Class AbstractTaxon
- All Implemented Interfaces:
Annotatable
,Taxon
,Changeable
- Direct Known Subclasses:
SimpleTaxon
,WeakTaxon
An abstract implementation of Taxon.
It is left up to the impementor to provide methods for accessing the parent and children. All other state is provided for here. A common pattern would be to route any Taxon.getParent() call back via a method on the TaxonFactory used to generate this instance.
- Since:
- 1.3
- Author:
- Matthew Pocock, Keith James
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
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Field Summary
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
Fields inherited from interface org.biojava.bio.taxa.Taxon
CHANGE_COMMON_NAME, CHANGE_SCIENTIFIC_NAME
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Constructor Summary
ConstructorsModifierConstructorDescriptionprotected
Deprecated.protected
AbstractTaxon
(String scientificName, String commonName) Deprecated. -
Method Summary
Modifier and TypeMethodDescriptionboolean
Deprecated.Two taxa are equal if they have equivalent children, common and scientific names.Deprecated.Should return the associated annotation object.protected ChangeSupport
Deprecated.Called to retrieve the ChangeSupport for this object.Deprecated.The common name of the Taxon.Deprecated.The scientific name of this taxon.int
hashCode()
Deprecated.The hash-code of a Taxon is equal to the hash-code of it's scientific name.void
setCommonName
(String commonName) Deprecated.Set the new common name of this Taxon.void
setScientificName
(String scientificName) Deprecated.Change the scientific name of this species.toString()
Deprecated.Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from interface org.biojava.bio.taxa.Taxon
getChildren, getParent
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Constructor Details
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AbstractTaxon
protected AbstractTaxon()Deprecated. -
AbstractTaxon
Deprecated.
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Method Details
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getChangeSupport
Deprecated.Description copied from class:AbstractChangeable
Called to retrieve the ChangeSupport for this object.Your implementation of this method should have the following structure:
It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register invalid input: '&' unregister the forwarder in the code that does the ChangeEvent handling in setter methods.ChangeSupport cs = super.getChangeSupport(ct); if(someForwarder == null invalid input: '&'invalid input: '&' ct.isMatching(SomeInterface.SomeChangeType)) { someForwarder = new ChangeForwarder(... this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange); } return cs;
- Overrides:
getChangeSupport
in classAbstractChangeable
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getCommonName
Deprecated.Description copied from interface:Taxon
The common name of the Taxon.
This is the normal name used in common speech, such as 'human'.
- Specified by:
getCommonName
in interfaceTaxon
- Returns:
- a String representing this Taxon's common name
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setCommonName
Deprecated.Description copied from interface:Taxon
Set the new common name of this Taxon.
- Specified by:
setCommonName
in interfaceTaxon
- Parameters:
commonName
- the new common name- Throws:
ChangeVetoException
- if the name can't be changed at this time
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getScientificName
Deprecated.Description copied from interface:Taxon
The scientific name of this taxon.
This will be the portion of the scientific classification pertaining to just this node within the classifictaion. It will be something like 'homo sapiens' or 'archaeal group 2', rather than the full classification list.
- Specified by:
getScientificName
in interfaceTaxon
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setScientificName
Deprecated.Description copied from interface:Taxon
Change the scientific name of this species.- Specified by:
setScientificName
in interfaceTaxon
- Parameters:
scientificName
- the new scientific name- Throws:
ChangeVetoException
- if the scientific name can't be changed at this time
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getAnnotation
Deprecated.Description copied from interface:Annotatable
Should return the associated annotation object.- Specified by:
getAnnotation
in interfaceAnnotatable
- Returns:
- an Annotation object, never null
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equals
Deprecated.Description copied from interface:Taxon
Two taxa are equal if they have equivalent children, common and scientific names.
Two different implementations of Taxon should be able to appropriately trans-class equality. The parent of a Taxon is not considered in testing equality as this potentially leads to combinatorial problems checking whole taxa hierachies against one another.
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toString
Deprecated. -
hashCode
Deprecated.Description copied from interface:Taxon
The hash-code of a Taxon is equal to the hash-code of it's scientific name.
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org.biojavax.bio.taxa