org.molgenis.omx.patient

Class Patient

java.lang.Object

org.molgenis.util.AbstractEntity

org.molgenis.omx.observ.Characteristic

org.molgenis.omx.observ.ObservationTarget

org.molgenis.omx.observ.target.Individual

org.molgenis.omx.patient.Patient

All Implemented Interfaces:

Serializable, Autoid, Identifiable, Entity

@Entity
public class Patient
extends Individual

Patient: .

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	ALLELE1
static String	ALLELE1_IDENTIFIER
static String	ALLELE2
static String	ALLELE2_IDENTIFIER
static String	ID
static String	PHENO
static String	PUBMEDID
static String	REFERENCE

Fields inherited from class org.molgenis.omx.observ.target.Individual

FATHER, FATHER_IDENTIFIER, MOTHER, MOTHER_IDENTIFIER

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

__TYPE, DESCRIPTION, IDENTIFIER, NAME

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
Patient	create(Entity entity)
boolean	equals(Object obj)
static List<? extends Patient>	find(Database db, QueryRule... rules) Shorthand for db.find(Patient.class, org.molgenis.framework.db.QueryRule ...
static Patient	findById(Database db, Integer id)
static Patient	findByIdentifier(Database db, String identifier)
Object	get(String name) Generic getter.
Integer	getAllele1_Id()
String	getAllele1_Identifier() Get a pretty label Identifier for cross reference Allele1 to Variant.Id.
Variant	getAllele1() Get the Allele1.
Variant	getAllele1(Database db) Deprecated.
Integer	getAllele2_Id()
String	getAllele2_Identifier() Get a pretty label Identifier for cross reference Allele2 to Variant.Id.
Variant	getAllele2() Get the Allele2.
Variant	getAllele2(Database db) Deprecated.
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of Patient.
String	getFields(String sep) Deprecated.
String	getIdField()
Object	getIdValue()
List<String>	getLabelFields()
String	getPheno() Get the Pheno.
String	getPheno(Database db) Deprecated.
String	getPubMedID() Get the PubMedID.
String	getPubMedID(Database db) Deprecated.
String	getReference() Get the Reference.
String	getReference(Database db) Deprecated.
String	getValues(String sep) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends Patient>	query(Database db) Shorthand for db.query(Patient.class).
void	set(Entity entity, boolean strict)
void	setAllele1_Id(Integer allele1_id) Set foreign key for field allele1.
void	setAllele1_Identifier(String allele1_Identifier) Set a pretty label for cross reference Allele1 to Variant.Id.
void	setAllele1(Integer allele1_id)
void	setAllele1(Variant allele1) Set the Allele1.
void	setAllele2_Id(Integer allele2_id) Set foreign key for field allele2.
void	setAllele2_Identifier(String allele2_Identifier) Set a pretty label for cross reference Allele2 to Variant.Id.
void	setAllele2(Integer allele2_id)
void	setAllele2(Variant allele2) Set the Allele2.
void	setPheno(String pheno) Set the Pheno.
void	setPubMedID(String pubMedID) Set the PubMedID.
void	setReference(String reference) Set the Reference.
String	toString()
String	toString(boolean verbose)
void	validate()

Methods inherited from class org.molgenis.omx.observ.target.Individual

getFather_Id, getFather_Identifier, getFather, getFather, getIndividualsPanelCollection, getIndividualsPanelCollection, getMother_Id, getMother_Identifier, getMother, getMother, setFather_Id, setFather_Identifier, setFather, setFather, setIndividualsPanelCollection, setMother_Id, setMother_Identifier, setMother, setMother

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

ALLELE1

public static final String ALLELE1

See Also:

Constant Field Values

ALLELE1_IDENTIFIER

public static final String ALLELE1_IDENTIFIER

See Also:

Constant Field Values

ALLELE2

public static final String ALLELE2

See Also:

Constant Field Values

ALLELE2_IDENTIFIER

public static final String ALLELE2_IDENTIFIER

See Also:

Constant Field Values

PHENO

public static final String PHENO

See Also:

Constant Field Values

PUBMEDID

public static final String PUBMEDID

See Also:

Constant Field Values

REFERENCE

public static final String REFERENCE

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

Constructor Detail

Patient

public Patient()

Patient

public Patient(Patient copyMe)
        throws Exception

copy constructor

Throws:

Exception

Method Detail

query

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

Shorthand for db.query(Patient.class).

find

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

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

Throws:

DatabaseException

findById

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

Throws:

DatabaseException

findByIdentifier

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

Throws:

DatabaseException

getAllele1

public Variant getAllele1()

Get the Allele1.

