org.molgenis.omx.ngs
Class FlowcellLane

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

All Implemented Interfaces:

Serializable, Autoid, Entity

@Entity
public class FlowcellLane
extends AbstractEntity
implements Autoid

FlowcellLane: A FlowcellLaneSampleBarcode bundles information about a sample which is added to a lane on a flowcell..

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

static String	FLOWCELL
static String	FLOWCELL_FLOWCELLNAME
static String	FLOWCELLLANECOMMENT
static String	ID
static String	LANE
static String	QCDRYDATE
static String	QCDRYMET
static String	QCDRYUSER
static String	QCDRYUSER_USERNAME
static String	QCWETDATE
static String	QCWETMET
static String	QCWETUSER
static String	QCWETUSER_USERNAME
static String	SAMPLE
static String	SAMPLE_INTERNALID

Constructor Summary

FlowcellLane()

FlowcellLane(FlowcellLane copyMe)
copy constructor

Method Summary

FlowcellLane	create(Tuple tuple)
boolean	equals(Object obj)
static List<? extends FlowcellLane>	find(Database db, QueryRule... rules) Shorthand for db.find(FlowcellLane.class, org.molgenis.framework.db.QueryRule ...
static FlowcellLane	findByFlowcellLaneSample(Database db, Integer flowcell, String lane, Integer sample)
static FlowcellLane	findById(Database db, Integer id)
Object	get(String name) Generic getter.
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of FlowcellLane.
String	getFields(String sep) Deprecated.
String	getFlowcell_FlowcellName() Get a pretty label FlowcellName for cross reference Flowcell to Flowcell.Id.
Integer	getFlowcell_Id()
Flowcell	getFlowcell() Get the The flowcell to which this lane belongs.
Flowcell	getFlowcell(Database db) Deprecated.
String	getFlowcellLaneComment() Get the Comment about the experiment..
String	getFlowcellLaneComment(Database db) Deprecated.
Integer	getId() Get the automatically generated internal id, only for internal use..
String	getIdField()
Object	getIdValue()
List<String>	getLabelFields()
String	getLane() Get the The lane number that is unique within a flow cell with a range of 1-8..
String	getLane(Database db) Deprecated.
String	getLaneLabel() Get tha label for enum Lane.
List<ValueLabel>	getLaneOptions() Lane is enum.
Date	getQcDryDate() Get the The date the QcWetUser selected the QcWetMet value.
Date	getQcDryDate(Database db) Deprecated.
String	getQcDryMet() Get the Variant calling quality criteria.
String	getQcDryMet(Database db) Deprecated.
String	getQcDryMetLabel() Get tha label for enum QcDryMet.
List<ValueLabel>	getQcDryMetOptions() QcDryMet is enum.
Integer	getQcDryUser_Id()
String	getQcDryUser_UserName() Get a pretty label UserName for cross reference QcDryUser to NgsUser.Id.
NgsUser	getQcDryUser() Get the The user who checked if the quality score of the analysis was met.
NgsUser	getQcDryUser(Database db) Deprecated.
Date	getQcWetDate() Get the The date the QcWetUser selected the QcWetMet value..
Date	getQcWetDate(Database db) Deprecated.
String	getQcWetMet() Get the Quality criteria of the wet lab met.
String	getQcWetMet(Database db) Deprecated.
String	getQcWetMetLabel() Get tha label for enum QcWetMet.
List<ValueLabel>	getQcWetMetOptions() QcWetMet is enum.
Integer	getQcWetUser_Id()
String	getQcWetUser_UserName() Get a pretty label UserName for cross reference QcWetUser to NgsUser.Id.
NgsUser	getQcWetUser() Get the The user who checked if the quality score on the wet-lab was met.
NgsUser	getQcWetUser(Database db) Deprecated.
Integer	getSample_Id()
String	getSample_InternalId() Get a pretty label InternalId for cross reference Sample to Sample.Id.
Sample	getSample() Get the Sample.
Sample	getSample(Database db) Deprecated.
String	getValues(String sep) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends FlowcellLane>	query(Database db) Shorthand for db.query(FlowcellLane.class).
void	set(Tuple tuple, boolean strict)
void	setFlowcell_FlowcellName(String flowcell_FlowcellName) Set a pretty label for cross reference Flowcell to Flowcell.Id.
void	setFlowcell_Id(Integer flowcell_id) Set foreign key for field flowcell.
void	setFlowcell(Flowcell flowcell) Set the The flowcell to which this lane belongs.
void	setFlowcell(Integer flowcell_id)
void	setFlowcellLaneComment(String flowcellLaneComment) Set the Comment about the experiment..
void	setId(Integer id) Set the automatically generated internal id, only for internal use..
void	setLane(String lane) Set the The lane number that is unique within a flow cell with a range of 1-8..
void	setQcDryDate(Date qcDryDate) Set the The date the QcWetUser selected the QcWetMet value.
void	setQcDryMet(String qcDryMet) Set the Variant calling quality criteria.
void	setQcDryUser_Id(Integer qcDryUser_id) Set foreign key for field qcDryUser.
void	setQcDryUser_UserName(String qcDryUser_UserName) Set a pretty label for cross reference QcDryUser to NgsUser.Id.
void	setQcDryUser(Integer qcDryUser_id)
void	setQcDryUser(NgsUser qcDryUser) Set the The user who checked if the quality score of the analysis was met.
void	setQcWetDate(Date qcWetDate) Set the The date the QcWetUser selected the QcWetMet value..
void	setQcWetMet(String qcWetMet) Set the Quality criteria of the wet lab met.
void	setQcWetUser_Id(Integer qcWetUser_id) Set foreign key for field qcWetUser.
void	setQcWetUser_UserName(String qcWetUser_UserName) Set a pretty label for cross reference QcWetUser to NgsUser.Id.
void	setQcWetUser(Integer qcWetUser_id)
void	setQcWetUser(NgsUser qcWetUser) Set the The user who checked if the quality score on the wet-lab was met.
void	setSample_Id(Integer sample_id) Set foreign key for field sample.
void	setSample_InternalId(String sample_InternalId) Set a pretty label for cross reference Sample to Sample.Id.
void	setSample(Integer sample_id)
void	setSample(Sample sample) Set the Sample.
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

