs(Set<JobData> jobs)

getExperimentalFactors

public Set<AnnotationTypeData> getExperimentalFactors()

The annotation types which describes the experimental factors for this experiment.

Hibernate: set

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

Hibernate: collection-key

column="`experiment_id`"

Hibernate: collection-many-to-many

column="`annotationtype_id`" class="net.sf.basedb.core.data.AnnotationTypeData"

setExperimentalFactors

void setExperimentalFactors(Set<AnnotationTypeData> experimentalFactors)

getReporterLists

Set<ReporterListData> getReporterLists()

This is the inverse end.

Since:

2.7

See Also:

ReporterListData.getExperiment()

Hibernate: set

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

Hibernate: collection-key

column="`experiment_id`"

Hibernate: collection-one-to-many

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

setReporterLists

void setReporterLists(Set<ReporterListData> reporterLists)