Package org.biojavax.bio.taxa

Class SimpleNCBITaxon

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.bio.taxa.SimpleNCBITaxon

All Implemented Interfaces:

Comparable, Changeable, NCBITaxon

public class SimpleNCBITaxon
extends AbstractChangeable
implements NCBITaxon

Reference implementation of NCBITaxon.

Since:

1.5

Author:

Richard Holland, Mark Schreiber, David Scott

Field Summary

Fields

Modifier and Type	Field	Description
protected Set	names

Fields inherited from interface org.biojavax.bio.taxa.NCBITaxon

ACRONYM, COMMON, EQUIVALENT, GENETICCODE, HIDDEN, LEFTVALUE, MITOGENETICCODE, NAMES, NODERANK, PARENT, RIGHTVALUE, SCIENTIFIC, SYNONYM

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	SimpleNCBITaxon()
	SimpleNCBITaxon(int NCBITaxID)	Creates a new instance of SimpleNCBITaxon based on the given taxon ID.
	SimpleNCBITaxon(Integer NCBITaxID)	Creates a new instance of SimpleNCBITaxon based on the given taxon ID.

Method Summary

Modifier and Type	Method	Description
void	addName(String nameClass, String name)	Adds the name to this taxon in the given name class.
int	compareTo(Object o)	NCBITaxon objects are compared only by their NCBITaxID fields.
boolean	containsName(String nameClass, String name)	Tests for the presence of a name in a given class.
boolean	equals(Object obj)	NCBITaxon objects are equal if their NCBITaxID fields match.
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.
Integer	getGeneticCode()	Returns the genetic code of this taxon, which may be null if not known.
Integer	getId()	Gets the Hibernate ID.
Integer	getLeftValue()	Gets the left value.
Integer	getMitoGeneticCode()	Getter for property mitoGeneticCode.
Set	getNameClasses()	Returns all the name classes available for a taxon.
String	getNameHierarchy()	Returns the taxonomy hierarchy of this taxon entry in the form: most specific; less specific; ...; least specific.
Set	getNames(String nameClass)	Returns all the names available for a taxon in a given class.
protected Set	getNameSet()
protected Map	getNamesMap()
int	getNCBITaxID()	Gets the NCBI taxon ID.
String	getNodeRank()	Gets the node rank of this taxon.
Integer	getParentNCBITaxID()	Returns the parent NCBI taxon ID, if known.
Integer	getRightValue()	Gets the right value.
int	hashCode()
boolean	isTaxonHidden()	Returns the taxonomy hierarchy of this taxon entry in the form: most specific; less specific; ...; least specific.
boolean	removeName(String nameClass, String name)	Removes the name from the given name class.
void	setGeneticCode(Integer geneticCode)	Sets the genetic code of this taxon, which may be null, which will unset it.
void	setId(Integer id)	Sets the Hibernate ID.
void	setLeftValue(Integer leftValue)	Sets the left value.
void	setMitoGeneticCode(Integer mitoGeneticCode)	Sets the mitochondrial genetic code of this taxon, which may be null, which will unset it.
void	setNodeRank(String nodeRank)	Setter for property nodeRank.
void	setParentNCBITaxID(Integer parent)	Sets the parent NCBI taxon ID.
void	setRightValue(Integer rightValue)	Sets the right value.
void	setTaxonHidden(boolean isTaxonHidden)	determines whether this taxonomy level is displayed in etNameHierarchy()
String	toString()	Form: "taxid:[name,name...]"

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, 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.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

names

protected Set names

Constructor Detail

SimpleNCBITaxon

public SimpleNCBITaxon(int NCBITaxID)

Creates a new instance of SimpleNCBITaxon based on the given taxon ID.

Parameters:

NCBITaxID - the underlying taxon ID from NCBI.

SimpleNCBITaxon

public SimpleNCBITaxon(Integer NCBITaxID)

Creates a new instance of SimpleNCBITaxon based on the given taxon ID. It may not be null, else you'll get exceptions.

Parameters:

NCBITaxID - the underlying taxon ID from NCBI.

SimpleNCBITaxon

protected SimpleNCBITaxon()

Method Detail

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.