FLOWCELL

public static final String FLOWCELL

See Also:

Constant Field Values

FLOWCELL_FLOWCELLNAME

public static final String FLOWCELL_FLOWCELLNAME

See Also:

Constant Field Values

LANE

public static final String LANE

See Also:

Constant Field Values

SAMPLE

public static final String SAMPLE

See Also:

Constant Field Values

SAMPLE_INTERNALID

public static final String SAMPLE_INTERNALID

See Also:

Constant Field Values

FLOWCELLLANECOMMENT

public static final String FLOWCELLLANECOMMENT

See Also:

Constant Field Values

QCWETMET

public static final String QCWETMET

See Also:

Constant Field Values

QCWETUSER

public static final String QCWETUSER

See Also:

Constant Field Values

QCWETUSER_USERNAME

public static final String QCWETUSER_USERNAME

See Also:

Constant Field Values

QCWETDATE

public static final String QCWETDATE

See Also:

Constant Field Values

QCDRYMET

public static final String QCDRYMET

See Also:

Constant Field Values

QCDRYUSER

public static final String QCDRYUSER

See Also:

Constant Field Values

QCDRYUSER_USERNAME

public static final String QCDRYUSER_USERNAME

See Also:

Constant Field Values

QCDRYDATE

public static final String QCDRYDATE

See Also:

Constant Field Values

Constructor Detail

FlowcellLane

public FlowcellLane()

FlowcellLane

public FlowcellLane(FlowcellLane copyMe)
             throws Exception

copy constructor

Throws:

Exception

Method Detail

query

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

Shorthand for db.query(FlowcellLane.class).

find

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

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

Throws:

DatabaseException

findById

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

Throws:

DatabaseException

findByFlowcellLaneSample

public static FlowcellLane findByFlowcellLaneSample(Database db,
                                                    Integer flowcell,
                                                    String lane,
                                                    Integer sample)
                                             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 -

getFlowcell

public Flowcell getFlowcell()

Get the The flowcell to which this lane belongs.

Returns:

flowcell.

getFlowcell

@Deprecated
public Flowcell getFlowcell(Database db)

Deprecated.

setFlowcell

public void setFlowcell(Flowcell flowcell)

Set the The flowcell to which this lane belongs.

Parameters:

flowcell -

setFlowcell_Id

public void setFlowcell_Id(Integer flowcell_id)

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

setFlowcell

public void setFlowcell(Integer flowcell_id)

getFlowcell_Id

public Integer getFlowcell_Id()

getFlowcell_FlowcellName

public String getFlowcell_FlowcellName()

Get a pretty label FlowcellName for cross reference Flowcell to Flowcell.Id.

setFlowcell_FlowcellName

public void setFlowcell_FlowcellName(String flowcell_FlowcellName)

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

getLane

public String getLane()

Get the The lane number that is unique within a flow cell with a range of 1-8..

Returns:

lane.

getLane

@Deprecated
public String getLane(Database db)

Deprecated.

setLane

public void setLane(String lane)

Set the The lane number that is unique within a flow cell with a range of 1-8..

Parameters:

lane -

getLaneLabel

public String getLaneLabel()

Get tha label for enum Lane.

getLaneOptions

public List<ValueLabel> getLaneOptions()

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

getSample

public Sample getSample()

Get the Sample.

Returns:

sample.

getSample

@Deprecated
public Sample getSample(Database db)

Deprecated.

setSample

public void setSample(Sample sample)

Set the Sample.

