| Package | Description |
|---|---|
| org.molgenis.omx.auth | |
| org.molgenis.omx.observ | |
| org.molgenis.omx.observ.db | |
| org.molgenis.omx.observ.target | |
| org.molgenis.omx.observ.value | |
| org.molgenis.service |
| Modifier and Type | Class and Description |
|---|---|
class |
Institute
Institute: A contact is either a person or an organization.
|
class |
Person
Person:
Person represents one or more people involved with an Investigation.
|
class |
PersonRole
PersonRole: Seperate type of ontologyTerm to administrate roles.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Category
Category: Category is partOf ObservableFeature to define categories for an
ObservableFeature, such as the categorical answer codes that are often used in Questionaires.
|
class |
DataSet
DataSet: Container for one or more observations that are measured
using the same protocol and by the same performer(s).
|
class |
ObservableFeature
ObservableFeature:
ObservableFeature defines anything that can be observed.
|
class |
ObservationTarget
ObservationTarget: ObservationTarget defines subjects of observation, such
as Individual, Panel, Sample, etc.
|
class |
Protocol
Protocol:
The Protocol class defines parameterizable descriptions of
(analysis)methods.
|
| Modifier and Type | Method and Description |
|---|---|
Characteristic |
Characteristic.create(Entity entity) |
static Characteristic |
Characteristic.findById(Database db,
Integer id) |
static Characteristic |
Characteristic.findByIdentifier(Database db,
String identifier) |
| Modifier and Type | Method and Description |
|---|---|
static List<? extends Characteristic> |
Characteristic.find(Database db,
QueryRule... rules)
Shorthand for db.find(Characteristic.class, org.molgenis.framework.db.QueryRule ...
|
static Query<? extends Characteristic> |
Characteristic.query(Database db)
Shorthand for db.query(Characteristic.class).
|
| Constructor and Description |
|---|
Characteristic(Characteristic copyMe)
copy constructor
|
| Modifier and Type | Class and Description |
|---|---|
class |
CharacteristicSecurityDecorator<E extends Characteristic>
TODO add column level security filters
|
| Modifier and Type | Method and Description |
|---|---|
Characteristic |
CharacteristicJpaMapper.create() |
| Modifier and Type | Method and Description |
|---|---|
List<Characteristic> |
CharacteristicJpaMapper.createList(int size)
Return EMPTY list of given allocated size
|
| Modifier and Type | Method and Description |
|---|---|
void |
CharacteristicJpaMapper.create(Characteristic entity)
This method first saves the objects that are being refered to by entity,
then the entity itself and
finally the objects that refer to this object
|
void |
CharacteristicJpaMapper.destroy(Characteristic characteristic) |
void |
CharacteristicJpaMapper.edit(Characteristic characteristic) |
| Modifier and Type | Method and Description |
|---|---|
int |
CharacteristicJpaMapper.executeAdd(List<? extends Characteristic> entities) |
int |
CharacteristicJpaMapper.executeRemove(List<? extends Characteristic> entities) |
int |
CharacteristicJpaMapper.executeUpdate(List<? extends Characteristic> entities) |
void |
CharacteristicJpaMapper.prepareFileAttachements(List<Characteristic> entities,
File baseDir) |
void |
CharacteristicJpaMapper.resolveForeignKeys(List<Characteristic> entities) |
boolean |
CharacteristicJpaMapper.saveFileAttachements(List<Characteristic> entities,
File baseDir) |
| Modifier and Type | Class and Description |
|---|---|
class |
Accession
Accession:
An external identifier for an annotation.
|
class |
Individual
Individual: The Individuals class defines the subjects that are
used
as observation target.
|
class |
OntologyTerm
OntologyTerm:
OntologyTerm defines a single entry (term) from an
ontology or a controlled vocabulary (defined by Ontology).
|
class |
Panel
Panel: The Panel class defines groups of individuals based on
cohort design, case/controls, families, etc.
|
class |
Species
Species: Ontology terms for species.
|
| Modifier and Type | Method and Description |
|---|---|
Characteristic |
XrefValue.getValue()
Get the Value.
|
Characteristic |
MrefValue_Value.getValue()
Get the .
|
Characteristic |
XrefValue.getValue(Database db)
Deprecated.
|
Characteristic |
MrefValue_Value.getValue(Database db)
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
List<Characteristic> |
MrefValue.getValue()
Get the Value.
|
List<Characteristic> |
MrefValue.getValue(Database db)
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
void |
MrefValue.setValue(Characteristic... value) |
void |
XrefValue.setValue(Characteristic value)
Set the Value.
|
void |
MrefValue_Value.setValue(Characteristic value)
Set the .
|
| Modifier and Type | Method and Description |
|---|---|
void |
MrefValue.setValue(List<Characteristic> value)
Set the Value.
|
| Modifier and Type | Method and Description |
|---|---|
Characteristic |
CharacteristicService.create(Characteristic characteristic) |
Characteristic |
CharacteristicService.read(Integer id) |
| Modifier and Type | Method and Description |
|---|---|
Iterable<Characteristic> |
CharacteristicService.readAll() |
EntityPager<Characteristic> |
CharacteristicService.readAll(int start,
int num,
List<QueryRule> queryRules) |
| Modifier and Type | Method and Description |
|---|---|
Characteristic |
CharacteristicService.create(Characteristic characteristic) |
void |
CharacteristicService.update(Characteristic characteristic) |
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