Class SimpleNCBITaxon

Method Details

• compareTo

  public int compareTo(Object o)

  NCBITaxon objects are compared only by their NCBITaxID fields.

  Specified by:

  compareTo in interface Comparable

• equals

  public boolean equals(Object obj)

  NCBITaxon objects are equal if their NCBITaxID fields match.

  Overrides:

  equals in class Object

• hashCode

  public int hashCode()

  Overrides:

  hashCode in class Object

• getNameClasses

  public Set getNameClasses()

  Returns all the name classes available for a taxon. These are Strings.

  Specified by:

  getNameClasses in interface NCBITaxon

  Returns:

  a set of name classes, or the empty set if there are none.

• getNames

  public Set getNames(String nameClass) throws IllegalArgumentException

  Returns all the names available for a taxon in a given class. These are Strings.

  Specified by:

  getNames in interface NCBITaxon

  Parameters:

  nameClass - the name class to retrieve names from.

  Returns:

  a set of names, or the empty set if there are none.

  Throws:

  IllegalArgumentException - if the name is null.

• getNameSet

  protected Set getNameSet()

• addName

  public void addName(String nameClass, String name) throws IllegalArgumentException, ChangeVetoException

  Adds the name to this taxon in the given name class. Neither can be null.

  Specified by:

  addName in interface NCBITaxon

  Parameters:

  nameClass - the class to add the name in.

  name - the name to add.

  Throws:

  IllegalArgumentException - if the name is null.

  ChangeVetoException - in case of objections.

• removeName

  public boolean removeName(String nameClass, String name) throws IllegalArgumentException, ChangeVetoException

  Removes the name from the given name class. Neither can be null.

  Specified by:

  removeName in interface NCBITaxon

  Parameters:

  nameClass - the class to remove the name from.

  name - the name to remove.

  Returns:

  True if the name was found and removed, false otherwise.

  Throws:

  IllegalArgumentException - if the name is null.

  ChangeVetoException - in case of objections.

• containsName

  public boolean containsName(String nameClass, String name) throws IllegalArgumentException

  Tests for the presence of a name in a given class. Neither can be null.

  Specified by:

  containsName in interface NCBITaxon

  Parameters:

  nameClass - the class to look the name up in.

  name - the name to text for existence of.

  Returns:

  True if the name exists in that class, false otherwise.

  Throws:

  IllegalArgumentException - if the name is null.

• getNamesMap

  protected final Map getNamesMap()

• getParentNCBITaxID

  public Integer getParentNCBITaxID()

  Returns the parent NCBI taxon ID, if known.

  Specified by:

  getParentNCBITaxID in interface NCBITaxon

  Returns:

  Value of property parent.

• setParentNCBITaxID

  public void setParentNCBITaxID(Integer parent) throws ChangeVetoException

  Sets the parent NCBI taxon ID. May be null if not known.

  Specified by:

  setParentNCBITaxID in interface NCBITaxon

  Parameters:

  parent - New value of property parent.

  Throws:

  ChangeVetoException - in case of objections.

• getNCBITaxID

  public int getNCBITaxID()

  Gets the NCBI taxon ID. This is never null and is immutable, as otherwise we would have no way of distinguishing between various taxa. It should be set by the constructor of an implementation.

  Specified by:

  getNCBITaxID in interface NCBITaxon

  Returns:

  Value of property NCBITaxID.

• getNodeRank

  public String getNodeRank()

  Gets the node rank of this taxon. May be null.

  Specified by:

  getNodeRank in interface NCBITaxon

  Returns:

  Value of property nodeRank.

• setNodeRank

  public void setNodeRank(String nodeRank) throws ChangeVetoException

  Setter for property nodeRank.

  Specified by:

  setNodeRank in interface NCBITaxon

  Parameters:

  nodeRank - New value of property nodeRank.

  Throws:

  ChangeVetoException - in case of objections.

• getGeneticCode

  public Integer getGeneticCode()

  Returns the genetic code of this taxon, which may be null if not known.

  Specified by:

  getGeneticCode in interface NCBITaxon

  Returns:

  Value of property geneticCode.

