org.molgenis.omx.xgap

Class Gene

java.lang.Object

org.molgenis.util.AbstractEntity

org.molgenis.omx.observ.Characteristic

org.molgenis.omx.observ.ObservationTarget

org.molgenis.omx.xgap.Gene

All Implemented Interfaces:

Serializable, Autoid, Identifiable, Locus, Entity

@Entity
public class Gene
extends ObservationTarget
implements Locus

Gene: Trait annotations specific for genes..

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	CHROMOSOME_IDENTIFIER
static String	CM
static String	CONTROL
static String	ID
static String	ORIENTATION
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
Gene()
Gene(Gene copyMe) copy constructor

Method Summary

Methods

Modifier and Type	Method and Description
Gene	create(Entity entity)
boolean	equals(Object obj)
static List<? extends Gene>	find(Database db, QueryRule... rules) Shorthand for db.find(Gene.class, org.molgenis.framework.db.QueryRule ...
static Gene	findById(Database db, Integer id)
static Gene	findByIdentifier(Database db, String identifier)
Object	get(String name) Generic getter.
Long	getBpEnd() Get the numeric basepair postion (3') on the chromosome.
Long	getBpEnd(Database db) Deprecated.
Long	getBpStart() Get the numeric basepair postion (5') on the chromosome.
Long	getBpStart(Database db) Deprecated.
Integer	getChromosome_Id()
String	getChromosome_Identifier() Get a pretty label Identifier for cross reference Chromosome to Chromosome.Id.
Chromosome	getChromosome() Get the Reference to the chromosome this position belongs to..
Chromosome	getChromosome(Database db) Deprecated.
Double	getCM() Get the genetic map position in centi morgan (cM)..
Double	getCM(Database db) Deprecated.
Boolean	getControl() Get the Indicating whether this is a 'housekeeping' gene that can be used as control..
Boolean	getControl(Database db) Deprecated.
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of Gene.
String	getFields(String sep) Deprecated.
String	getIdField()
Object	getIdValue()
List<String>	getLabelFields()
String	getOrientation() Get the Orientation of the gene on the genome (F=forward, R=reverse).
String	getOrientation(Database db) Deprecated.
String	getOrientationLabel() Get tha label for enum Orientation.
List<ValueLabel>	getOrientationOptions() Orientation is enum.
String	getSeq() Get the The FASTA text representation of the sequence..
String	getSeq(Database db) Deprecated.
String	getSymbol() Get the Main symbol this gene is known by (not necessarily unique, in constrast to 'name').
String	getSymbol(Database db) Deprecated.
String	getValues(String sep) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends Gene>	query(Database db) Shorthand for db.query(Gene.class).
void	set(Entity entity, boolean strict)
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_Id(Integer chromosome_id) Set foreign key for field chromosome.
void	setChromosome_Identifier(String chromosome_Identifier) Set a pretty label for cross reference Chromosome to Chromosome.Id.
void	setChromosome(Chromosome chromosome) Set the Reference to the chromosome this position belongs to..
void	setChromosome(Integer chromosome_id)
void	setCM(Double cM) Set the genetic map position in centi morgan (cM)..
void	setControl(Boolean control) Set the Indicating whether this is a 'housekeeping' gene that can be used as control..
void	setOrientation(String orientation) Set the Orientation of the gene on the genome (F=forward, R=reverse).
void	setSeq(String seq) Set the The FASTA text representation of the sequence..
void	setSymbol(String symbol) Set the Main symbol this gene is known by (not necessarily unique, in constrast to 'name').
String	toString()
String	toString(boolean verbose)
void	validate()

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

CHROMOSOME

public static final String CHROMOSOME

See Also:

Constant Field Values

CHROMOSOME_IDENTIFIER

public static final String CHROMOSOME_IDENTIFIER

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

ORIENTATION

public static final String ORIENTATION

See Also:

Constant Field Values

CONTROL

public static final String CONTROL

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

Constructor Detail

Gene

public Gene()

Gene

public Gene(Gene copyMe)
     throws Exception

copy constructor

Throws:

Exception

Method Detail

query

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

Shorthand for db.query(Gene.class).

find

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

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

Throws:

DatabaseException

findById

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

Throws:

DatabaseException

findByIdentifier

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

Throws:

DatabaseException

getChromosome

public Chromosome getChromosome()

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

Specified by:

getChromosome in interface Locus

Returns:

chromosome.

getChromosome

@Deprecated
public Chromosome getChromosome(Database db)

Deprecated.

setChromosome

public void setChromosome(Chromosome chromosome)

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

Specified by:

setChromosome in interface Locus

Parameters:

chromosome -

setChromosome_Id

public void setChromosome_Id(Integer chromosome_id)

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

Specified by:

setChromosome_Id in interface Locus

setChromosome

public void setChromosome(Integer chromosome_id)

getChromosome_Id

public Integer getChromosome_Id()

Specified by:

getChromosome_Id in interface Locus

getChromosome_Identifier

public String getChromosome_Identifier()

Get a pretty label Identifier for cross reference Chromosome to Chromosome.Id.

