org.molgenis.omx.ngs
Class Sample

java.lang.Object
  org.molgenis.util.AbstractEntity
      org.molgenis.omx.ngs.Sample

All Implemented Interfaces:

Serializable, Autoid, Entity

@Entity
public class Sample
extends AbstractEntity
implements Autoid

Sample: A Sample bundles information about a sample. Sample can be pooled. A pooled sample is just another sample, but with a additional mref (many to many) linking to the samples inside the pool..

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

static String	ARRAYFILE
static String	ARRAYID
static String	CAPTURINGKIT
static String	CAPTURINGKIT_CAPTURINGKITNAME
static String	EXTERNALID
static String	ID
static String	INTERNALID
static String	LABSTATUS
static String	PROJECTID
static String	PROJECTID_PROJECTNAME
static String	SAMPLEBARCODE
static String	SAMPLEBARCODE_SAMPLEBARCODENAME
static String	SAMPLECOMMENT
static String	SAMPLEINPOOL
static String	SAMPLEINPOOL_INTERNALID

Constructor Summary

Sample()

Sample(Sample copyMe)
copy constructor

Method Summary

Sample	create(Tuple tuple)
boolean	equals(Object obj)
static List<? extends Sample>	find(Database db, QueryRule... rules) Shorthand for db.find(Sample.class, org.molgenis.framework.db.QueryRule ...
static Sample	findById(Database db, Integer id)
static Sample	findByInternalId(Database db, String internalId)
Object	get(String name) Generic getter.
String	getArrayFile() Get the Location of arrayfile for the sample in this lane-barcode.
String	getArrayFile(Database db) Deprecated.
String	getArrayId() Get the ID of the sample on the arrayFile.
String	getArrayId(Database db) Deprecated.
String	getCapturingKit_CapturingKitName() Get a pretty label CapturingKitName for cross reference CapturingKit to CapturingKit.Id.
Integer	getCapturingKit_Id()
CapturingKit	getCapturingKit() Get the Capturing kit used..
CapturingKit	getCapturingKit(Database db) Deprecated.
String	getExternalId() Get the The name of a sample as known by the customer.
String	getExternalId(Database db) Deprecated.
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of Sample.
String	getFields(String sep) Deprecated.
Integer	getId() Get the automatically generated internal id, only for internal use..
String	getIdField()
Object	getIdValue()
String	getInternalId() Get the The number of a sample as used in-house.
String	getInternalId(Database db) Deprecated.
List<String>	getLabelFields()
String	getLabStatus() Get the Lab status phase of this sample.
String	getLabStatus(Database db) Deprecated.
String	getLabStatusLabel() Get tha label for enum LabStatus.
List<ValueLabel>	getLabStatusOptions() LabStatus is enum.
Integer	getProjectId_Id()
String	getProjectId_ProjectName() Get a pretty label ProjectName for cross reference ProjectId to Project.Id.
Project	getProjectId() Get the the sample that this sample is part of.
Project	getProjectId(Database db) Deprecated.
Integer	getSampleBarcode_Id()
String	getSampleBarcode_SampleBarcodeName() Get a pretty label SampleBarcodeName for cross reference SampleBarcode to SampleBarcode.Id.
SampleBarcode	getSampleBarcode() Get the Multiple samples can be on one flowcell using barcodes..
SampleBarcode	getSampleBarcode(Database db) Deprecated.
String	getSampleComment() Get the Comments about the sample.
String	getSampleComment(Database db) Deprecated.
List<Integer>	getSampleInPool_Id()
List<String>	getSampleInPool_InternalId() Get a pretty label for cross reference SampleInPool to Sample.Id.
List<Sample>	getSampleInPool() Get the List of samples inside the pool.
List<Sample>	getSampleInPool(Database db) Deprecated.
Collection<Sample>	getSampleInPoolSampleCollection()
Collection<Sample>	getSampleInPoolSampleCollection(Database db)
String	getValues(String sep) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends Sample>	query(Database db) Shorthand for db.query(Sample.class).
void	set(Tuple tuple, boolean strict)
void	setArrayFile(String arrayFile) Set the Location of arrayfile for the sample in this lane-barcode.
void	setArrayId(String arrayId) Set the ID of the sample on the arrayFile.
void	setCapturingKit_CapturingKitName(String capturingKit_CapturingKitName) Set a pretty label for cross reference CapturingKit to CapturingKit.Id.
void	setCapturingKit_Id(Integer capturingKit_id) Set foreign key for field capturingKit.
void	setCapturingKit(CapturingKit capturingKit) Set the Capturing kit used..
void	setCapturingKit(Integer capturingKit_id)
void	setExternalId(String externalId) Set the The name of a sample as known by the customer.
void	setId(Integer id) Set the automatically generated internal id, only for internal use..
void	setInternalId(String internalId) Set the The number of a sample as used in-house.
void	setLabStatus(String labStatus) Set the Lab status phase of this sample.
void	setProjectId_Id(Integer projectId_id) Set foreign key for field projectId.
void	setProjectId_ProjectName(String projectId_ProjectName) Set a pretty label for cross reference ProjectId to Project.Id.
void	setProjectId(Integer projectId_id)
void	setProjectId(Project projectId) Set the the sample that this sample is part of.
void	setSampleBarcode_Id(Integer sampleBarcode_id) Set foreign key for field sampleBarcode.
void	setSampleBarcode_SampleBarcodeName(String sampleBarcode_SampleBarcodeName) Set a pretty label for cross reference SampleBarcode to SampleBarcode.Id.
void	setSampleBarcode(Integer sampleBarcode_id)
void	setSampleBarcode(SampleBarcode sampleBarcode) Set the Multiple samples can be on one flowcell using barcodes..
void	setSampleComment(String sampleComment) Set the Comments about the sample.
void	setSampleInPool_Id(Integer... sampleInPool)
void	setSampleInPool_Id(List<Integer> sampleInPool_id) Set foreign key for field sampleInPool.
void	setSampleInPool_InternalId(List<String> sampleInPool_InternalId) Update the foreign key SampleInPool This sets sampleInPool to null until next database transaction.
void	setSampleInPool(List<Sample> sampleInPool) Set the List of samples inside the pool.
void	setSampleInPool(Sample... sampleInPool)
void	setSampleInPoolSampleCollection(Collection<Sample> collection)
String	toString()
String	toString(boolean verbose)
void	validate()

