org.molgenis.omx.xgap

Class ProbeSet

java.lang.Object

org.molgenis.data.support.AbstractEntity

org.molgenis.omx.observ.Characteristic

org.molgenis.omx.observ.ObservationTarget

org.molgenis.omx.xgap.ProbeSet

All Implemented Interfaces:

Serializable, Entity, Autoid, Identifiable, Locus

@Entity
public class ProbeSet
extends ObservationTarget
implements Entity, Locus

ProbeSet: A set of Probes. E.g. an Affymetrix probeset has multiple probes. It implements locus because sometimes you want to give the complete set of probes a range, for example: indicating that this set of probes spans basepair 0 through 10.000.000 on chromosome 3. The same information could arguably also be queried from the probes themselves, but if you have 40k probes, retrieving the same information from only ProbeSet (if annotated so) would be much faster..

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	BPEND
static String	BPSTART
static String	CHROMOSOME
static String	CM
static String	ENTITY_NAME
static String	ID
static String	SEQ
static String	SYMBOL

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

__TYPE, DESCRIPTION, IDENTIFIER, NAME

Constructor Summary

Constructors

Constructor and Description
ProbeSet()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object obj)
Object	get(String name) Generic getter.
Iterable<String>	getAttributeNames()
Long	getBpEnd() Get the numeric basepair postion (3') on the chromosome.
Long	getBpStart() Get the numeric basepair postion (5') on the chromosome.
Chromosome	getChromosome() Get the Reference to the chromosome this position belongs to..
Double	getCM() Get the genetic map position in centi morgan (cM)..
EntityMetaData	getEntityMetaData()
String	getEntityName()
Integer	getIdValue()
List<String>	getLabelAttributeNames()
String	getSeq() Get the The FASTA text representation of the sequence..
String	getSymbol() Get the todo.
int	hashCode()
void	set(Entity entity, boolean strict)
void	set(String attributeName, Object value)
void	setBpEnd(Long bpEnd) Set the numeric basepair postion (3') on the chromosome.
void	setBpStart(Long bpStart) Set the numeric basepair postion (5') on the chromosome.
void	setChromosome(Chromosome chromosome) Set the Reference to the chromosome this position belongs to..
void	setCM(Double cM) Set the genetic map position in centi morgan (cM)..
void	setSeq(String seq) Set the The FASTA text representation of the sequence..
void	setSymbol(String symbol) Set the todo.
String	toString()
String	toString(boolean verbose)

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

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

Methods inherited from class org.molgenis.data.support.AbstractEntity

getBoolean, getDate, getDouble, getEntities, getEntity, getInt, getIntList, getLabelValue, getList, getLong, getString, getTimestamp, getUtilDate, isObjectRepresentation, set, setValuesFromString

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.molgenis.data.Entity

getBoolean, getDate, getDouble, getEntities, getEntity, getInt, getIntList, getLabelValue, getList, getLong, getString, getTimestamp, getUtilDate, set

Field Detail

ENTITY_NAME

public static final String ENTITY_NAME

See Also:

Constant Field Values

CHROMOSOME

public static final String CHROMOSOME

See Also:

Constant Field Values

CM

public static final String CM

See Also:

Constant Field Values

BPSTART

public static final String BPSTART

See Also:

Constant Field Values

BPEND

public static final String BPEND

See Also:

Constant Field Values

SEQ

public static final String SEQ

See Also:

Constant Field Values

SYMBOL

public static final String SYMBOL

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

Constructor Detail

ProbeSet

public ProbeSet()

Method Detail

getEntityName

public String getEntityName()

Overrides:

getEntityName in class ObservationTarget

getChromosome

public Chromosome getChromosome()

Get the Reference to the chromosome this position belongs to..

Specified by:

getChromosome in interface Locus

Returns:

chromosome.

setChromosome

public void setChromosome(Chromosome chromosome)

Set the Reference to the chromosome this position belongs to..

Specified by:

setChromosome in interface Locus

Parameters:

chromosome -

getCM

public Double getCM()

Get the genetic map position in centi morgan (cM)..

Specified by:

getCM in interface Locus

Returns:

cM.

setCM

public void setCM(Double cM)

Set the genetic map position in centi morgan (cM)..

Specified by:

setCM in interface Locus

Parameters:

cM -

getBpStart

public Long getBpStart()

Get the numeric basepair postion (5') on the chromosome.

Specified by:

getBpStart in interface Locus

Returns:

bpStart.

setBpStart

public void setBpStart(Long bpStart)

Set the numeric basepair postion (5') on the chromosome.

Specified by:

setBpStart in interface Locus

Parameters:

bpStart -

getBpEnd

public Long getBpEnd()

Get the numeric basepair postion (3') on the chromosome.

Specified by:

getBpEnd in interface Locus

Returns:

bpEnd.

setBpEnd

public void setBpEnd(Long bpEnd)

Set the numeric basepair postion (3') on the chromosome.

Specified by:

setBpEnd in interface Locus

Parameters:

bpEnd -

getSeq

public String getSeq()

Get the The FASTA text representation of the sequence..

Specified by:

getSeq in interface Locus

Returns:

seq.

setSeq

public void setSeq(String seq)

Set the The FASTA text representation of the sequence..

Specified by:

setSeq in interface Locus

Parameters:

seq -

getSymbol

public String getSymbol()

Get the todo.

Specified by:

getSymbol in interface Locus

Returns:

symbol.

setSymbol

public void setSymbol(String symbol)

Set the todo.

Specified by:

setSymbol in interface Locus

Parameters:

symbol -

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 ObservationTarget

set

public void set(Entity entity,
       boolean strict)

Specified by:

set in interface Entity

Overrides:

set in class ObservationTarget

toString

public String toString()

Overrides:

toString in class ObservationTarget

toString

public String toString(boolean verbose)

Overrides:

toString in class ObservationTarget

getIdValue

public Integer getIdValue()

Specified by:

getIdValue in interface Entity

Overrides:

getIdValue in class ObservationTarget

getAttributeNames

public Iterable<String> getAttributeNames()

Specified by:

getAttributeNames in interface Entity

Overrides:

getAttributeNames in class ObservationTarget

getLabelAttributeNames

public List<String> getLabelAttributeNames()

Specified by:

getLabelAttributeNames in interface Entity

Overrides:

getLabelAttributeNames in class ObservationTarget

set

public void set(String attributeName,
       Object value)

Specified by:

set in interface Entity

Overrides:

set in class ObservationTarget

equals

public boolean equals(Object obj)

Overrides:

equals in class ObservationTarget

hashCode

public int hashCode()

Overrides:

hashCode in class ObservationTarget

getEntityMetaData

public EntityMetaData getEntityMetaData()

Specified by:

getEntityMetaData in interface Entity

Overrides:

getEntityMetaData in class ObservationTarget