Parameters:

sample -

setSample_Id

public void setSample_Id(Integer sample_id)

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

setSample

public void setSample(Integer sample_id)

getSample_Id

public Integer getSample_Id()

getSample_InternalId

public String getSample_InternalId()

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

setSample_InternalId

public void setSample_InternalId(String sample_InternalId)

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

getFlowcellLaneComment

public String getFlowcellLaneComment()

Get the Comment about the experiment..

Returns:

flowcellLaneComment.

getFlowcellLaneComment

@Deprecated
public String getFlowcellLaneComment(Database db)

Deprecated.

setFlowcellLaneComment

public void setFlowcellLaneComment(String flowcellLaneComment)

Set the Comment about the experiment..

Parameters:

flowcellLaneComment -

getQcWetMet

public String getQcWetMet()

Get the Quality criteria of the wet lab met.

Returns:

qcWetMet.

getQcWetMet

@Deprecated
public String getQcWetMet(Database db)

Deprecated.

setQcWetMet

public void setQcWetMet(String qcWetMet)

Set the Quality criteria of the wet lab met.

Parameters:

qcWetMet -

getQcWetMetLabel

public String getQcWetMetLabel()

Get tha label for enum QcWetMet.

getQcWetMetOptions

public List<ValueLabel> getQcWetMetOptions()

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

getQcWetUser

public NgsUser getQcWetUser()

Get the The user who checked if the quality score on the wet-lab was met.

Returns:

qcWetUser.

getQcWetUser

@Deprecated
public NgsUser getQcWetUser(Database db)

Deprecated.

setQcWetUser

public void setQcWetUser(NgsUser qcWetUser)

Set the The user who checked if the quality score on the wet-lab was met.

Parameters:

qcWetUser -

setQcWetUser_Id

public void setQcWetUser_Id(Integer qcWetUser_id)

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

setQcWetUser

public void setQcWetUser(Integer qcWetUser_id)

getQcWetUser_Id

public Integer getQcWetUser_Id()

getQcWetUser_UserName

public String getQcWetUser_UserName()

Get a pretty label UserName for cross reference QcWetUser to NgsUser.Id.

setQcWetUser_UserName

public void setQcWetUser_UserName(String qcWetUser_UserName)

Set a pretty label for cross reference QcWetUser to NgsUser.Id. Implies setQcWetUser(null) until save

getQcWetDate

public Date getQcWetDate()

Get the The date the QcWetUser selected the QcWetMet value..

Returns:

qcWetDate.

getQcWetDate

@Deprecated
public Date getQcWetDate(Database db)

Deprecated.

setQcWetDate

public void setQcWetDate(Date qcWetDate)

Set the The date the QcWetUser selected the QcWetMet value..

Parameters:

qcWetDate -

getQcDryMet

public String getQcDryMet()

Get the Variant calling quality criteria.

Returns:

qcDryMet.

getQcDryMet

@Deprecated
public String getQcDryMet(Database db)

Deprecated.

setQcDryMet

public void setQcDryMet(String qcDryMet)

Set the Variant calling quality criteria.

Parameters:

qcDryMet -

getQcDryMetLabel

public String getQcDryMetLabel()

Get tha label for enum QcDryMet.

getQcDryMetOptions

public List<ValueLabel> getQcDryMetOptions()

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

getQcDryUser

public NgsUser getQcDryUser()

Get the The user who checked if the quality score of the analysis was met.

Returns:

qcDryUser.

getQcDryUser

@Deprecated
public NgsUser getQcDryUser(Database db)

Deprecated.

setQcDryUser

public void setQcDryUser(NgsUser qcDryUser)

Set the The user who checked if the quality score of the analysis was met.

Parameters:

qcDryUser -

setQcDryUser_Id

public void setQcDryUser_Id(Integer qcDryUser_id)

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

setQcDryUser

public void setQcDryUser(Integer qcDryUser_id)

getQcDryUser_Id

public Integer getQcDryUser_Id()

getQcDryUser_UserName

public String getQcDryUser_UserName()

Get a pretty label UserName for cross reference QcDryUser to NgsUser.Id.

setQcDryUser_UserName

public void setQcDryUser_UserName(String qcDryUser_UserName)

Set a pretty label for cross reference QcDryUser to NgsUser.Id. Implies setQcDryUser(null) until save

getQcDryDate

public Date getQcDryDate()

Get the The date the QcWetUser selected the QcWetMet value.

Returns:

qcDryDate.

getQcDryDate

@Deprecated
public Date getQcDryDate(Database db)

Deprecated.

setQcDryDate

public void setQcDryDate(Date qcDryDate)

Set the The date the QcWetUser selected the QcWetMet value.

Parameters:

qcDryDate -

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 FlowcellLane.

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 FlowcellLane create(Tuple tuple)
                    throws Exception

Specified by:

create in interface Entity

Throws:

Exception

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object