AbstractTaxon (BioJava-1.5-beta API)
Keywords: org.biojava.bio.taxa.AbstractTaxon class

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## 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

Deprecated. replaced by classes in `org.biojavax.bio.taxa`

    public abstract class AbstractTaxon

extends AbstractChangeable
implements Taxon

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

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
`Annotatable.AnnotationForwarder`

Field Summary

Fields inherited from interface org.biojava.bio.taxa.Taxon
`CHANGE_COMMON_NAME, CHANGE_SCIENTIFIC_NAME`

Fields inherited from interface org.biojava.bio.Annotatable
`ANNOTATION`

Constructor Summary
`protected` | `AbstractTaxon()` Deprecated.
`protected` | `AbstractTaxon(String scientificName, String commonName)` Deprecated.

Method Summary
`boolean` | `equals(Object o)` Deprecated. Two taxa are equal if they have equivalent children, common and scientific names.
`Annotation` | `getAnnotation()` Deprecated. Should return the associated annotation object.
`protected ChangeSupport` | `getChangeSupport(ChangeType ct)` Deprecated. Called to retrieve the ChangeSupport for this object.
`String` | `getCommonName()` Deprecated. The common name of the Taxon.
`String` | `getScientificName()` 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.
`String` | `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.bio.taxa.Taxon
`getChildren, getParent`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Constructor Detail

### AbstractTaxon

    protected AbstractTaxon()

  Deprecated.

### AbstractTaxon

    protected AbstractTaxon(String scientificName,
                            String commonName)

  Deprecated.

Method Detail

### 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`

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