Methods inherited from class org.molgenis.util.AbstractEntity

get__Type, get__TypeLabel, get__TypeOptions, getLabelValue, getValues, isObjectRepresentation, isReadonly, set__Type, set, set, setReadonly, setValuesFromString, string2date

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.molgenis.util.Entity

getLabelValue, getValues, isReadonly, set, set, setReadonly

Field Detail

ID

public static final String ID

See Also:

Constant Field Values

INTERNALID

public static final String INTERNALID

See Also:

Constant Field Values

EXTERNALID

public static final String EXTERNALID

See Also:

Constant Field Values

SAMPLECOMMENT

public static final String SAMPLECOMMENT

See Also:

Constant Field Values

PROJECTID

public static final String PROJECTID

See Also:

Constant Field Values

PROJECTID_PROJECTNAME

public static final String PROJECTID_PROJECTNAME

See Also:

Constant Field Values

ARRAYFILE

public static final String ARRAYFILE

See Also:

Constant Field Values

ARRAYID

public static final String ARRAYID

See Also:

Constant Field Values

CAPTURINGKIT

public static final String CAPTURINGKIT

See Also:

Constant Field Values

CAPTURINGKIT_CAPTURINGKITNAME

public static final String CAPTURINGKIT_CAPTURINGKITNAME

See Also:

Constant Field Values

SAMPLEBARCODE

public static final String SAMPLEBARCODE

See Also:

Constant Field Values

SAMPLEBARCODE_SAMPLEBARCODENAME

public static final String SAMPLEBARCODE_SAMPLEBARCODENAME

See Also:

Constant Field Values

SAMPLEINPOOL

public static final String SAMPLEINPOOL

See Also:

Constant Field Values

SAMPLEINPOOL_INTERNALID

public static final String SAMPLEINPOOL_INTERNALID

See Also:

Constant Field Values

LABSTATUS

public static final String LABSTATUS

See Also:

Constant Field Values

Constructor Detail

Sample

public Sample()

Sample

public Sample(Sample copyMe)
       throws Exception

copy constructor

Throws:

Exception

Method Detail

query

public static Query<? extends Sample> query(Database db)

Shorthand for db.query(Sample.class).

find

public static List<? extends Sample> find(Database db,
                                          QueryRule... rules)
                                   throws DatabaseException

Shorthand for db.find(Sample.class, org.molgenis.framework.db.QueryRule ... rules).