Returns:

allele1.

getAllele1

@Deprecated
public Variant getAllele1(Database db)

Deprecated.

setAllele1

public void setAllele1(Variant allele1)

Set the Allele1.

Parameters:

allele1 -

setAllele1_Id

public void setAllele1_Id(Integer allele1_id)

Set foreign key for field allele1. This will erase any foreign key objects currently set. FIXME: can we autoload the new object?

setAllele1

public void setAllele1(Integer allele1_id)

getAllele1_Id

public Integer getAllele1_Id()

getAllele1_Identifier

public String getAllele1_Identifier()

Get a pretty label Identifier for cross reference Allele1 to Variant.Id.

setAllele1_Identifier

public void setAllele1_Identifier(String allele1_Identifier)

Set a pretty label for cross reference Allele1 to Variant.Id. Implies setAllele1(null) until save

getAllele2

public Variant getAllele2()

Get the Allele2.

Returns:

allele2.

getAllele2

@Deprecated
public Variant getAllele2(Database db)

Deprecated.

setAllele2

public void setAllele2(Variant allele2)

Set the Allele2.

Parameters:

allele2 -

setAllele2_Id

public void setAllele2_Id(Integer allele2_id)

Set foreign key for field allele2. This will erase any foreign key objects currently set. FIXME: can we autoload the new object?

setAllele2

public void setAllele2(Integer allele2_id)

getAllele2_Id

public Integer getAllele2_Id()

getAllele2_Identifier

public String getAllele2_Identifier()

Get a pretty label Identifier for cross reference Allele2 to Variant.Id.

setAllele2_Identifier

public void setAllele2_Identifier(String allele2_Identifier)

Set a pretty label for cross reference Allele2 to Variant.Id. Implies setAllele2(null) until save

getPheno

public String getPheno()

Get the Pheno.

Returns:

pheno.

getPheno

@Deprecated
public String getPheno(Database db)

Deprecated.

setPheno

public void setPheno(String pheno)

Set the Pheno.

Parameters:

pheno -

getPubMedID

public String getPubMedID()

Get the PubMedID.

Returns:

pubMedID.

getPubMedID

@Deprecated
public String getPubMedID(Database db)

Deprecated.

setPubMedID

public void setPubMedID(String pubMedID)

Set the PubMedID.

Parameters:

pubMedID -

getReference

public String getReference()

Get the Reference.

Returns:

reference.

getReference

@Deprecated
public String getReference(Database db)

Deprecated.

setReference

public void setReference(String reference)

Set the Reference.

Parameters:

reference -

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 Individual

validate

public void validate()
              throws DatabaseException

Specified by:

validate in interface Entity

Overrides:

validate in class Individual

Throws:

DatabaseException

set

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

Specified by:

set in interface Entity

Overrides:

set in class Individual

Throws:

Exception

toString

public String toString()

Overrides:

toString in class Individual

toString

public String toString(boolean verbose)

Overrides:

toString in class Individual

getFields

public Vector<String> getFields(boolean skipAutoIds)

Get the names of all public properties of Patient.

Specified by:

getFields in interface Entity

Overrides:

getFields in class Individual

getFields

public Vector<String> getFields()

Specified by:

getFields in interface Entity

Overrides:

getFields in class Individual

getIdField

public String getIdField()

Specified by:

getIdField in interface Entity

Overrides:

getIdField in class Individual

getLabelFields

public List<String> getLabelFields()

Specified by:

getLabelFields in interface Entity

Overrides:

getLabelFields in class Individual

getFields

@Deprecated
public String getFields(String sep)

Deprecated.

Specified by:

getFields in interface Entity

Overrides:

getFields in class Individual

getIdValue

public Object getIdValue()

Specified by:

getIdValue in interface Entity

Overrides:

getIdValue in class Individual

getXrefIdFieldName

public String getXrefIdFieldName(String fieldName)

Specified by:

getXrefIdFieldName in interface Entity

Overrides:

getXrefIdFieldName in class Individual

getValues

@Deprecated
public String getValues(String sep)

Deprecated.

Specified by:

getValues in interface Entity

Overrides:

getValues in class Individual

create

public Patient create(Entity entity)
               throws Exception

Specified by:

create in interface Entity

Overrides:

create in class Individual

Throws:

Exception

equals

public boolean equals(Object obj)

Overrides:

equals in class Individual

hashCode

public int hashCode()

Overrides:

hashCode in class Individual