Package net.sf.basedb.core.data

Class BioAssaySetData

java.lang.Object
net.sf.basedb.core.data.BasicData
net.sf.basedb.core.data.BioAssaySetData
All Implemented Interfaces:
AnnotatableData, FileStoreEnabledData, IdentifiableData, NameableData, RemovableData
public class BioAssaySetData extends BasicData implements NameableData, RemovableData, AnnotatableData, FileStoreEnabledData
This class holds information about a bioassayset.
Version:
2.0
Author:
Nicklas
See Also:
Last modified
$Date: 2016-04-27 08:38:21 +0200 (on, 27 apr 2016) $
Hibernate: class
table="`BioAssaySets`" lazy="true"

  • Field Details

  • Constructor Details

    • BioAssaySetData

      public BioAssaySetData()

  • Method Details

    • getName

      public String getName()
      Description copied from interface: NameableData
      Get the name of the item.
      Specified by:
      getName in interface NameableData
      Returns:
      A String with the name of the item

    • setName

      public void setName(String name)
      Description copied from interface: NameableData
      Set the name of the item. The name cannot be null and mustn't be longer than the value specified by the MAX_NAME_LENGTH constant.
      Specified by:
      setName in interface NameableData
      Parameters:
      name - The new name for the item

    • getDescription

      public String getDescription()
      Description copied from interface: NameableData
      Get the description for the item.
      Specified by:
      getDescription in interface NameableData
      Returns:
      A String with a description of the item

    • setDescription

      public void setDescription(String description)
      Description copied from interface: NameableData
      Set the description for the item. The description can be null but mustn't be longer than the value specified by the MAX_DESCRIPTION_LENGTH constant.
      Specified by:
      setDescription in interface NameableData
      Parameters:
      description - The new description for the item

    • getRemovedBy

      public Integer getRemovedBy()
      Description copied from interface: RemovableData
      Get the ID of the user that removed this item.
      Specified by:
      getRemovedBy in interface RemovableData
      Returns:
      The ID of a user or null if the item is not removed

    • setRemovedBy

      public void setRemovedBy(Integer removedBy)
      Description copied from interface: RemovableData
      Set the ID of the user that removed this item or null to restore the item.
      Specified by:
      setRemovedBy in interface RemovableData

    • getAnnotationSet

      public AnnotationSetData getAnnotationSet()
      Description copied from interface: AnnotatableData
      Get the annotation set that holds the annotations for an item.
      Specified by:
      getAnnotationSet in interface AnnotatableData
      Returns:
      An AnnotationSetData item or null if no annotations exist
      Since:
      2.2

    • setAnnotationSet

      public void setAnnotationSet(AnnotationSetData annotationSet)
      Description copied from interface: AnnotatableData
      Change the annotation set. Use null to remove the annotations.
      Specified by:
      setAnnotationSet in interface AnnotatableData
      Parameters:
      annotationSet - Annotation set to change to.
      Since:
      2.2

    • getAnnotations

      public Set<AnnotationLink> getAnnotations()
      Description copied from interface: AnnotatableData
      Short-cut to all annotations belonging to this item. Used for HQL queries only. This is the inverse end. NOTE! The property-ref="annotationSet" require that AnnotationSetData implements Serializable
      Specified by:
      getAnnotations in interface AnnotatableData

    • setAnnotations

      void setAnnotations(Set<AnnotationLink> links)

    • 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

    • getExperiment

      public ExperimentData getExperiment()
      Get the experiment this bioassayset belongs to.
      Hibernate: many-to-one
      column="`experiment_id`" not-null="true" outer-join="false" update="false"

    • setExperiment

      public void setExperiment(ExperimentData experiment)

    • getTransformation

      public TransformationData getTransformation()
      Get the transformation that created this bioassayset.
      Hibernate: many-to-one
      column="`transformation_id`" not-null="true" outer-join="false" update="false"

    • setTransformation

      public void setTransformation(TransformationData transformation)