• setGeneticCode

  public void setGeneticCode(Integer geneticCode) throws ChangeVetoException

  Sets the genetic code of this taxon, which may be null, which will unset it.

  Specified by:

  setGeneticCode in interface NCBITaxon

  Parameters:

  geneticCode - New value of property geneticCode.

  Throws:

  ChangeVetoException - in case of objections.

• getMitoGeneticCode

  public Integer getMitoGeneticCode()

  Getter for property mitoGeneticCode. Returns Persistent.NULL_INTEGER if null.

  Specified by:

  getMitoGeneticCode in interface NCBITaxon

  Returns:

  Value of property mitoGeneticCode.

• setMitoGeneticCode

  public void setMitoGeneticCode(Integer mitoGeneticCode) throws ChangeVetoException

  Sets the mitochondrial genetic code of this taxon, which may be null, which will unset it.

  Specified by:

  setMitoGeneticCode in interface NCBITaxon

  Parameters:

  mitoGeneticCode - New value of property mitoGeneticCode.

  Throws:

  ChangeVetoException - in case of objections.

• getLeftValue

  public Integer getLeftValue()

  Gets the left value. May be null.

  Specified by:

  getLeftValue in interface NCBITaxon

  Returns:

  Value of property leftValue.

• setLeftValue

  public void setLeftValue(Integer leftValue) throws ChangeVetoException

  Sets the left value. May be null.

  Specified by:

  setLeftValue in interface NCBITaxon

  Parameters:

  leftValue - New value of property leftValue.

  Throws:

  ChangeVetoException - in case of objections.

• getRightValue

  public Integer getRightValue()

  Gets the right value. May be null.

  Specified by:

  getRightValue in interface NCBITaxon

  Returns:

  Value of property rightValue.

• setRightValue

  public void setRightValue(Integer rightValue) throws ChangeVetoException

  Sets the right value. May be null.

  Specified by:

  setRightValue in interface NCBITaxon

  Parameters:

  rightValue - New value of property rightValue.

  Throws:

  ChangeVetoException - in case of objections.

• getDisplayName

  public String getDisplayName()

  Returns the name of this taxon entry in the form: scientific (common) or if there is no common name: scientific or if there are no scientific names at all, the empty string.

  Specified by:

  getDisplayName in interface NCBITaxon

  Returns:

  the display name as described above.

• isTaxonHidden

  public final boolean isTaxonHidden()

  Returns the taxonomy hierarchy of this taxon entry in the form: most specific; less specific; ...; least specific. It follows the chain up the tree as far as it can, and will stop at the first one it comes to that returns null for getParentNCBITaxID(). If this taxon entry has no scientific name, you will get the string ".".

  Specified by:

  isTaxonHidden in interface NCBITaxon

  Returns:

  the display name as described above.

• setTaxonHidden

  public final void setTaxonHidden(boolean isTaxonHidden) throws ChangeVetoException

  Description copied from interface: NCBITaxon

  determines whether this taxonomy level is displayed in etNameHierarchy()

  Specified by:

  setTaxonHidden in interface NCBITaxon

  Parameters:

  isTaxonHidden - - if true it is displayed

  Throws:

  ChangeVetoException

• getNameHierarchy

  public String getNameHierarchy()

  Returns the taxonomy hierarchy of this taxon entry in the form: most specific; less specific; ...; least specific. It follows the chain up the tree as far as it can, and will stop at the first one it comes to that returns null for getParentNCBITaxID(). If this taxon entry has no scientific name, you will get the string ".".

  Specified by:

  getNameHierarchy in interface NCBITaxon

  Returns:

  the display name as described above.

• toString

  public String toString()

  Form: "taxid:[name,name...]"

  Overrides:

  toString in class Object

• getId

  public Integer getId()

  Gets the Hibernate ID. Should be used with caution.

  Returns:

  the Hibernate ID, if using Hibernate.

• setId

  public void setId(Integer id)

  Sets the Hibernate ID. Should be used with caution.

  Parameters:

  id - the Hibernate ID, if using Hibernate.