phenote.datamodel
Class AnnotationCharacter

java.lang.Object
  phenote.datamodel.AbstractCharacter
      phenote.datamodel.AnnotationCharacter

All Implemented Interfaces:

CharacterI

public class AnnotationCharacter
extends AbstractCharacter

CharacterI for OBOAnnotations

Field Summary

protected org.obo.annotation.datamodel.Annotation	annotation underlying obo annotation - cant be null actually
protected AnnotationMappingDriver	driver
protected static int	idgen

Constructor Summary

AnnotationCharacter(org.obo.annotation.datamodel.Annotation annotation, AnnotationMappingDriver driver)

AnnotationCharacter(AnnotationMappingDriver driver)

AnnotationCharacter(java.lang.String id, AnnotationMappingDriver driver)

Method Summary

void	addComparison(org.obo.datamodel.OBOProperty relation, CharacterI relatedChar) Make comparison relationship between 2 annotations
CharacterI	cloneCharacter()
protected CharFieldValue	getCharFieldValue(org.obo.datamodel.DanglingObject oboInst, CharacterI character, CharField field)
protected CharFieldValue	getCharFieldValue(org.obo.datamodel.Instance oboInst, CharacterI character, CharField field)
protected CharFieldValue	getCharFieldValue(org.obo.datamodel.OBOClass oboClass, CharacterI character, CharField field)
protected CharFieldValue	getCharFieldValue(java.lang.String s, CharacterI character, CharField field)
protected org.obo.datamodel.OBOProperty	getDefaultRelationship()
protected org.obo.datamodel.OBOProperty	getPropertyForField(CharField cf)
CharFieldValue	getValue(CharField cf)
java.util.List<CharFieldValue>	getValueList(CharField cf) im wondering if a better way is to make CFVs recursive, so a CFV can be a list of CFV's - that might be easier - not sure
protected boolean	isObjectField(CharField cf)
protected boolean	isSubjectField(CharField cf)
protected void	resetRelationshipField()
protected void	setPropertyValue(org.obo.annotation.datamodel.Annotation annotation, org.obo.datamodel.OBOProperty property, org.obo.datamodel.OBOClass value)
protected void	setPropertyValue(org.obo.annotation.datamodel.Annotation annotation, org.obo.datamodel.OBOProperty property, java.lang.String value)
void	setValue(CharField cf, CharFieldValue cfv)
boolean	supportsComparisons() Returns true if charI implementation supports comparisons, eg Character doesnt AnnotChar does

Methods inherited from class phenote.datamodel.AbstractCharacter

eq, equals, fieldEquals, getAllCharFields, getCharFieldForName, getEntity, getEntityField, getGenConField, getGeneticContext, getGenotype, getGenotypeField, getOboAnnotation, getPub, getPubField, getQualField, getQuality, getTerm, getTerm, getValueString, getValueString, hasGeneticContext, hasNoContent, hasOboAnnotation, hasPub, hasValue, hasValue, setEntity, setGeneticContext, setGenotype, setPub, setQuality, setValue, setValue, setValue, setValue, setValue

Methods inherited from class java.lang.Object

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

Field Detail

idgen

protected static int idgen

annotation

protected org.obo.annotation.datamodel.Annotation annotation

underlying obo annotation - cant be null actually

driver

protected AnnotationMappingDriver driver

Constructor Detail

AnnotationCharacter

public AnnotationCharacter(AnnotationMappingDriver driver)

AnnotationCharacter

public AnnotationCharacter(java.lang.String id,
                           AnnotationMappingDriver driver)

AnnotationCharacter

public AnnotationCharacter(org.obo.annotation.datamodel.Annotation annotation,
                           AnnotationMappingDriver driver)

Method Detail

getPropertyForField

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

setPropertyValue

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

setPropertyValue

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

getDefaultRelationship

protected org.obo.datamodel.OBOProperty getDefaultRelationship()

isSubjectField

protected boolean isSubjectField(CharField cf)

isObjectField

protected boolean isObjectField(CharField cf)

resetRelationshipField

protected void resetRelationshipField()

setValue

public void setValue(CharField cf,
                     CharFieldValue cfv)

getValue

public CharFieldValue getValue(CharField cf)

getValueList

public java.util.List<CharFieldValue> getValueList(CharField cf)

Description copied from interface: CharacterI

im wondering if a better way is to make CFVs recursive, so a CFV can be a list of CFV's - that might be easier - not sure

getCharFieldValue

protected CharFieldValue getCharFieldValue(org.obo.datamodel.OBOClass oboClass,
                                           CharacterI character,
                                           CharField field)

getCharFieldValue

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

getCharFieldValue

protected CharFieldValue getCharFieldValue(org.obo.datamodel.DanglingObject oboInst,
                                           CharacterI character,
                                           CharField field)

getCharFieldValue

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

cloneCharacter

public CharacterI cloneCharacter()

supportsComparisons

public boolean supportsComparisons()

Description copied from interface: CharacterI

Returns true if charI implementation supports comparisons, eg Character doesnt AnnotChar does

addComparison

public void addComparison(org.obo.datamodel.OBOProperty relation,
                          CharacterI relatedChar)
                   throws CharacterEx

Make comparison relationship between 2 annotations

Specified by:

addComparison in interface CharacterI

Specified by:

addComparison in class AbstractCharacter

Throws:

CharacterEx