Throws:

DatabaseException

findById

public static Sample findById(Database db,
                              Integer id)
                       throws DatabaseException

Throws:

DatabaseException

findByInternalId

public static Sample findByInternalId(Database db,
                                      String internalId)
                               throws DatabaseException

Throws:

DatabaseException

getId

public Integer getId()

Get the automatically generated internal id, only for internal use..

Specified by:

getId in interface Autoid

Returns:

id.

setId

public void setId(Integer id)

Set the automatically generated internal id, only for internal use..

Specified by:

setId in interface Autoid

Parameters:

id -

getInternalId

public String getInternalId()

Get the The number of a sample as used in-house.

Returns:

internalId.

getInternalId

@Deprecated
public String getInternalId(Database db)

Deprecated.

setInternalId

public void setInternalId(String internalId)

Set the The number of a sample as used in-house.

Parameters:

internalId -

getExternalId

public String getExternalId()

Get the The name of a sample as known by the customer.

Returns:

externalId.

getExternalId

@Deprecated
public String getExternalId(Database db)

Deprecated.

setExternalId

public void setExternalId(String externalId)

Set the The name of a sample as known by the customer.

Parameters:

externalId -

getSampleComment

public String getSampleComment()

Get the Comments about the sample.

Returns:

sampleComment.

getSampleComment

@Deprecated
public String getSampleComment(Database db)

Deprecated.

setSampleComment

public void setSampleComment(String sampleComment)

Set the Comments about the sample.

Parameters:

sampleComment -

getProjectId

public Project getProjectId()

Get the the sample that this sample is part of.

Returns:

projectId.

getProjectId

@Deprecated
public Project getProjectId(Database db)

Deprecated.

setProjectId

public void setProjectId(Project projectId)

Set the the sample that this sample is part of.

Parameters:

projectId -

setProjectId_Id

public void setProjectId_Id(Integer projectId_id)

Set foreign key for field projectId. This will erase any foreign key objects currently set. FIXME: can we autoload the new object?

setProjectId

public void setProjectId(Integer projectId_id)

getProjectId_Id

public Integer getProjectId_Id()

getProjectId_ProjectName

public String getProjectId_ProjectName()

Get a pretty label ProjectName for cross reference ProjectId to Project.Id.

setProjectId_ProjectName

public void setProjectId_ProjectName(String projectId_ProjectName)

Set a pretty label for cross reference ProjectId to Project.Id. Implies setProjectId(null) until save

getArrayFile

public String getArrayFile()

Get the Location of arrayfile for the sample in this lane-barcode.

Returns:

arrayFile.

getArrayFile

@Deprecated
public String getArrayFile(Database db)

Deprecated.

setArrayFile

public void setArrayFile(String arrayFile)

Set the Location of arrayfile for the sample in this lane-barcode.

Parameters:

arrayFile -

getArrayId

public String getArrayId()

Get the ID of the sample on the arrayFile.

Returns:

arrayId.

getArrayId

@Deprecated
public String getArrayId(Database db)

Deprecated.

setArrayId

public void setArrayId(String arrayId)

Set the ID of the sample on the arrayFile.

Parameters:

arrayId -

getCapturingKit

public CapturingKit getCapturingKit()

Get the Capturing kit used..

Returns:

capturingKit.

getCapturingKit

@Deprecated
public CapturingKit getCapturingKit(Database db)

Deprecated.

setCapturingKit

public void setCapturingKit(CapturingKit capturingKit)

Set the Capturing kit used..

Parameters:

capturingKit -

setCapturingKit_Id

public void setCapturingKit_Id(Integer capturingKit_id)

Set foreign key for field capturingKit. This will erase any foreign key objects currently set. FIXME: can we autoload the new object?

setCapturingKit

public void setCapturingKit(Integer capturingKit_id)

getCapturingKit_Id

public Integer getCapturingKit_Id()

getCapturingKit_CapturingKitName

public String getCapturingKit_CapturingKitName()

Get a pretty label CapturingKitName for cross reference CapturingKit to CapturingKit.Id.

setCapturingKit_CapturingKitName

public void setCapturingKit_CapturingKitName(String capturingKit_CapturingKitName)

Set a pretty label for cross reference CapturingKit to CapturingKit.Id. Implies setCapturingKit(null) until save

getSampleBarcode

public SampleBarcode getSampleBarcode()

Get the Multiple samples can be on one flowcell using barcodes..

Returns:

sampleBarcode.

getSampleBarcode

@Deprecated
public SampleBarcode getSampleBarcode(Database db)

Deprecated.

setSampleBarcode

public void setSampleBarcode(SampleBarcode sampleBarcode)

Set the Multiple samples can be on one flowcell using barcodes..

