Package org.biojava.bio.taxa

Class WeakTaxonFactory

java.lang.Object
org.biojava.bio.taxa.WeakTaxonFactory
All Implemented Interfaces:
TaxonFactory
public class WeakTaxonFactory extends Object implements TaxonFactory
Deprecated.
replaced by classes in org.biojavax.bio.taxa

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

  • Field Details

    • GLOBAL

      public static final WeakTaxonFactory GLOBAL
      Deprecated.
      The TaxonFactory that the biojava system should use for storing the taxonomy used by swissprot and embl as in-memory objects.

  • Constructor Details

  • Method Details

    • getRoot

      public Taxon 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 interface TaxonFactory
      Returns:
      the 'root' Taxon

    • getName

      public String getName()
      Deprecated.
      Description copied from interface: TaxonFactory

      Name for this TaxonFactory.

      Specified by:
      getName in interface TaxonFactory
      Returns:
      the name of this TaxonFactory

    • importTaxon

      public Taxon importTaxon(Taxon taxon)
      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 interface TaxonFactory
      Parameters:
      taxon - the Taxon to copy
      Returns:
      a new Taxon

    • createTaxon

      public Taxon createTaxon(String scientificName, String commonName)
      Deprecated.
      Description copied from interface: TaxonFactory

      Create a new orphan Taxon with a given scientific and common name.

      Specified by:
      createTaxon in interface TaxonFactory
      Parameters:
      scientificName - the scientificName to give the Taxon
      commonName - the common name to give the Taxon
      Returns:
      a new Taxon with no parent and no children

    • addChild

      public Taxon addChild(Taxon parent, Taxon child)
      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 interface TaxonFactory
      Parameters:
      parent - the parent Taxon to add the child to
      child - the Taxon to add as a child
      Returns:
      the Taxon object actualy present as the child

    • removeChild

      public Taxon removeChild(Taxon parent, Taxon child)
      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 interface TaxonFactory
      Parameters:
      parent - the parent Taxon to remove the child from
      child - the Taxon to remove as a child
      Returns:
      the actual Taxon removed, or null if none were removed

    • search

      public Taxon search(Object id)
      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 interface TaxonFactory
      Parameters:
      id - the Object identifying a Taxon
      Returns:
      the Taxon matching the ID, or null if none match