Package net.sf.basedb.core.data

Class RawBioAssayData

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.RawBioAssayData
All Implemented Interfaces:
AnnotatableData, DiskConsumableData, FileStoreEnabledData, IdentifiableData, LoggableData, NameableData, OwnableData, RegisteredData, RemovableData, ShareableData
public class RawBioAssayData
extends AnnotatedData
implements DiskConsumableData, FileStoreEnabledData, RegisteredData
This class holds information about a raw bioassay, which is the raw data extracted from a scan.
Version:
2.0
Author:
Nicklas
See Also:
RawBioAssay, Developer documentation: Bioassays and raw data
Last modified
$Date: 2019-03-11 12:51:33 +0100 (mån, 11 mars 2019) $
Hibernate: class
table="`RawBioAssays`" lazy="true"

  • Field Details

  • Constructor Details

    • RawBioAssayData

      public RawBioAssayData()

  • 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)

    • 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 raw data to this raw bioassay
      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

    • getSoftware

      public SoftwareData getSoftware()
      Get the software used to analyse the scanned image and produce the raw data.
      Hibernate: many-to-one
      column="`software_id`" not-null="false" outer-join="false"

    • setSoftware

      public void setSoftware​(SoftwareData software)

    • getProtocol

      public ProtocolData getProtocol()
      Get the protocol used for the image analysis.
      Hibernate: many-to-one
      column="`protocol_id`" not-null="false" outer-join="false"

    • setProtocol

      public void setProtocol​(ProtocolData protocol)

    • getArrayDesign

      public ArrayDesignData getArrayDesign()
      Get the array design used for the hybridization this raw bio assay comes from.
      Hibernate: many-to-one
      column="`arraydesign_id`" not-null="false" outer-join="false"

    • setArrayDesign

      public void setArrayDesign​(ArrayDesignData arrayDesign)

    • getParentBioAssay

      public DerivedBioAssayData getParentBioAssay()
      Get the derived bioassay that this raw bioassay has been created from.
      Hibernate: many-to-one
      column="`bioassay_id`" not-null="false" outer-join="false"

    • setParentBioAssay

      public void setParentBioAssay​(DerivedBioAssayData bioAssay)

    • getParentExtract

      public ExtractData getParentExtract()
      Get the derived bioassay that this raw bioassay has been created from.
      Hibernate: many-to-one
      column="`extract_id`" not-null="false" outer-join="false"

    • setParentExtract

      public void setParentExtract​(ExtractData extract)

    • getRawDataType

      public String getRawDataType()
      Get the name of the raw data type used by this raw bio assay.
      Hibernate: property
      column="`rawdatatype`" type="string" length="255" not-null="true"

    • setRawDataType

      public void setRawDataType​(String rawDataType)

    • getHasData

      public boolean getHasData()
      If the raw bioassay has data or not.
      Hibernate: property
      column="`has_data`" type="boolean" not-null="true"

    • setHasData

      public void setHasData​(boolean hasData)

    • getSpots

      public int getSpots()
      The number of data spots in this raw bio assay, that are stored in the database.
      Since:
      2.5
      Hibernate: property
      column="`spots`" type="int" not-null="true"

    • setSpots

      public void setSpots​(int spots)

    • getNumFileSpots

      public int getNumFileSpots()
      The number of spots on this raw bioassay that are stored inside files.
      Since:
      2.5
      Hibernate: property
      column="`file_spots`" type="int" not-null="true"

    • setNumFileSpots

      public void setNumFileSpots​(int fileSpots)

    • getBytes

      public long getBytes()
      The number of bytes the raw data occupies on disk.
      Hibernate: property
      column="`bytes`" type="long" not-null="true"

    • setBytes

      public void setBytes​(long bytes)

    • getHeaders

      public Map<String,​String> getHeaders()
      File headers from the raw data file.
      Hibernate: map
      table="`RawBioAssayHeaders`" lazy="true" cascade="all"
      Hibernate: collection-key
      column="`rawbioassay_id`"
      Hibernate: collection-index
      column="`name`" type="string" length="255" not-null="true"
      Hibernate: collection-element
      column="`value`" type="text" not-null="true"

    • setHeaders

      void setHeaders​(Map<String,​String> headers)

    • getExperiments

      Set<ExperimentData> getExperiments()
      This is the inverse end. The real end is mapped by RootRawBioAssayData but we skip directly to the experiment.
      See Also:
      ExperimentData.getRawBioAssays()
      Hibernate: set
      table="`RootRawBioAssays`" lazy="true" inverse="true"
      Hibernate: collection-key
      column="`rawbioassay_id`"
      Hibernate: collection-many-to-many
      column="`experiment_id`" class="net.sf.basedb.core.data.ExperimentData"

    • setExperiments

      void setExperiments​(Set<ExperimentData> experiments)

    • getTransformations

      Set<TransformationData> getTransformations()
      This is the inverse end. We keep the inverse="true" attribute because we don't want to remove a raw bioassay that is used by a transformation.
      See Also:
      TransformationData.getRawSources()
      Hibernate: set
      table="`TransformationRawBioAssays`" lazy="true" inverse="true"
      Hibernate: collection-key
      column="`rawbioassay_id`"
      Hibernate: collection-many-to-many
      column="`transformation_id`" class="net.sf.basedb.core.data.TransformationData"

    • setTransformations

      void setTransformations​(Set<TransformationData> transformations)

    • getBioAssays

      Set<BioAssayData> getBioAssays()
      This is the inverse end. We keep the inverse="true" attribute because we don't want to remove a raw bioassay that is used by a bioassay.
      See Also:
      BioAssayData.getRawParents()
      Hibernate: set
      table="`BioAssayRawParents`" lazy="true" inverse="true"
      Hibernate: collection-key
      column="`parent_id`"
      Hibernate: collection-many-to-many
      column="`bioassay_id`" class="net.sf.basedb.core.data.BioAssayData"

    • setBioAssays

      void setBioAssays​(Set<BioAssayData> bioAssays)