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:
- Last modified
- $Date: 2019-03-11 12:51:33 +0100 (mån, 11 mars 2019) $
- Hibernate: class
- table="`RawBioAssays`" lazy="true"
-
Field Summary
Modifier and TypeFieldDescriptionprivate ArrayDesignData
private DerivedBioAssayData
private Set<BioAssayData>
private long
private DiskUsageData
private Date
private Set<ExperimentData>
private ExtractData
private FileSetData
private int
private boolean
private JobData
static final int
static final int
private PlatformData
private ProtocolData
private String
private SoftwareData
private int
private Set<TransformationData>
private PlatformVariantData
Fields inherited from interface net.sf.basedb.core.data.NameableData
MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH
-
Constructor Summary
-
Method Summary
Modifier and TypeMethodDescriptionGet the array design used for the hybridization this raw bio assay comes from.(package private) Set<BioAssayData>
This is the inverse end.long
getBytes()
The number of bytes the raw data occupies on disk.Get theDiskUsageData
that this item use.Get the date this item was added to the database.(package private) Set<ExperimentData>
This is the inverse end.Get the file set attached to this item.boolean
If the raw bioassay has data or not.File headers from the raw data file.getJob()
Get the job that was used to import raw data to this raw bioassayint
The number of spots on this raw bioassay that are stored inside files.Get the derived bioassay that this raw bioassay has been created from.Get the derived bioassay that this raw bioassay has been created from.Get the platform this raw bioassay uses.Get the protocol used for the image analysis.Get the name of the raw data type used by this raw bio assay.Get the software used to analyse the scanned image and produce the raw data.int
getSpots()
The number of data spots in this raw bio assay, that are stored in the database.(package private) Set<TransformationData>
This is the inverse end.Get the platform variant this raw bioassay uses, or null.void
setArrayDesign
(ArrayDesignData arrayDesign) (package private) void
setBioAssays
(Set<BioAssayData> bioAssays) void
setBytes
(long bytes) (package private) void
setDiskUsage
(DiskUsageData diskUsage) void
setEntryDate
(Date entryDate) (package private) void
setExperiments
(Set<ExperimentData> experiments) void
setFileSet
(FileSetData fileSet) Attach a file set to the item.void
setHasData
(boolean hasData) (package private) void
setHeaders
(Map<String, String> headers) void
void
setNumFileSpots
(int fileSpots) void
setParentBioAssay
(DerivedBioAssayData bioAssay) void
setParentExtract
(ExtractData extract) void
setPlatform
(PlatformData platform) void
setProtocol
(ProtocolData protocol) void
setRawDataType
(String rawDataType) void
setSoftware
(SoftwareData software) void
setSpots
(int spots) (package private) void
setTransformations
(Set<TransformationData> transformations) void
setVariant
(PlatformVariantData variant) Methods inherited from class net.sf.basedb.core.data.AnnotatedData
getAnnotations, getAnnotationSet, setAnnotations, setAnnotationSet
Methods inherited from class net.sf.basedb.core.data.CommonData
getDescription, getName, getRemovedBy, setDescription, setName, setRemovedBy
Methods inherited from class net.sf.basedb.core.data.SharedData
getItemKey, getProjectKey, setItemKey, setProjectKey
Methods inherited from class net.sf.basedb.core.data.BasicData
equals, getId, getVersion, hashCode, setId, setVersion, toString
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
Methods inherited from interface net.sf.basedb.core.data.IdentifiableData
getId, getVersion
Methods inherited from interface net.sf.basedb.core.data.OwnableData
getOwner, setOwner
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Field Details
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diskUsage
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fileSet
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entryDate
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platform
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variant
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job
-
software
-
protocol
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arrayDesign
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bioAssay
-
extract
-
rawDataType
-
hasData
private boolean hasData -
spots
private int spots -
fileSpots
private int fileSpots -
bytes
private long bytes -
MAX_HEADER_NAME_LENGTH
public static final int MAX_HEADER_NAME_LENGTH- See Also:
-
MAX_HEADER_VALUE_LENGTH
public static final int MAX_HEADER_VALUE_LENGTH- See Also:
-
headers
-
experiments
-
transformations
-
bioAssays
-
-
Constructor Details
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RawBioAssayData
public RawBioAssayData()
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Method Details
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getDiskUsage
Description copied from interface:DiskConsumableData
Get theDiskUsageData
that this item use.- Specified by:
getDiskUsage
in interfaceDiskConsumableData
-
setDiskUsage
-
getFileSet
Description copied from interface:FileStoreEnabledData
Get the file set attached to this item.- Specified by:
getFileSet
in interfaceFileStoreEnabledData
- Returns:
- A
FileSetData
object or null if no files are attached
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setFileSet
Description copied from interface:FileStoreEnabledData
Attach a file set to the item. Null is allowed to unlink it.- Specified by:
setFileSet
in interfaceFileStoreEnabledData
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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 interfaceRegisteredData
-
setEntryDate
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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
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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
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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
- Since:
- 2.7
-
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
-
getProtocol
Get the protocol used for the image analysis.- Hibernate: many-to-one
- column="`protocol_id`" not-null="false" outer-join="false"
-
setProtocol
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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
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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
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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
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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
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getHasData
public boolean getHasData()If the raw bioassay has data or not.- Hibernate: property
- column="`has_data`" type="boolean" not-null="true"
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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"
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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
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
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getExperiments
Set<ExperimentData> getExperiments()This is the inverse end. The real end is mapped byRootRawBioAssayData
but we skip directly to the experiment.- See Also:
- 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"
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setExperiments
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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:
- 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
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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:
- 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"
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setBioAssays
-