org.biojavax.bio.taxa

Interface NCBITaxon

All Superinterfaces:

Changeable, Comparable

All Known Implementing Classes:

SimpleNCBITaxon

public interface NCBITaxon
extends Comparable, Changeable

Represents an NCBI Taxon entry, a combination of the taxon and taxon_name tables in BioSQL.

Since:

1.5

Author:

Mark Schreiber, Richard Holland

Field Summary

Fields

Modifier and Type	Field and Description
static String	ACRONYM Use this to define acronyms for things.
static String	COMMON Use this to define common names for things.
static String	EQUIVALENT Use this to define equivalent names for things.
static ChangeType	GENETICCODE
static ChangeType	HIDDEN
static ChangeType	LEFTVALUE
static ChangeType	MITOGENETICCODE
static ChangeType	NAMES
static ChangeType	NODERANK
static ChangeType	PARENT
static ChangeType	RIGHTVALUE
static String	SCIENTIFIC Use this to define scientific names for things.
static String	SYNONYM Use this to define common names for things.

Method Summary

Methods

Modifier and Type	Method and Description
void	addName(String nameClass, String name) Adds the name to this taxon in the given name class.
boolean	containsName(String nameClass, String name) Tests for the presence of a name in a given class.
String	getDisplayName() Returns the name of this taxon entry in the form: scientific (common) or if there is no common name: scientific
Integer	getGeneticCode() Returns the genetic code of this taxon, which may be null if not known.
Integer	getLeftValue() Gets the left value.
Integer	getMitoGeneticCode() Returns the mitochondrial genetic code of this taxon, which may be null if not known.
Set	getNameClasses() Returns all the name classes available for a taxon.
String	getNameHierarchy() Returns the taxonomy hierarchy of this taxon entry in the form: least specific; more specific; ...; most specific.
Set	getNames(String nameClass) Returns all the names available for a taxon in a given class.
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.
boolean	isTaxonHidden() used in getNameHierarchy() to determine whether this taxonomy level is displayed
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	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) Sets the node rank of this taxon.
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()

Methods inherited from interface java.lang.Comparable

compareTo

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

NAMES

static final ChangeType NAMES

PARENT

static final ChangeType PARENT

NODERANK

static final ChangeType NODERANK

GENETICCODE

static final ChangeType GENETICCODE

MITOGENETICCODE

static final ChangeType MITOGENETICCODE

LEFTVALUE

static final ChangeType LEFTVALUE

RIGHTVALUE

static final ChangeType RIGHTVALUE

HIDDEN

static final ChangeType HIDDEN

SCIENTIFIC

static final String SCIENTIFIC

Use this to define scientific names for things. There should usually only be one scientific name for an organism.

See Also:

Constant Field Values

COMMON

static final String COMMON

Use this to define common names for things. There can be as many common names as you like.

See Also:

Constant Field Values

SYNONYM

static final String SYNONYM

Use this to define common names for things. There can be as many synonyms as you like.

See Also:

Constant Field Values

ACRONYM

static final String ACRONYM

Use this to define acronyms for things. There can be as many acronyms as you like.

See Also:

Constant Field Values

EQUIVALENT

static final String EQUIVALENT

Use this to define equivalent names for things. There can be as many equivalent names as you like.

See Also:

Constant Field Values

Method Detail

getNameClasses

Set getNameClasses()

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

Returns:

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

getNames

Set getNames(String nameClass)
             throws IllegalArgumentException

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

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.

addName

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

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

Parameters:

nameClass - the class to add the name in.

name - the name to add.

Throws:

ChangeVetoException - in case of objections.

IllegalArgumentException - if the name is null.

removeName

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

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

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:

ChangeVetoException - in case of objections.

IllegalArgumentException - if the name is null.

containsName

boolean containsName(String nameClass,
                   String name)
                     throws IllegalArgumentException

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

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.

getParentNCBITaxID

Integer getParentNCBITaxID()

Returns the parent NCBI taxon ID, if known.

Returns:

Value of property parent.

setParentNCBITaxID

void setParentNCBITaxID(Integer parent)
                        throws ChangeVetoException

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

Parameters:

parent - New value of property parent.

Throws:

ChangeVetoException - in case of objections.

getNCBITaxID

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.

Returns:

Value of property NCBITaxID.

getNodeRank

String getNodeRank()

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

Returns:

Value of property nodeRank.

setNodeRank

void setNodeRank(String nodeRank)
                 throws ChangeVetoException

Sets the node rank of this taxon. May be null, in which case it is unset.

Parameters:

nodeRank - New value of property nodeRank.

Throws:

ChangeVetoException - in case of objections.

getGeneticCode

Integer getGeneticCode()

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

Returns:

Value of property geneticCode.

setGeneticCode

void setGeneticCode(Integer geneticCode)
                    throws ChangeVetoException

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

Parameters:

geneticCode - New value of property geneticCode.

Throws:

ChangeVetoException - in case of objections.

getMitoGeneticCode

Integer getMitoGeneticCode()

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

Returns:

Value of property mitoGeneticCode.

setMitoGeneticCode

void setMitoGeneticCode(Integer mitoGeneticCode)
                        throws ChangeVetoException

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

Parameters:

mitoGeneticCode - New value of property mitoGeneticCode.

Throws:

ChangeVetoException - in case of objections.

getLeftValue

Integer getLeftValue()

Gets the left value. May be null.

Returns:

Value of property leftValue.

setLeftValue

void setLeftValue(Integer leftValue)
                  throws ChangeVetoException

Sets the left value. May be null.

Parameters:

leftValue - New value of property leftValue.

Throws:

ChangeVetoException - in case of objections.

getRightValue

Integer getRightValue()

Gets the right value. May be null.

Returns:

Value of property rightValue.

setRightValue

void setRightValue(Integer rightValue)
                   throws ChangeVetoException

Sets the right value. May be null.

Parameters:

rightValue - New value of property rightValue.

Throws:

ChangeVetoException - in case of objections.

getDisplayName

String getDisplayName()

Returns the name of this taxon entry in the form: scientific (common) or if there is no common name: scientific

Returns:

the display name as described above.

getNameHierarchy

String getNameHierarchy()

Returns the taxonomy hierarchy of this taxon entry in the form: least specific; more specific; ...; most 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()

Returns:

the display name as described above.

isTaxonHidden

boolean isTaxonHidden()

used in getNameHierarchy() to determine whether this taxonomy level is displayed

setTaxonHidden

void setTaxonHidden(boolean isTaxonHidden)
                    throws ChangeVetoException

determines whether this taxonomy level is displayed in etNameHierarchy()

Parameters:

isTaxonHidden - - if true it is displayed

Throws:

ChangeVetoException