Parameters:

sampleBarcode -

setSampleBarcode_Id

public void setSampleBarcode_Id(Integer sampleBarcode_id)

Set foreign key for field sampleBarcode. This will erase any foreign key objects currently set. FIXME: can we autoload the new object?

setSampleBarcode

public void setSampleBarcode(Integer sampleBarcode_id)

getSampleBarcode_Id

public Integer getSampleBarcode_Id()

getSampleBarcode_SampleBarcodeName

public String getSampleBarcode_SampleBarcodeName()

Get a pretty label SampleBarcodeName for cross reference SampleBarcode to SampleBarcode.Id.

setSampleBarcode_SampleBarcodeName

public void setSampleBarcode_SampleBarcodeName(String sampleBarcode_SampleBarcodeName)

Set a pretty label for cross reference SampleBarcode to SampleBarcode.Id. Implies setSampleBarcode(null) until save

getSampleInPool

public List<Sample> getSampleInPool()

Get the List of samples inside the pool.

Returns:

sampleInPool.

getSampleInPool

@Deprecated
public List<Sample> getSampleInPool(Database db)

Deprecated.

setSampleInPool

public void setSampleInPool(List<Sample> sampleInPool)

Set the List of samples inside the pool.

Parameters:

sampleInPool -

setSampleInPool_Id

public void setSampleInPool_Id(Integer... sampleInPool)

setSampleInPool

public void setSampleInPool(Sample... sampleInPool)

setSampleInPool_Id

public void setSampleInPool_Id(List<Integer> sampleInPool_id)

Set foreign key for field sampleInPool. This will erase any foreign key objects currently set. FIXME: can we autoload the new object?

getSampleInPool_Id

public List<Integer> getSampleInPool_Id()

getSampleInPool_InternalId

public List<String> getSampleInPool_InternalId()

Get a pretty label for cross reference SampleInPool to Sample.Id.

setSampleInPool_InternalId

public void setSampleInPool_InternalId(List<String> sampleInPool_InternalId)

Update the foreign key SampleInPool This sets sampleInPool to null until next database transaction.

getLabStatus

public String getLabStatus()

Get the Lab status phase of this sample.

Returns:

labStatus.

getLabStatus

@Deprecated
public String getLabStatus(Database db)

Deprecated.

setLabStatus

public void setLabStatus(String labStatus)

Set the Lab status phase of this sample.

Parameters:

labStatus -

getLabStatusLabel

public String getLabStatusLabel()

Get tha label for enum LabStatus.

getLabStatusOptions

public List<ValueLabel> getLabStatusOptions()

LabStatus is enum. This method returns all available enum options.

get

public Object get(String name)

Generic getter. Get the property by using the name.

Specified by:

get in interface Entity

validate

public void validate()
              throws DatabaseException

Specified by:

validate in interface Entity

Throws:

DatabaseException

set

public void set(Tuple tuple,
                boolean strict)
         throws Exception

Specified by:

set in interface Entity

Throws:

Exception

toString

public String toString()

Overrides:

toString in class Object

toString

public String toString(boolean verbose)

getFields

public Vector<String> getFields(boolean skipAutoIds)

Get the names of all public properties of Sample.

Specified by:

getFields in interface Entity

getFields

public Vector<String> getFields()

Specified by:

getFields in interface Entity

getIdField

public String getIdField()

Specified by:

getIdField in interface Entity

getLabelFields

public List<String> getLabelFields()

Specified by:

getLabelFields in interface Entity

getFields

@Deprecated
public String getFields(String sep)

Deprecated.

Specified by:

getFields in interface Entity

getIdValue

public Object getIdValue()

Specified by:

getIdValue in interface Entity

getXrefIdFieldName

public String getXrefIdFieldName(String fieldName)

Specified by:

getXrefIdFieldName in interface Entity

getValues

@Deprecated
public String getValues(String sep)

Deprecated.

Specified by:

getValues in interface Entity

Overrides:

getValues in class AbstractEntity

create

public Sample create(Tuple tuple)
              throws Exception

Specified by:

create in interface Entity

Throws:

Exception

getSampleInPoolSampleCollection

public Collection<Sample> getSampleInPoolSampleCollection()

getSampleInPoolSampleCollection

public Collection<Sample> getSampleInPoolSampleCollection(Database db)

setSampleInPoolSampleCollection

public void setSampleInPoolSampleCollection(Collection<Sample> collection)

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object