Interface Taxon
- All Superinterfaces:
Annotatable
,Changeable
- All Known Implementing Classes:
AbstractTaxon
,SimpleTaxon
,WeakTaxon
A taxon within a classification.
Taxa may be 'leaf' nodes specifying species, or 'internal' nodes specifying kingdoms and the like.
- Author:
- Matthew Pocock
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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
FieldsModifier and TypeFieldDescriptionstatic final ChangeType
Deprecated.Change type to indicate that the common name of this Taxon is changing.static final ChangeType
Deprecated.Change type to indicate that the scientific name of this Taxon is changing.Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
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Method Summary
Modifier and TypeMethodDescriptionboolean
Deprecated.Two taxa are equal if they have equivalent children, common and scientific names.Deprecated.The children of this Taxon.Deprecated.The common name of the Taxon.Deprecated.The parent of this 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.Methods inherited from interface org.biojava.bio.Annotatable
getAnnotation
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Field Details
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CHANGE_COMMON_NAME
Deprecated.Change type to indicate that the common name of this Taxon is changing. -
CHANGE_SCIENTIFIC_NAME
Deprecated.Change type to indicate that the scientific name of this Taxon is changing.
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Method Details
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getCommonName
Deprecated.The common name of the Taxon.
This is the normal name used in common speech, such as 'human'.
- Returns:
- a String representing this Taxon's common name
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setCommonName
Deprecated.Set the new common name of this Taxon.
- Parameters:
commonName
- the new common name- Throws:
ChangeVetoException
- if the name can't be changed at this time
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getScientificName
Deprecated.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.
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setScientificName
Deprecated.Change the scientific name of this species.- Parameters:
scientificName
- the new scientific name- Throws:
ChangeVetoException
- if the scientific name can't be changed at this time
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getParent
Deprecated.The parent of this Taxon.
Taxa live within a tree data-structure, so every taxon has a single parent except for the root type. This has the null parent.
- Returns:
- the parent Taxon, or null if this is the root type.
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getChildren
Deprecated.The children of this Taxon.
Taxa live within a tree data-structure, so every taxon has zero or more children. In the case of zero children, the empty set is returned.
? read-only ? dynamicaly updated with taxon object ? copy of data ?
- Returns:
- the Set (possibly empty) of all child Taxa
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equals
Deprecated.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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hashCode
int hashCode()Deprecated.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