Class RawBioAssayData

    • Constructor Detail

      • RawBioAssayData

        public RawBioAssayData()
    • Method Detail

      • 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"
      • 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"
      • 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"
      • 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"
      • 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"
      • 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"