Package org.biojava.bio.taxa

Class AbstractTaxon

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.taxa.AbstractTaxon
All Implemented Interfaces:
Annotatable, Taxon, Changeable
Direct Known Subclasses:
SimpleTaxon, WeakTaxon
public abstract class AbstractTaxon extends AbstractChangeable implements Taxon
Deprecated.
replaced by classes in org.biojavax.bio.taxa

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

  • Constructor Details

  • Method Details

    • getChangeSupport

      protected ChangeSupport getChangeSupport(ChangeType ct)
      Deprecated.
      Description copied from class: AbstractChangeable
      Called to retrieve the ChangeSupport for this object.

      Your implementation of this method should have the following structure: 

       ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
      It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.
      Overrides:
      getChangeSupport in class AbstractChangeable

    • getCommonName

      public String 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 interface Taxon
      Returns:
      a String representing this Taxon's common name

    • setCommonName

      public void setCommonName(String commonName) throws ChangeVetoException
      Deprecated.
      Description copied from interface: Taxon

      Set the new common name of this Taxon.

      Specified by:
      setCommonName in interface Taxon
      Parameters:
      commonName - the new common name
      Throws:
      ChangeVetoException - if the name can't be changed at this time

    • getScientificName

      public String 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 interface Taxon

    • setScientificName

      public void setScientificName(String scientificName) throws ChangeVetoException
      Deprecated.
      Description copied from interface: Taxon
      Change the scientific name of this species.
      Specified by:
      setScientificName in interface Taxon
      Parameters:
      scientificName - the new scientific name
      Throws:
      ChangeVetoException - if the scientific name can't be changed at this time

    • getAnnotation

      public Annotation getAnnotation()
      Deprecated.
      Description copied from interface: Annotatable
      Should return the associated annotation object.
      Specified by:
      getAnnotation in interface Annotatable
      Returns:
      an Annotation object, never null

    • equals

      public boolean equals(Object o)
      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.

      Specified by:
      equals in interface Taxon
      Overrides:
      equals in class Object
      Parameters:
      o - the object to check
      Returns:
      true if o is a Taxon instance and has the same properties as this

    • toString

      public String toString()
      Deprecated.
      Overrides:
      toString in class Object

    • hashCode

      public int hashCode()
      Deprecated.
      Description copied from interface: Taxon
      The hash-code of a Taxon is equal to the hash-code of it's scientific name.
      Specified by:
      hashCode in interface Taxon
      Overrides:
      hashCode in class Object