org.molgenis.omx.xgap

Class Spot

java.lang.Object

org.molgenis.util.AbstractEntity

org.molgenis.omx.observ.Characteristic

org.molgenis.omx.observ.ObservationTarget

org.molgenis.omx.xgap.Probe

org.molgenis.omx.xgap.Spot

All Implemented Interfaces:

Serializable, Autoid, Identifiable, Locus, Entity

@Entity
public class Spot
extends Probe

Spot: This is the spot on a microarray.
Note: We don't distinquish between probes (the sequence) and spots (the sequence as spotted on the array). .

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	GRIDX
static String	GRIDY
static String	ID
static String	X
static String	Y

Fields inherited from class org.molgenis.omx.xgap.Probe

BPEND, BPSTART, CHROMOSOME, CHROMOSOME_IDENTIFIER, CM, MISMATCH, PROBESET, PROBESET_IDENTIFIER, REPORTSFOR, REPORTSFOR_IDENTIFIER, SEQ, SYMBOL

Fields inherited from class org.molgenis.omx.observ.Characteristic

__TYPE, DESCRIPTION, IDENTIFIER, NAME

Constructor Summary

Constructors

Constructor and Description
Spot()
Spot(Spot copyMe) copy constructor

Method Summary

Methods

Modifier and Type	Method and Description
Spot	create(Entity entity)
boolean	equals(Object obj)
static List<? extends Spot>	find(Database db, QueryRule... rules) Shorthand for db.find(Spot.class, org.molgenis.framework.db.QueryRule ...
static Spot	findById(Database db, Integer id)
static Spot	findByIdentifier(Database db, String identifier)
static Spot	findByXYGridXGridY(Database db, Integer x, Integer y, Integer gridX, Integer gridY)
Object	get(String name) Generic getter.
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of Spot.
String	getFields(String sep) Deprecated.
Integer	getGridX() Get the Meta Row.
Integer	getGridX(Database db) Deprecated.
Integer	getGridY() Get the Meta Column.
Integer	getGridY(Database db) Deprecated.
String	getIdField()
Object	getIdValue()
List<String>	getLabelFields()
String	getValues(String sep) Deprecated.
Integer	getX() Get the Row.
Integer	getX(Database db) Deprecated.
String	getXrefIdFieldName(String fieldName)
Integer	getY() Get the Column.
Integer	getY(Database db) Deprecated.
int	hashCode()
static Query<? extends Spot>	query(Database db) Shorthand for db.query(Spot.class).
void	set(Entity entity, boolean strict)
void	setGridX(Integer gridX) Set the Meta Row.
void	setGridY(Integer gridY) Set the Meta Column.
void	setX(Integer x) Set the Row.
void	setY(Integer y) Set the Column.
String	toString()
String	toString(boolean verbose)
void	validate()

Methods inherited from class org.molgenis.omx.xgap.Probe

getBpEnd, getBpEnd, getBpStart, getBpStart, getChromosome_Id, getChromosome_Identifier, getChromosome, getChromosome, getCM, getCM, getMismatch, getMismatch, getProbeSet_Id, getProbeSet_Identifier, getProbeSet, getProbeSet, getReportsFor_Id, getReportsFor_Identifier, getReportsFor, getReportsFor, getSeq, getSeq, getSymbol, getSymbol, setBpEnd, setBpStart, setChromosome_Id, setChromosome_Identifier, setChromosome, setChromosome, setCM, setMismatch, setProbeSet_Id, setProbeSet_Identifier, setProbeSet, setProbeSet, setReportsFor_Id, setReportsFor_Identifier, setReportsFor, setReportsFor, setSeq, setSymbol

Methods inherited from class org.molgenis.omx.observ.Characteristic

get__Type, get__Type, get__TypeLabel, get__TypeOptions, getDescription, getDescription, getId, getIdentifier, getIdentifier, getName, getName, getValueMrefValueCollection, getValueMrefValueCollection, set__Type, setDescription, setId, setIdentifier, setName, setValueMrefValueCollection

