Package net.sf.basedb.core.data
Class ExperimentData
- java.lang.Object
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- net.sf.basedb.core.data.BasicData
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- net.sf.basedb.core.data.OwnedData
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- net.sf.basedb.core.data.SharedData
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- net.sf.basedb.core.data.CommonData
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- net.sf.basedb.core.data.AnnotatedData
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- net.sf.basedb.core.data.ExperimentData
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- All Implemented Interfaces:
AnnotatableData
,DiskConsumableData
,IdentifiableData
,LoggableData
,NameableData
,OwnableData
,RegisteredData
,RemovableData
,ShareableData
public class ExperimentData extends AnnotatedData implements DiskConsumableData, RegisteredData, LoggableData
Holds information about an experiment.- Version:
- 2.0
- Author:
- Nicklas
- See Also:
Experiment
, Developer documentation: Experiments and analysis- Last modified
- $Date: 2015-05-13 11:36:12 +0200 (on, 13 maj 2015) $
- Hibernate: class
- table="`Experiments`" lazy="true"
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Field Summary
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Fields inherited from interface net.sf.basedb.core.data.NameableData
MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH
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Constructor Summary
Constructors Constructor Description ExperimentData()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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 associatedDirectoryData
item directory where it is recommended for plugins to save files related to the experiment.DiskUsageData
getDiskUsage()
Get theDiskUsageData
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.(package private) Set<RawBioAssayData>
getRawBioAssays()
Duplicates the mappinggetRootRawBioAssays()
.String
getRawDataType()
Get the name of the raw data type used in this experiment.(package private) Set<ReporterListData>
getReporterLists()
This is the inverse end.Map<RawBioAssayData,RootRawBioAssayData>
getRootRawBioAssays()
Manages which raw bioassays are available in the experiment.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)
(package private) void
setRootRawBioAssays(Map<RawBioAssayData,RootRawBioAssayData> rootRawBioAssays)
void
setTitle(String title)
(package private) void
setTransformations(Set<TransformationData> transformations)
void
setVirtualDb(VirtualDbData virtualDb)
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Methods inherited from class net.sf.basedb.core.data.AnnotatedData
getAnnotations, getAnnotationSet, setAnnotations, setAnnotationSet
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Methods inherited from class net.sf.basedb.core.data.CommonData
getDescription, getName, getRemovedBy, setDescription, setName, setRemovedBy
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Methods inherited from class net.sf.basedb.core.data.SharedData
getItemKey, getProjectKey, setItemKey, setProjectKey
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Methods inherited from class net.sf.basedb.core.data.BasicData
equals, getId, getVersion, hashCode, setId, setVersion, toString
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Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
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Methods inherited from interface net.sf.basedb.core.data.IdentifiableData
getId, getVersion
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Methods inherited from interface net.sf.basedb.core.data.OwnableData
getOwner, setOwner
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Field Detail
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diskUsage
private DiskUsageData diskUsage
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entryDate
private Date entryDate
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bytes
private long bytes
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rawDataType
private String rawDataType
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directory
private DirectoryData directory
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MAX_AUTHORS_LENGTH
public static final int MAX_AUTHORS_LENGTH
- See Also:
- Constant Field Values
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authors
private String authors
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MAX_AFFILIATIONS_LENGTH
public static final int MAX_AFFILIATIONS_LENGTH
- See Also:
- Constant Field Values
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affiliations
private String affiliations
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MAX_TITLE_LENGTH
public static final int MAX_TITLE_LENGTH
- See Also:
- Constant Field Values
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title
private String title
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MAX_ABSTRACT_LENGTH
public static final int MAX_ABSTRACT_LENGTH
- See Also:
- Constant Field Values
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theAbstract
private String theAbstract
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MAX_EXPERIMENT_DESIGN_LENGTH
public static final int MAX_EXPERIMENT_DESIGN_LENGTH
- See Also:
- Constant Field Values
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experimentDesign
private String experimentDesign
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MAX_EXPERIMENT_TYPE_LENGTH
public static final int MAX_EXPERIMENT_TYPE_LENGTH
- See Also:
- Constant Field Values
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experimentType
private String experimentType
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MAX_PUBLICATION_LENGTH
public static final int MAX_PUBLICATION_LENGTH
- See Also:
- Constant Field Values
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publication
private String publication
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MAX_PUBMEDID_LENGTH
public static final int MAX_PUBMEDID_LENGTH
- See Also:
- Constant Field Values
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pubMedId
private String pubMedId
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publicationDate
private Date publicationDate
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virtualDb
private VirtualDbData virtualDb
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rootRawBioAssays
private Map<RawBioAssayData,RootRawBioAssayData> rootRawBioAssays
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rawBioAssays
private Set<RawBioAssayData> rawBioAssays
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bioAssaySets
private Set<BioAssaySetData> bioAssaySets
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transformations
private Set<TransformationData> transformations
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experimentalFactors
private Set<AnnotationTypeData> experimentalFactors
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reporterLists
