Package net.sf.basedb.core.data
Class RawBioAssayData
- java.lang.Object
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- net.sf.basedb.core.data.BasicData
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- net.sf.basedb.core.data.OwnedData
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- net.sf.basedb.core.data.SharedData
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- net.sf.basedb.core.data.CommonData
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- net.sf.basedb.core.data.AnnotatedData
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- net.sf.basedb.core.data.RawBioAssayData
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- 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"
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Field Summary
Fields Modifier and Type Field Description private ArrayDesignData
arrayDesign
private DerivedBioAssayData
bioAssay
private Set<BioAssayData>
bioAssays
private long
bytes
private DiskUsageData
diskUsage
private Date
entryDate
private Set<ExperimentData>
experiments
private ExtractData
extract
private FileSetData
fileSet
private int
fileSpots
private boolean
hasData
private Map<String,String>
headers
private JobData
job
static int
MAX_HEADER_NAME_LENGTH
static int
MAX_HEADER_VALUE_LENGTH
private PlatformData
platform
private ProtocolData
protocol
private String
rawDataType
private SoftwareData
software
private int
spots
private Set<TransformationData>
transformations
private PlatformVariantData
variant
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Fields inherited from interface net.sf.basedb.core.data.NameableData
MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH
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Constructor Summary
Constructors Constructor Description RawBioAssayData()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description ArrayDesignData
getArrayDesign()
Get the array design used for the hybridization this raw bio assay comes from.(package private) Set<BioAssayData>
getBioAssays()
This is the inverse end.long
getBytes()
The number of bytes the raw data occupies on disk.DiskUsageData
getDiskUsage()
Get theDiskUsageData
that this item use.Date
getEntryDate()
Get the date this item was added to the database.(package private) Set<ExperimentData>
getExperiments()
This is the inverse end.FileSetData
getFileSet()
Get the file set attached to this item.boolean
getHasData()
If the raw bioassay has data or not.Map<String,String>
getHeaders()
File headers from the raw data file.JobData
getJob()
Get the job that was used to import raw data to this raw bioassayint
getNumFileSpots()
The number of spots on this raw bioassay that are stored inside files.DerivedBioAssayData
getParentBioAssay()
Get the derived bioassay that this raw bioassay has been created from.ExtractData
getParentExtract()
Get the derived bioassay that this raw bioassay has been created from.PlatformData
getPlatform()
Get the platform this raw bioassay uses.ProtocolData
getProtocol()
Get the protocol used for the image analysis.String
getRawDataType()
Get the name of the raw data type used by this raw bio assay.SoftwareData
getSoftware()
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>
getTransformations()
This is the inverse end.PlatformVariantData
getVariant()
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
setJob(JobData job)
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)
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Methods inherited from class net.sf.basedb.core.data.AnnotatedData
getAnnotations, getAnnotationSet, setAnnotations, setAnnotationSet
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Methods inherited from class net.sf.basedb.core.data.CommonData
getDescription, getName, getRemovedBy, setDescription, setName, setRemovedBy
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Methods inherited from class net.sf.basedb.core.data.SharedData
getItemKey, getProjectKey, setItemKey, setProjectKey
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Methods inherited from class net.sf.basedb.core.data.BasicData
equals, getId, getVersion, hashCode, setId, setVersion, toString
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Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
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Methods inherited from interface net.sf.basedb.core.data.IdentifiableData
getId, getVersion
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Methods inherited from interface net.sf.basedb.core.data.OwnableData
getOwner, setOwner
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Field Detail
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diskUsage
private DiskUsageData diskUsage
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fileSet
private FileSetData fileSet
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entryDate
private Date entryDate
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platform
private PlatformData platform
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variant
private PlatformVariantData variant
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job
private JobData job
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software
private SoftwareData software
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protocol
private ProtocolData protocol
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arrayDesign
private ArrayDesignData arrayDesign
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bioAssay
private DerivedBioAssayData bioAssay
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extract
private ExtractData extract
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rawDataType
private String rawDataType
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hasData
private boolean hasData
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spots
private int spots
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fileSpots
private int fileSpots
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bytes
private long bytes
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MAX_HEADER_NAME_LENGTH
public static final int MAX_HEADER_NAME_LENGTH
- See Also:
- Constant Field Values
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MAX_HEADER_VALUE_LENGTH
public static final int MAX_HEADER_VALUE_LENGTH
- See Also:
- Constant Field Values
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experiments
private Set<ExperimentData> experiments
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transformations
private Set<TransformationData> transformations
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bioAssays
private Set<BioAssayData> bioAssays
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Method Detail
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getDiskUsage
public DiskUsageData getDiskUsage()
Description copied from interface:DiskConsumableData
Get theDiskUsageData
that this item use.- Specified by:
getDiskUsage
in interfaceDiskConsumableData
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setDiskUsage
void setDiskUsage(DiskUsageData diskUsage)
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getFileSet
public FileSetData 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
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 interfaceFileStoreEnabledData
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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 interfaceRegisteredData
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setEntryDate
public void setEntryDate(Date entryDate)
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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"
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setPlatform
public void setPlatform(PlatformData platform)
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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"
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setVariant
public void setVariant(PlatformVariantData variant)
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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"
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setJob
public void setJob(JobData job)
- Since:
- 2.7
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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"
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setSoftware
public void setSoftware(SoftwareData software)
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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"
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setProtocol
public void setProtocol(ProtocolData protocol)
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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"
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setArrayDesign
public void setArrayDesign(ArrayDesignData arrayDesign)
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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"
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setParentBioAssay
public void setParentBioAssay(DerivedBioAssayData bioAssay)
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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"
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setParentExtract
public void setParentExtract(ExtractData extract)
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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"
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setRawDataType
public void setRawDataType(String rawDataType)
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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)
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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)
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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"
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setNumFileSpots
public void setNumFileSpots(int fileSpots)
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getBytes
public long getBytes()
The number of bytes the raw data occupies on disk.- Hibernate: property
- column="`bytes`" type="long" not-null="true"
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setBytes
public void setBytes(long bytes)
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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"
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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:
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"
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setExperiments
void setExperiments(Set<ExperimentData> experiments)
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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:
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"
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setTransformations
void setTransformations(Set<TransformationData> transformations)
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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:
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"
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setBioAssays
void setBioAssays(Set<BioAssayData> bioAssays)
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