Methods inherited from class org.molgenis.util.AbstractEntity

getLabelValue, getValues, isObjectRepresentation, isReadonly, 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

X

public static final String X

See Also:

Constant Field Values

Y

public static final String Y

See Also:

Constant Field Values

GRIDX

public static final String GRIDX

See Also:

Constant Field Values

GRIDY

public static final String GRIDY

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

Constructor Detail

Spot

public Spot()

Spot

public Spot(Spot copyMe)
     throws Exception

copy constructor

Throws:

Exception

Method Detail

query

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

Shorthand for db.query(Spot.class).

find

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

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

Throws:

DatabaseException

findById

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

Throws:

DatabaseException

findByIdentifier

public static Spot findByIdentifier(Database db,
                    String identifier)
                             throws DatabaseException

Throws:

DatabaseException

findByXYGridXGridY

public static Spot findByXYGridXGridY(Database db,
                      Integer x,
                      Integer y,
                      Integer gridX,
                      Integer gridY)
                               throws DatabaseException

Throws:

DatabaseException

getX

public Integer getX()

Get the Row.

Returns:

x.

getX

@Deprecated
public Integer getX(Database db)

Deprecated.

setX

public void setX(Integer x)

Set the Row.

Parameters:

x -

getY

public Integer getY()

Get the Column.

Returns:

y.

getY

@Deprecated
public Integer getY(Database db)

Deprecated.

setY

public void setY(Integer y)

Set the Column.

Parameters:

y -

getGridX

public Integer getGridX()

Get the Meta Row.

Returns:

gridX.

getGridX

@Deprecated
public Integer getGridX(Database db)

Deprecated.

setGridX

public void setGridX(Integer gridX)

Set the Meta Row.

Parameters:

gridX -

getGridY

public Integer getGridY()

Get the Meta Column.

Returns:

gridY.

getGridY

@Deprecated
public Integer getGridY(Database db)

Deprecated.

setGridY

public void setGridY(Integer gridY)

Set the Meta Column.

Parameters:

gridY -

get

public Object get(String name)

Generic getter. Get the property by using the name.

Specified by:

get in interface Entity

Overrides:

get in class Probe

validate

public void validate()
              throws DatabaseException

Specified by:

validate in interface Entity

Overrides:

validate in class Probe

Throws:

DatabaseException

set

public void set(Entity entity,
       boolean strict)
         throws Exception

Specified by:

set in interface Entity

Overrides:

set in class Probe

Throws:

Exception

toString

public String toString()

Overrides:

toString in class Probe

toString

public String toString(boolean verbose)

Overrides:

toString in class Probe

getFields

public Vector<String> getFields(boolean skipAutoIds)

Get the names of all public properties of Spot.

Specified by:

getFields in interface Entity

Overrides:

getFields in class Probe

getFields

public Vector<String> getFields()

Specified by:

getFields in interface Entity

Overrides:

getFields in class Probe

getIdField

public String getIdField()

Specified by:

getIdField in interface Entity

Overrides:

getIdField in class Probe

getLabelFields

public List<String> getLabelFields()

Specified by:

getLabelFields in interface Entity

Overrides:

getLabelFields in class Probe

getFields

@Deprecated
public String getFields(String sep)

Deprecated.

Specified by:

getFields in interface Entity

Overrides:

getFields in class Probe

getIdValue

public Object getIdValue()

Specified by:

getIdValue in interface Entity

Overrides:

getIdValue in class Probe

getXrefIdFieldName

public String getXrefIdFieldName(String fieldName)

Specified by:

getXrefIdFieldName in interface Entity

Overrides:

getXrefIdFieldName in class Probe

getValues

@Deprecated
public String getValues(String sep)

Deprecated.

Specified by:

getValues in interface Entity

Overrides:

getValues in class Probe

create

public Spot create(Entity entity)
            throws Exception

Specified by:

create in interface Entity

Overrides:

create in class Probe

Throws:

Exception

equals

public boolean equals(Object obj)

Overrides:

equals in class Probe

hashCode

public int hashCode()

Overrides:

hashCode in class Probe