@Entity public class Marker extends ObservationTarget implements Locus
| Modifier and Type | Field and Description |
|---|---|
static String |
BPEND |
static String |
BPSTART |
static String |
CHROMOSOME |
static String |
CHROMOSOME_IDENTIFIER |
static String |
CM |
static String |
ID |
static String |
REPORTSFOR |
static String |
REPORTSFOR_IDENTIFIER |
static String |
SEQ |
static String |
SYMBOL |
__TYPE, DESCRIPTION, IDENTIFIER, NAME| Constructor and Description |
|---|
Marker() |
Marker(Marker copyMe)
copy constructor
|
| Modifier and Type | Method and Description |
|---|---|
Marker |
create(Entity entity) |
boolean |
equals(Object obj) |
static List<? extends Marker> |
find(Database db,
QueryRule... rules)
Shorthand for db.find(Marker.class, org.molgenis.framework.db.QueryRule ...
|
static Marker |
findById(Database db,
Integer id) |
static Marker |
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.
|
Vector<String> |
getFields() |
Vector<String> |
getFields(boolean skipAutoIds)
Get the names of all public properties of Marker.
|
String |
getFields(String sep)
Deprecated.
|
String |
getIdField() |
Object |
getIdValue() |
List<String> |
getLabelFields() |
List<Integer> |
getReportsFor_Id() |
List<String> |
getReportsFor_Identifier()
Get a pretty label for cross reference ReportsFor to Marker.Id.
|
List<Marker> |
getReportsFor()
Get the The marker (or a subclass like 'SNP') this marker (or a subclass like 'SNP') reports for..
|
List<Marker> |
getReportsFor(Database db)
Deprecated.
|
Collection<Marker> |
getReportsForMarkerCollection() |
Collection<Marker> |
getReportsForMarkerCollection(Database db) |
String |
getSeq()
Get the The FASTA text representation of the sequence..
|
String |
getSeq(Database db)
Deprecated.
|
String |
getSymbol()
Get the todo.
|
String |
getSymbol(Database db)
Deprecated.
|
String |
getValues(String sep)
Deprecated.
|
String |
getXrefIdFieldName(String fieldName) |
int |
hashCode() |
static Query<? extends Marker> |
query(Database db)
Shorthand for db.query(Marker.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 |
setReportsFor_Id(Integer... reportsFor) |
void |
setReportsFor_Id(List<Integer> reportsFor_id)
Set foreign key for field reportsFor.
|
void |
setReportsFor_Identifier(List<String> reportsFor_Identifier)
Update the foreign key ReportsFor
This sets reportsFor to null until next database transaction.
|
void |
setReportsFor(List<Marker> reportsFor)
Set the The marker (or a subclass like 'SNP') this marker (or a subclass like 'SNP') reports for..
|
void |
setReportsFor(Marker... reportsFor) |
void |
setReportsForMarkerCollection(Collection<Marker> collection) |
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) |
void |
validate() |
get__Type, get__Type, get__TypeLabel, get__TypeOptions, getDescription, getDescription, getId, getIdentifier, getIdentifier, getName, getName, getValueMrefValueCollection, getValueMrefValueCollection, set__Type, setDescription, setId, setIdentifier, setName, setValueMrefValueCollectiongetLabelValue, getValues, isObjectRepresentation, isReadonly, set, set, setReadonly, setValuesFromString, string2dateclone, finalize, getClass, notify, notifyAll, wait, wait, waitgetLabelValue, getValues, isReadonly, set, set, setReadonlypublic static final String CHROMOSOME
public static final String CHROMOSOME_IDENTIFIER
public static final String CM
public static final String BPSTART
public static final String BPEND
public static final String SEQ
public static final String SYMBOL
public static final String REPORTSFOR
public static final String REPORTSFOR_IDENTIFIER
public static final String ID
public static Query<? extends Marker> query(Database db)
public static List<? extends Marker> find(Database db, QueryRule... rules) throws DatabaseException
DatabaseExceptionpublic static Marker findById(Database db, Integer id) throws DatabaseException
DatabaseExceptionpublic static Marker findByIdentifier(Database db, String identifier) throws DatabaseException
DatabaseExceptionpublic Chromosome getChromosome()
getChromosome in interface Locus@Deprecated public Chromosome getChromosome(Database db)
public void setChromosome(Chromosome chromosome)
setChromosome in interface Locuschromosome - public void setChromosome_Id(Integer chromosome_id)
setChromosome_Id in interface Locuspublic void setChromosome(Integer chromosome_id)
public Integer getChromosome_Id()
getChromosome_Id in interface Locuspublic String getChromosome_Identifier()
getChromosome_Identifier in interface Locuspublic void setChromosome_Identifier(String chromosome_Identifier)
setChromosome_Identifier in interface Locuspublic Double getCM()
@Deprecated public Double getCM(Database db)
public void setCM(Double cM)
public Long getBpStart()
getBpStart in interface Locus@Deprecated public Long getBpStart(Database db)
public void setBpStart(Long bpStart)
setBpStart in interface LocusbpStart - public Long getBpEnd()
@Deprecated public Long getBpEnd(Database db)
public void setBpEnd(Long bpEnd)
public String getSeq()
@Deprecated public String getSeq(Database db)
public void setSeq(String seq)
public String getSymbol()
@Deprecated public String getSymbol(Database db)
public void setSymbol(String symbol)
public List<Marker> getReportsFor()
@Deprecated public List<Marker> getReportsFor(Database db)
public void setReportsFor(List<Marker> reportsFor)
reportsFor - public void setReportsFor_Id(Integer... reportsFor)
public void setReportsFor(Marker... reportsFor)
public void setReportsFor_Id(List<Integer> reportsFor_id)
public List<String> getReportsFor_Identifier()
public void setReportsFor_Identifier(List<String> reportsFor_Identifier)
public Object get(String name)
get in interface Entityget in class ObservationTargetpublic void validate()
throws DatabaseException
validate in interface Entityvalidate in class ObservationTargetDatabaseExceptionpublic void set(Entity entity, boolean strict) throws Exception
set in interface Entityset in class ObservationTargetExceptionpublic String toString()
toString in class ObservationTargetpublic String toString(boolean verbose)
toString in class ObservationTargetpublic Vector<String> getFields(boolean skipAutoIds)
getFields in interface EntitygetFields in class ObservationTargetpublic Vector<String> getFields()
getFields in interface EntitygetFields in class ObservationTargetpublic String getIdField()
getIdField in interface EntitygetIdField in class ObservationTargetpublic List<String> getLabelFields()
getLabelFields in interface EntitygetLabelFields in class ObservationTarget@Deprecated public String getFields(String sep)
getFields in interface EntitygetFields in class ObservationTargetpublic Object getIdValue()
getIdValue in interface EntitygetIdValue in class ObservationTargetpublic String getXrefIdFieldName(String fieldName)
getXrefIdFieldName in interface EntitygetXrefIdFieldName in class ObservationTarget@Deprecated public String getValues(String sep)
getValues in interface EntitygetValues in class ObservationTargetpublic Marker create(Entity entity) throws Exception
create in interface Entitycreate in class ObservationTargetExceptionpublic Collection<Marker> getReportsForMarkerCollection()
public Collection<Marker> getReportsForMarkerCollection(Database db)
public void setReportsForMarkerCollection(Collection<Marker> collection)
public boolean equals(Object obj)
equals in class ObservationTargetpublic int hashCode()
hashCode in class ObservationTargetCopyright © 2013. All Rights Reserved.