Package 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.AnnotatedData
net.sf.basedb.core.data.ExperimentData
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"

  • Field Details

  • Constructor Details

    • ExperimentData

      public ExperimentData()

  • Method Details

    • 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)

    • 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"

    • setRootRawBioAssays

      void setRootRawBioAssays​(Map<RawBioAssayData,​RootRawBioAssayData> rootRawBioAssays)

    • getRawBioAssays

      Set<RawBioAssayData> getRawBioAssays()
      Duplicates the mapping getRootRawBioAssays(). 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"

    • 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)