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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Description.Ontology.BioMaterialCharacteristic
org.biomage.Description.OntologyEntry
public class OntologyEntry
A single entry from an ontology or a controlled vocabulary. For instance, category could be 'species name', value could be 'homo sapiens' and ontology would be taxonomy database, NCBI.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasAssociations |
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HasAssociations.Associations_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets |
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HasPropertySets.PropertySets_list |
Field Summary | |
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protected DatabaseEntry |
ontologyReference
Many ontology entries will not yet have formalized ontologies. |
Fields inherited from class org.biomage.Description.Ontology.BioMaterialCharacteristic |
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ojbConcreteClass |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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OntologyEntry()
Default constructor. |
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OntologyEntry(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToAssociations(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Associations_list |
void |
addToAssociations(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Associations_list |
boolean |
emptyMAGEobject()
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HasAssociations.Associations_list |
getAssociations()
Get method for associations |
java.lang.String |
getCategory()
Get method for category |
java.lang.String |
getDescription()
Get method for description |
OntologyEntry |
getFromAssociations(int position)
Method to get OntologyEntry from Associations_list |
java.lang.String |
getModelClassName()
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DatabaseEntry |
getOntologyReference()
Get method for ontologyReference |
java.lang.String |
getValue()
Get method for value |
void |
removeElementAtFromAssociations(int position)
Method to remove by position from Associations_list |
void |
removeFromAssociations(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Associations_list |
void |
setAssociations(HasAssociations.Associations_list associations)
Set method for associations |
void |
setCategory(java.lang.String category)
Set method for category |
void |
setDescription(java.lang.String description)
Set method for description |
void |
setOntologyReference(DatabaseEntry ontologyReference)
Set method for ontologyReference |
void |
setValue(java.lang.String value)
Set method for value |
void |
writeAssociations(java.io.Writer out)
writeAssociations This method is responsible for assembling the association data into XML. |
void |
writeAttributes(java.io.Writer out)
writeAttributes This method is responsible for assembling the attribute data into XML. |
void |
writeMAGEML(java.io.Writer out)
writeMAGEML This method is responsible for assembling the attribute and association data into XML. |
Methods inherited from class org.biomage.Description.Ontology.BioMaterialCharacteristic |
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createMGEDMeasurementRestriction |
Methods inherited from class org.biomage.Common.Extendable |
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addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setAttributes, setId, setIsEditable, setPropertySets, setSecuredElementId, toString |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected DatabaseEntry ontologyReference
Constructor Detail |
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public OntologyEntry()
public OntologyEntry(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Extendable
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Extendable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Extendable
java.io.IOException
public void setCategory(java.lang.String category)
setCategory
in class BioMaterialCharacteristic
value
- to setpublic java.lang.String getCategory()
getCategory
in class BioMaterialCharacteristic
public void setValue(java.lang.String value)
setValue
in class BioMaterialCharacteristic
value
- to setpublic java.lang.String getValue()
getValue
in class BioMaterialCharacteristic
public void setDescription(java.lang.String description)
setDescription
in class BioMaterialCharacteristic
value
- to setpublic java.lang.String getDescription()
getDescription
in class BioMaterialCharacteristic
public java.lang.String getModelClassName()
getModelClassName
in class Extendable
public void setOntologyReference(DatabaseEntry ontologyReference)
setOntologyReference
in interface HasOntologyReference
setOntologyReference
in class BioMaterialCharacteristic
value
- to setpublic DatabaseEntry getOntologyReference()
getOntologyReference
in interface HasOntologyReference
getOntologyReference
in class BioMaterialCharacteristic
public void setAssociations(HasAssociations.Associations_list associations)
setAssociations
in interface HasAssociations
setAssociations
in class BioMaterialCharacteristic
value
- to setpublic HasAssociations.Associations_list getAssociations()
getAssociations
in interface HasAssociations
getAssociations
in class BioMaterialCharacteristic
public void addToAssociations(OntologyEntry ontologyEntry)
addToAssociations
in interface HasAssociations
addToAssociations
in class BioMaterialCharacteristic
public void addToAssociations(int position, OntologyEntry ontologyEntry)
addToAssociations
in interface HasAssociations
addToAssociations
in class BioMaterialCharacteristic
public OntologyEntry getFromAssociations(int position)
getFromAssociations
in interface HasAssociations
getFromAssociations
in class BioMaterialCharacteristic
public void removeElementAtFromAssociations(int position)
removeElementAtFromAssociations
in interface HasAssociations
removeElementAtFromAssociations
in class BioMaterialCharacteristic
public void removeFromAssociations(OntologyEntry ontologyEntry)
removeFromAssociations
in interface HasAssociations
removeFromAssociations
in class BioMaterialCharacteristic
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