phenote.datamodel
Class BasicAnnotationMappingDriver

java.lang.Object
  phenote.datamodel.BasicAnnotationMappingDriver

All Implemented Interfaces:

AnnotationMappingDriver

Direct Known Subclasses:

DefaultMappingDriver, PhenotypeAssociationMappingDriver

public class BasicAnnotationMappingDriver
extends java.lang.Object
implements AnnotationMappingDriver

Maps ENTITY to subject and QUALITY to object but is this proper? shouldnt genotype be subject?

Field Summary

protected boolean	auditHistoryMode
protected boolean	changeObjectsMode
protected static org.obo.datamodel.OBOProperty	GENOTYPE_REL We probably want to create a special static ontology that extends AnnotationOntology to contain these properties.
protected static org.obo.datamodel.OBOProperty	HAS_QUALITY_REL
protected java.util.List<org.obo.history.HistoryItem>	historyItems

Constructor Summary

BasicAnnotationMappingDriver()

Method Summary

void	addHistoryItem(org.obo.history.HistoryItem item)
void	clearProperty(org.obo.annotation.datamodel.Annotation annotation, org.obo.datamodel.OBOProperty property)
boolean	getAuditHistoryMode()
boolean	getChangeObjectsMode()
CharFieldValue	getCharFieldValue(org.obo.datamodel.Instance oboInst, CharacterI character, CharField field)
CharFieldValue	getCharFieldValue(org.obo.datamodel.OBOClass oboclass, CharacterI character, CharField field)
CharFieldValue	getCharFieldValue(java.lang.String s, CharacterI character, CharField field)
org.obo.datamodel.OBOProperty	getDefaultRelationship()
org.obo.datamodel.OBOProperty	getPropertyForField(CharField cf)
protected org.obo.datamodel.OBOProperty	getRelation(java.lang.String id, java.lang.String name) retrieves prop from obo session by id, if not there then creates one
boolean	isObjectDifferentiaField(CharField cf)
boolean	isObjectField(CharField cf)
boolean	isObjectGenusField(CharField cf)
boolean	isSubjectField(CharField cf)
java.util.List<org.obo.history.HistoryItem>	popHistoryList()
void	setAuditHistoryMode(boolean auditHistoryMode)
void	setChangeObjectsMode(boolean changeObjectsMode)
void	setPropertyValue(org.obo.annotation.datamodel.Annotation annotation, org.obo.datamodel.OBOProperty property, org.obo.datamodel.OBOClass value)
void	setPropertyValue(org.obo.annotation.datamodel.Annotation annotation, org.obo.datamodel.OBOProperty property, java.lang.String value)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

auditHistoryMode

protected boolean auditHistoryMode

changeObjectsMode

protected boolean changeObjectsMode

historyItems

protected java.util.List<org.obo.history.HistoryItem> historyItems

GENOTYPE_REL

protected static final org.obo.datamodel.OBOProperty GENOTYPE_REL

We probably want to create a special static ontology that extends AnnotationOntology to contain these properties. This is here just to keep the example simple

HAS_QUALITY_REL

protected static final org.obo.datamodel.OBOProperty HAS_QUALITY_REL

Constructor Detail

BasicAnnotationMappingDriver

public BasicAnnotationMappingDriver()

Method Detail

getPropertyForField

public org.obo.datamodel.OBOProperty getPropertyForField(CharField cf)

Specified by:

getPropertyForField in interface AnnotationMappingDriver

getRelation

protected org.obo.datamodel.OBOProperty getRelation(java.lang.String id,
                                                    java.lang.String name)

retrieves prop from obo session by id, if not there then creates one

popHistoryList

public java.util.List<org.obo.history.HistoryItem> popHistoryList()

Specified by:

popHistoryList in interface AnnotationMappingDriver

getCharFieldValue

public CharFieldValue getCharFieldValue(org.obo.datamodel.OBOClass oboclass,
                                        CharacterI character,
                                        CharField field)

Specified by:

getCharFieldValue in interface AnnotationMappingDriver

getCharFieldValue

public CharFieldValue getCharFieldValue(org.obo.datamodel.Instance oboInst,
                                        CharacterI character,
                                        CharField field)

getCharFieldValue

public CharFieldValue getCharFieldValue(java.lang.String s,
                                        CharacterI character,
                                        CharField field)

Specified by:

getCharFieldValue in interface AnnotationMappingDriver

setPropertyValue

public void setPropertyValue(org.obo.annotation.datamodel.Annotation annotation,
                             org.obo.datamodel.OBOProperty property,
                             org.obo.datamodel.OBOClass value)

Specified by:

setPropertyValue in interface AnnotationMappingDriver

setPropertyValue

public void setPropertyValue(org.obo.annotation.datamodel.Annotation annotation,
                             org.obo.datamodel.OBOProperty property,
                             java.lang.String value)

Specified by:

setPropertyValue in interface AnnotationMappingDriver

clearProperty

public void clearProperty(org.obo.annotation.datamodel.Annotation annotation,
                          org.obo.datamodel.OBOProperty property)

Specified by:

clearProperty in interface AnnotationMappingDriver

getDefaultRelationship

public org.obo.datamodel.OBOProperty getDefaultRelationship()

Specified by:

getDefaultRelationship in interface AnnotationMappingDriver

isSubjectField

public boolean isSubjectField(CharField cf)

Specified by:

isSubjectField in interface AnnotationMappingDriver

isObjectField

public boolean isObjectField(CharField cf)

Specified by:

isObjectField in interface AnnotationMappingDriver

isObjectGenusField

public boolean isObjectGenusField(CharField cf)

Specified by:

isObjectGenusField in interface AnnotationMappingDriver

isObjectDifferentiaField

public boolean isObjectDifferentiaField(CharField cf)

Specified by:

isObjectDifferentiaField in interface AnnotationMappingDriver

getAuditHistoryMode

public boolean getAuditHistoryMode()

Specified by:

getAuditHistoryMode in interface AnnotationMappingDriver

setAuditHistoryMode

public void setAuditHistoryMode(boolean auditHistoryMode)

getChangeObjectsMode

public boolean getChangeObjectsMode()

Specified by:

getChangeObjectsMode in interface AnnotationMappingDriver

setChangeObjectsMode

public void setChangeObjectsMode(boolean changeObjectsMode)

addHistoryItem

public void addHistoryItem(org.obo.history.HistoryItem item)

Specified by:

addHistoryItem in interface AnnotationMappingDriver