Class BioAssaySetData

    • Constructor Detail

      • BioAssaySetData

        public BioAssaySetData()
    • Method Detail

      • 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
      • 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:
        BioAssayData.getBioAssaySet()
        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"
      • getTransformations

        Set<TransformationData> getTransformations()
        This is the inverse end.
        See Also:
        TransformationData.getSource()
        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"
      • 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:
        ExtraValueData.getBioAssaySet(), ExtraValueData.getExtraValueType()
        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"
      • 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