private Set<ReporterListData> reporterLists
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Method Detail
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getDiskUsage
public DiskUsageData getDiskUsage()
Description copied from interface:DiskConsumableData
Get theDiskUsageData
that this item use.- Specified by:
getDiskUsage
in interfaceDiskConsumableData
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setDiskUsage
void setDiskUsage(DiskUsageData diskUsage)
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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 interfaceRegisteredData
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setEntryDate
public void setEntryDate(Date entryDate)
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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"
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setBytes
public void setBytes(long bytes)
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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"
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setRawDataType
public void setRawDataType(String rawDataType)
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getDirectory
public DirectoryData getDirectory()
Get the associatedDirectoryData
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"
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setDirectory
public void setDirectory(DirectoryData directory)
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getAuthors
public String getAuthors()
Get the authors for this experiment.- Hibernate: property
- column="`authors`" type="text" not-null="false"
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setAuthors
public void setAuthors(String authors)
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getAffiliations
public String getAffiliations()
Get the affiliations for this experiment.- Hibernate: property
- column="`affiliations`" type="text" not-null="false"
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setAffiliations
public void setAffiliations(String affiliations)
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getTitle
public String getTitle()
Get the title for this experiment.- Hibernate: property
- column="`title`" type="text" not-null="false"
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setTitle
public void setTitle(String title)
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getAbstract
public String getAbstract()
Get the abstract for this experiment.- Hibernate: property
- column="`abstract`" type="text" not-null="false"
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setAbstract
public void setAbstract(String theAbstract)
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getExperimentDesign
public String getExperimentDesign()
Get the experimental design for this experiment.- Hibernate: property
- column="`experiment_design`" type="text" not-null="false"
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setExperimentDesign
public void setExperimentDesign(String experimentDesign)
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getExperimentType
public String getExperimentType()
Get the experimental type for this experiment.- Hibernate: property
- column="`experiment_type`" type="text" not-null="false"
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setExperimentType
public void setExperimentType(String experimentType)
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getPublication
public String getPublication()
Get the publication for this experiment.- Hibernate: property
- column="`publication`" type="text" not-null="false"
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setPublication
public void setPublication(String publication)
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getPubMedId
public String getPubMedId()
Get the publication for this experiment.- Hibernate: property
- column="`pubmed_id`" type="string" not-null="false" length="255"
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setPubMedId
public void setPubMedId(String pubMedId)
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getPublicationDate
public Date getPublicationDate()
Get the publication date for this experiment.- Hibernate: property
- column="`publication_date`" type="date" not-null="false"
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setPublicationDate
public void setPublicationDate(Date publicationDate)
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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"
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setVirtualDb
public void setVirtualDb(VirtualDbData virtualDb)
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getRootRawBioAssays
public Map<RawBioAssayData,RootRawBioAssayData> getRootRawBioAssays()
Manages which raw bioassays are available in the experiment. This is the inverse end.- Hibernate: map
- lazy="true" cascade="all-delete-orphan" inverse="true"
- Hibernate: index-many-to-many
- column="`rawbioassay_id`" class="net.sf.basedb.core.data.RawBioAssayData"
- Hibernate: collection-key
- column="`experiment_id`"
- Hibernate: collection-one-to-many
- class="net.sf.basedb.core.data.RootRawBioAssayData"
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setRootRawBioAssays
void setRootRawBioAssays(Map<RawBioAssayData,RootRawBioAssayData> rootRawBioAssays)
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getRawBioAssays
Set<RawBioAssayData> getRawBioAssays()
Duplicates the mappinggetRootRawBioAssays()
. Kept for backwards compatibility with queries that join raw bioassays.- Hibernate: set
- table="`RootRawBioAssays`" lazy="true" inverse="true"
- Hibernate: collection-key
- column="`experiment_id`"
- Hibernate: collection-many-to-many
- column="`rawbioassay_id`" class="net.sf.basedb.core.data.RawBioAssayData"
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setRawBioAssays
void setRawBioAssays(Set<RawBioAssayData> rawBioAssays)
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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"
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setBioAssaySets
void setBioAssaySets(Set<BioAssaySetData> bioAssaySets)
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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"
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setTransformations
void setTransformations(Set<TransformationData> transformations)
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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"
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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"
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setExperimentalFactors
void setExperimentalFactors(Set<AnnotationTypeData> experimentalFactors)
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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"
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setReporterLists
void setReporterLists(Set<ReporterListData> reporterLists)
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-