    • getDataCubeLayer

      public DataCubeLayerData getDataCubeLayer()
      Get the layer this bioassayset stores it's data in.
      Hibernate: many-to-one
      column="`datacubelayer_id`" not-null="true" outer-join="false" update="false"

    • setDataCubeLayer

      public void setDataCubeLayer(DataCubeLayerData dataCubeLayer)

    • getDataCubeFilter

      public DataCubeFilterData getDataCubeFilter()
      Get the filter used by this bioassayset. Null = no filter
      Hibernate: many-to-one
      column="`datacubefilter_id`" not-null="false" outer-join="false" update="false" cascade="save-update"

    • setDataCubeFilter

      public void setDataCubeFilter(DataCubeFilterData dataCubeFilter)

    • getNumReporters

      public int getNumReporters()
      The number of unique reporters in this bioassayset.
      Hibernate: property
      column="`reporters`" type="int" not-null="true" update="false"

    • setNumReporters

      public void setNumReporters(int numReporters)

    • getNumSpots

      public int getNumSpots()
      The number of unique spots in this bioassayset.
      Hibernate: property
      column="`spots`" type="int" not-null="true" update="false"

    • setNumSpots

      public void setNumSpots(int numSpots)

    • getNumFileReporters

      public int getNumFileReporters()
      The number of unique reporters as stored in files in this bioassayset.
      Since:
      2.8
      Hibernate: property
      column="`file_reporters`" type="int" not-null="true"

    • setNumFileReporters

      public void setNumFileReporters(int numFileReporters)
      Since:
      2.8

    • getNumFileSpots

      public int getNumFileSpots()
      The number of unique spots in this bioassayset.
      Since:
      2.8
      Hibernate: property
      column="`file_spots`" type="int" not-null="true"

    • setNumFileSpots

      public void setNumFileSpots(int numFileSpots)
      Since:
      2.8

    • getBioAssays

      Set<BioAssayData> getBioAssays()
      This is the inverse end.
      See Also:
      Hibernate: set
      lazy="true" inverse="true" cascade="delete"
      Hibernate: collection-key
      column="`bioassayset_id`"
      Hibernate: collection-one-to-many
      class="net.sf.basedb.core.data.BioAssayData"

    • setBioAssays

      void setBioAssays(Set<BioAssayData> bioAssays)

    • getTransformations

      Set<TransformationData> getTransformations()
      This is the inverse end.
      See Also:
      Hibernate: set
      lazy="true" inverse="true" cascade="delete"
      Hibernate: collection-key
      column="`bioassayset_id`"
      Hibernate: collection-one-to-many
      class="net.sf.basedb.core.data.TransformationData"

    • setTransformations

      void setTransformations(Set<TransformationData> transformations)

    • getExtraValues

      public Map<ExtraValueTypeData,ExtraValueData> getExtraValues()
      The extra values calculated for this bioassayset. This is the inverse end. This method is public since we need it for reading extra values from the bioassayset. The map should never be modified by the core.
      See Also:
      Hibernate: map
      lazy="true" cascade="all" inverse="true"
      Hibernate: index-many-to-many
      column="`extravaluetype_id`" class="net.sf.basedb.core.data.ExtraValueTypeData"
      Hibernate: collection-key
      column="`bioassayset_id`"
      Hibernate: collection-one-to-many
      column="`extravalue_id`" class="net.sf.basedb.core.data.ExtraValueData"

    • setExtraValues

      void setExtraValues(Map<ExtraValueTypeData,ExtraValueData> extraValues)

    • getIntensityTransform

      public int getIntensityTransform()
      A flag indicating how the spot intensities has been transformed before it was stored in the database: 0 = no transformation; 1 = 2-log; 2 = 10-log
      Since:
      2.12
      Hibernate: property
      column="`intensity_transform`" type="int" not-null="true"

    • setIntensityTransform

      public void setIntensityTransform(int intensityTransform)
      Since:
      2.12