Specified by:

getChromosome_Identifier in interface Locus

setChromosome_Identifier

public void setChromosome_Identifier(String chromosome_Identifier)

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

Specified by:

setChromosome_Identifier in interface Locus

getCM

public Double getCM()

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

Specified by:

getCM in interface Locus

Returns:

cM.

getCM

@Deprecated
public Double getCM(Database db)

Deprecated.

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.

getBpStart

@Deprecated
public Long getBpStart(Database db)

Deprecated.

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.

getBpEnd

@Deprecated
public Long getBpEnd(Database db)

Deprecated.

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.

getSeq

@Deprecated
public String getSeq(Database db)

Deprecated.

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 Main symbol this gene is known by (not necessarily unique, in constrast to 'name').

Specified by:

getSymbol in interface Locus

Returns:

symbol.

getSymbol

@Deprecated
public String getSymbol(Database db)

Deprecated.

setSymbol

public void setSymbol(String symbol)

Set the Main symbol this gene is known by (not necessarily unique, in constrast to 'name').

Specified by:

setSymbol in interface Locus

Parameters:

symbol -

getOrientation

public String getOrientation()

Get the Orientation of the gene on the genome (F=forward, R=reverse).

Returns:

orientation.

getOrientation

@Deprecated
public String getOrientation(Database db)

Deprecated.

setOrientation

public void setOrientation(String orientation)

Set the Orientation of the gene on the genome (F=forward, R=reverse).

Parameters:

orientation -

getOrientationLabel

public String getOrientationLabel()

Get tha label for enum Orientation.

getOrientationOptions

public List<ValueLabel> getOrientationOptions()

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

getControl

public Boolean getControl()

Get the Indicating whether this is a 'housekeeping' gene that can be used as control..

Returns:

control.

getControl

@Deprecated
public Boolean getControl(Database db)

Deprecated.

setControl

public void setControl(Boolean control)

Set the Indicating whether this is a 'housekeeping' gene that can be used as control..

Parameters:

control -

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

validate

public void validate()
              throws DatabaseException

Specified by:

validate in interface Entity

Overrides:

validate in class ObservationTarget

Throws:

DatabaseException

set

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

Specified by:

set in interface Entity

Overrides:

set in class ObservationTarget

Throws:

Exception

toString

public String toString()

Overrides:

toString in class ObservationTarget

toString

public String toString(boolean verbose)

Overrides:

toString in class ObservationTarget

getFields

public Vector<String> getFields(boolean skipAutoIds)

Get the names of all public properties of Gene.

Specified by:

getFields in interface Entity

Overrides:

getFields in class ObservationTarget

getFields

public Vector<String> getFields()

Specified by:

getFields in interface Entity

Overrides:

getFields in class ObservationTarget

getIdField

public String getIdField()

Specified by:

getIdField in interface Entity

Overrides:

getIdField in class ObservationTarget

getLabelFields

public List<String> getLabelFields()

Specified by:

getLabelFields in interface Entity

Overrides:

getLabelFields in class ObservationTarget

getFields

@Deprecated
public String getFields(String sep)

Deprecated.

Specified by:

getFields in interface Entity

Overrides:

getFields in class ObservationTarget

getIdValue

public Object getIdValue()

Specified by:

getIdValue in interface Entity

Overrides:

getIdValue in class ObservationTarget

getXrefIdFieldName

public String getXrefIdFieldName(String fieldName)

Specified by:

getXrefIdFieldName in interface Entity

Overrides:

getXrefIdFieldName in class ObservationTarget

getValues

@Deprecated
public String getValues(String sep)

Deprecated.

Specified by:

getValues in interface Entity

Overrides:

getValues in class ObservationTarget

create

public Gene create(Entity entity)
            throws Exception

Specified by:

create in interface Entity

Overrides:

create in class ObservationTarget

Throws:

Exception

equals

public boolean equals(Object obj)

Overrides:

equals in class ObservationTarget

hashCode

public int hashCode()

Overrides:

hashCode in class ObservationTarget