Class WeakTaxonFactory
- All Implemented Interfaces:
TaxonFactory
An implementation of TaxonFactory that builds a weak in-memory Taxon tree.
This implementation holds only weak references to the Taxon instances it knows about. This means that WeakTaxonFactory may not be appropriate for situations where you wish to browse the taxon tree. It does, however, mean that massive taxa can be represented, by effectively reflecting the currently useful rooted sub-tree in memory.
- Author:
- Matthew Pocock
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final WeakTaxonFactory
Deprecated.The TaxonFactory that the biojava system should use for storing the taxonomy used by swissprot and embl as in-memory objects. -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionDeprecated.Add a taxon as a child to a parent.createTaxon
(String scientificName, String commonName) Deprecated.Create a new orphan Taxon with a given scientific and common name.getName()
Deprecated.Name for this TaxonFactory.getRoot()
Deprecated.Retrieve the root upon which all rooted Taxon that this factory knows about are rooted.importTaxon
(Taxon taxon) Deprecated.Import a Taxon and all its children into the implementation provided by this factory.removeChild
(Taxon parent, Taxon child) Deprecated.Remove a Taxon as a child to this one.Deprecated.Retrieve a Taxon that matches some ID.
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Field Details
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GLOBAL
Deprecated.The TaxonFactory that the biojava system should use for storing the taxonomy used by swissprot and embl as in-memory objects.
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Constructor Details
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WeakTaxonFactory
Deprecated.
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Method Details
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getRoot
Deprecated.Description copied from interface:TaxonFactory
Retrieve the root upon which all rooted Taxon that this factory knows about are rooted.
- Specified by:
getRoot
in interfaceTaxonFactory
- Returns:
- the 'root' Taxon
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getName
Deprecated.Description copied from interface:TaxonFactory
Name for this TaxonFactory.
- Specified by:
getName
in interfaceTaxonFactory
- Returns:
- the name of this TaxonFactory
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importTaxon
Deprecated.Description copied from interface:TaxonFactory
Import a Taxon and all its children into the implementation provided by this factory.
The return value of this method should be .equals() and .hasCode() compatable with the taxon parameter. It may not be implemented by the same underlying implementation.
- Specified by:
importTaxon
in interfaceTaxonFactory
- Parameters:
taxon
- the Taxon to copy- Returns:
- a new Taxon
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createTaxon
Deprecated.Description copied from interface:TaxonFactory
Create a new orphan Taxon with a given scientific and common name.
- Specified by:
createTaxon
in interfaceTaxonFactory
- Parameters:
scientificName
- the scientificName to give the TaxoncommonName
- the common name to give the Taxon- Returns:
- a new Taxon with no parent and no children
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addChild
Deprecated.Description copied from interface:TaxonFactory
Add a taxon as a child to a parent.
The TaxonFactory may chose to add the child directly, or make a new object which is .equals() compatable with child. The actual Taxon instance inserted into the child set is returned by the add method.
- Specified by:
addChild
in interfaceTaxonFactory
- Parameters:
parent
- the parent Taxon to add the child tochild
- the Taxon to add as a child- Returns:
- the Taxon object actualy present as the child
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removeChild
Deprecated.Description copied from interface:TaxonFactory
Remove a Taxon as a child to this one.
This Taxon should attempt to remove a child that is .equals() compatable with child. If it is sucessful, it should return the Taxon instance that was removed. If not, it should return null.
- Specified by:
removeChild
in interfaceTaxonFactory
- Parameters:
parent
- the parent Taxon to remove the child fromchild
- the Taxon to remove as a child- Returns:
- the actual Taxon removed, or null if none were removed
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search
Deprecated.Description copied from interface:TaxonFactory
Retrieve a Taxon that matches some ID.
This method is here out of desperation. It's nasty and should be replaced by some propper querying API. Without having different methods for every TaxonFactory I don't know what to do. All ideas appreciated.
- Specified by:
search
in interfaceTaxonFactory
- Parameters:
id
- the Object identifying a Taxon- Returns:
- the Taxon matching the ID, or null if none match
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org.biojavax.bio.taxa