org.molgenis.omx.xgap

Class Protein

java.lang.Object

org.molgenis.util.AbstractEntity

org.molgenis.omx.observ.Characteristic

org.molgenis.omx.observ.ObservationTarget

org.molgenis.omx.xgap.Protein

All Implemented Interfaces:

Serializable, Autoid, Identifiable, Entity

@Entity
public class Protein
extends ObservationTarget

Protein: Trait annotations specific for proteins..

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	AMINOSEQUENCE
static String	GENE
static String	GENE_IDENTIFIER
static String	ID
static String	MASS
static String	TRANSCRIPT
static String	TRANSCRIPT_IDENTIFIER

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

__TYPE, DESCRIPTION, IDENTIFIER, NAME

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
Protein	create(Entity entity)
boolean	equals(Object obj)
static List<? extends Protein>	find(Database db, QueryRule... rules) Shorthand for db.find(Protein.class, org.molgenis.framework.db.QueryRule ...
static Protein	findById(Database db, Integer id)
static Protein	findByIdentifier(Database db, String identifier)
Object	get(String name) Generic getter.
String	getAminoSequence() Get the The aminoacid sequence..
String	getAminoSequence(Database db) Deprecated.
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of Protein.
String	getFields(String sep) Deprecated.
Integer	getGene_Id()
String	getGene_Identifier() Get a pretty label Identifier for cross reference Gene to Gene.Id.
Gene	getGene() Get the The gene that produces this protein.
Gene	getGene(Database db) Deprecated.
String	getIdField()
Object	getIdValue()
List<String>	getLabelFields()
Double	getMass() Get the The mass of this metabolite.
Double	getMass(Database db) Deprecated.
Integer	getTranscript_Id()
String	getTranscript_Identifier() Get a pretty label Identifier for cross reference Transcript to Transcript.Id.
Transcript	getTranscript() Get the The transcript variant that produces this protein.
Transcript	getTranscript(Database db) Deprecated.
String	getValues(String sep) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends Protein>	query(Database db) Shorthand for db.query(Protein.class).
void	set(Entity entity, boolean strict)
void	setAminoSequence(String aminoSequence) Set the The aminoacid sequence..
void	setGene_Id(Integer gene_id) Set foreign key for field gene.
void	setGene_Identifier(String gene_Identifier) Set a pretty label for cross reference Gene to Gene.Id.
void	setGene(Gene gene) Set the The gene that produces this protein.
void	setGene(Integer gene_id)
void	setMass(Double mass) Set the The mass of this metabolite.
void	setTranscript_Id(Integer transcript_id) Set foreign key for field transcript.
void	setTranscript_Identifier(String transcript_Identifier) Set a pretty label for cross reference Transcript to Transcript.Id.
void	setTranscript(Integer transcript_id)
void	setTranscript(Transcript transcript) Set the The transcript variant that produces this protein.
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

GENE

public static final String GENE

See Also:

Constant Field Values

GENE_IDENTIFIER

public static final String GENE_IDENTIFIER

See Also:

Constant Field Values

TRANSCRIPT

public static final String TRANSCRIPT

See Also:

Constant Field Values

TRANSCRIPT_IDENTIFIER

public static final String TRANSCRIPT_IDENTIFIER

See Also:

Constant Field Values

AMINOSEQUENCE

public static final String AMINOSEQUENCE

See Also:

Constant Field Values

MASS

public static final String MASS

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

Constructor Detail

Protein

public Protein()

Protein

public Protein(Protein copyMe)
        throws Exception

copy constructor

Throws:

Exception

Method Detail

query

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

Shorthand for db.query(Protein.class).

find

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

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

Throws:

DatabaseException

findById

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

Throws:

DatabaseException

findByIdentifier

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

Throws:

DatabaseException

getGene

public Gene getGene()

Get the The gene that produces this protein.

Returns:

gene.

getGene

@Deprecated
public Gene getGene(Database db)

Deprecated.

setGene

public void setGene(Gene gene)

Set the The gene that produces this protein.

Parameters:

gene -

setGene_Id

public void setGene_Id(Integer gene_id)

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

setGene

public void setGene(Integer gene_id)

getGene_Id

public Integer getGene_Id()

getGene_Identifier

public String getGene_Identifier()

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

setGene_Identifier

public void setGene_Identifier(String gene_Identifier)

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

getTranscript

public Transcript getTranscript()

Get the The transcript variant that produces this protein.

Returns:

transcript.

getTranscript

@Deprecated
public Transcript getTranscript(Database db)

Deprecated.

setTranscript

public void setTranscript(Transcript transcript)

Set the The transcript variant that produces this protein.

Parameters:

transcript -

setTranscript_Id

public void setTranscript_Id(Integer transcript_id)

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

setTranscript

public void setTranscript(Integer transcript_id)

getTranscript_Id

public Integer getTranscript_Id()

getTranscript_Identifier

public String getTranscript_Identifier()

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

setTranscript_Identifier

public void setTranscript_Identifier(String transcript_Identifier)

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

getAminoSequence

public String getAminoSequence()

Get the The aminoacid sequence..

Returns:

aminoSequence.

getAminoSequence

@Deprecated
public String getAminoSequence(Database db)

Deprecated.

setAminoSequence

public void setAminoSequence(String aminoSequence)

Set the The aminoacid sequence..

Parameters:

aminoSequence -

getMass

public Double getMass()

Get the The mass of this metabolite.

Returns:

mass.

getMass

@Deprecated
public Double getMass(Database db)

Deprecated.

setMass

public void setMass(Double mass)

Set the The mass of this metabolite.

Parameters:

mass -

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 Protein.

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 Protein 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