Interface Taxon

All Superinterfaces:
Annotatable, Changeable
All Known Implementing Classes:
AbstractTaxon, SimpleTaxon, WeakTaxon

public interface Taxon extends Annotatable
Deprecated.
replaced by classes in org.biojavax.bio.taxa

A taxon within a classification.

Taxa may be 'leaf' nodes specifying species, or 'internal' nodes specifying kingdoms and the like.

Author:
Matthew Pocock
  • Field Details

    • 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.
  • Method Details

    • 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
    • setCommonName

      void setCommonName(String commonName) throws ChangeVetoException
      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
    • 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.

    • setScientificName

      void setScientificName(String scientificName) throws ChangeVetoException
      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
    • 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.
    • 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
    • equals

      boolean equals(Object o)
      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.

      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
    • hashCode

      int hashCode()
      Deprecated.
      The hash-code of a Taxon is equal to the hash-code of it's scientific name.
      Overrides:
      hashCode in class Object