uk.ac.ebi.intenz.domain.enzyme
Class EnzymeEntry

java.lang.Object
  uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry

public class EnzymeEntry
extends Object

This class stores the information of an IntEnz enzyme.

Such an enzyme includes information from three different sources:

• NC-IUBMB (the official data)
• enzyme.dat (Amos' enzyme file)
• BRENDA (enzyme database from the University of Cologne)

Version:

$Revision: 1.4 $ $Date: 2009/04/20 13:44:24 $

Author:

Michael Darsow

Constructor Summary

EnzymeEntry()
The default source is INTENZ.

Method Summary

void	addCofactor(Cofactor cofactor) Deprecated. use addCofactor(Object) instead
void	addCofactor(Object cofactor) Adds a cofactor to the list of cofactors.
void	addCommonName(EnzymeName commonName) Adds a common name to the list of common names.
void	addEnzymaticReaction(uk.ac.ebi.rhea.domain.Reaction reaction, String view, boolean iubmb) Adds a reaction to the list of alternative reactions.
void	addLink(EnzymeLink link) Adds a link to the list of additional links.
void	addReaction(uk.ac.ebi.rhea.domain.Reaction reaction) Deprecated. use addEnzymaticReaction instead
void	addReference(Reference reference) Adds a reference to the list of references.
void	addSynonym(EnzymeName synonym) Adds a synonsm to the list of synonyms.
boolean	equals(Object o) Standard equals method.
SortedSet<EnzymeLink>	getCasNumbers() CAS numbers for IntEnz and IUBMB views.
String	getClassName()
Set<Object>	getCofactors()
List<EnzymeComment>	getComments()
List<EnzymeComment>	getComments(EnzymeViewConstant view) Deprecated. use getComments(String) instead
List<EnzymeComment>	getComments(String view)
List<EnzymeComment>	getComments(View theView)
EnzymeName	getCommonName()
EnzymeName	getCommonName(EnzymeViewConstant view) Returns the first common name which view value matches the parameter's view value.
List<EnzymeName>	getCommonNames()
EnzymeCommissionNumber	getEc()
EnzymaticReactions	getEnzymaticReactions()
EnzymaticReactions	getEnzymaticReactions(View view) Gets a collection of enzymatic reactions for the given view.
HistoryGraph	getHistory()
Long	getId()
SortedSet<EnzymeLink>	getLinks()
SortedSet<EnzymeLink>	getLinks(EnzymeViewConstant view) Deprecated. use getLinks(String) instead
SortedSet<EnzymeLink>	getLinks(String view)
SortedSet<EnzymeLink>	getLinks(View theView) Return the links to entries in external databases.
String	getNote()
List<uk.ac.ebi.rhea.domain.Reaction>	getReactions() Deprecated. use getEnzymaticReactions instead
List<uk.ac.ebi.rhea.domain.Reaction>	getReactions(EnzymeViewConstant view) Deprecated. use getReactions(View) or getReactions(String) instead.
List<uk.ac.ebi.rhea.domain.Reaction>	getReactions(String view)
List<uk.ac.ebi.rhea.domain.Reaction>	getReactions(View view)
List<Reference>	getReferences()
EnzymeSourceConstant	getSource()
Status	getStatus()
String	getSubclassName()
String	getSubSubclassName()
List<EnzymeName>	getSynonyms()
List<EnzymeName>	getSynonyms(EnzymeViewConstant view) Deprecated. use getSynonyms(String) or getSynonyms(View) instead.
List<EnzymeName>	getSynonyms(String view)
List<EnzymeName>	getSynonyms(View theView)
EnzymeName	getSystematicName()
SortedSet<EnzymeLink>	getUniProtLinks()
int	hashCode() Returns the hash code of this object.
boolean	hasNames()
boolean	isActive()
boolean	isGhost()
void	removeCofactor(Cofactor cofactor) Deprecated. use removeCofactor(Object) instead
void	removeCofactor(Object cofactor) Removes a cofactor from the list of cofactors.
void	removeCofactor(String cofactorString) Deprecated. use removeCofactor(Object) instead
void	removeEnzymaticReaction(uk.ac.ebi.rhea.domain.Reaction reaction)
void	removeLink(EnzymeLink link) Removes a link from the list of additional links.
void	removeReaction(String equation) Deprecated. use removeEnzymaticReaction instead
void	removeReference(Reference reference) Removes a reference from the list of references.
void	removeSynonym(String synonym) Removes a synonsm from the list of synonyms.
void	setActive(boolean active)
void	setClassName(String className) Sets the class name.
void	setCofactors(Set<Object> cofactors)
void	setComments(List<EnzymeComment> comments) Sets the list of comments.
void	setCommonNames(List<EnzymeName> commonNames) Sets the list of common names.
void	setEc(EnzymeCommissionNumber ec) Sets the EC number.
void	setEnzymaticReactions(EnzymaticReactions enzymaticReactions)
void	setGhost(boolean ghost)
void	setHistory(HistoryGraph historyGraph) Sets the history graph.
void	setId(Long id)
void	setLinks(SortedSet<EnzymeLink> links) Sets the list of links.
void	setNote(String note) Sets the note.
void	setReactions(List<uk.ac.ebi.rhea.domain.Reaction> reactions) Sets the list of reactions.
void	setReferences(List<Reference> references) Sets the list of refernces.
void	setSource(EnzymeSourceConstant source) Sets the enzyme's source.
void	setStatus(Status status) Sets the enzyme's status.
void	setSubclassName(String subclassName) Sets the subclass name.
void	setSubSubclassName(String subSubclassName) Sets the sub-subclass name.
void	setSynonyms(List<EnzymeName> synonyms) Sets the list of synonyms.
void	setSystematicName(EnzymeName systematicName) Sets the systematic name of the enzyme.

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

EnzymeEntry

public EnzymeEntry()

The default source is INTENZ. Every new instance is active by default.

Method Detail

addReaction

public void addReaction(uk.ac.ebi.rhea.domain.Reaction reaction)

Deprecated. use addEnzymaticReaction instead

Adds a reaction to the list of reactions.

Duplicates are not stored.

Parameters:

reaction - The reaction to be added.

Throws:

NullPointerException - if reaction is null.

addEnzymaticReaction

public void addEnzymaticReaction(uk.ac.ebi.rhea.domain.Reaction reaction,
                                 String view,
                                 boolean iubmb)

Adds a reaction to the list of alternative reactions.

Parameters:

reaction -

view -

iubmb - the IUBMB flag.

addCofactor

public void addCofactor(Cofactor cofactor)

Deprecated. use addCofactor(Object) instead

Adds a cofactor to the list of cofactors.

Duplicates are not stored.

Parameters:

cofactor - The cofactor to be added.

Throws:

NullPointerException - if cofactor is null.

addCofactor

public void addCofactor(Object cofactor)

Adds a cofactor to the list of cofactors.

Parameters:

cofactor - A Cofactor or OperatorSet object.

removeReaction

public void removeReaction(String equation)

Deprecated. use removeEnzymaticReaction instead

Removes a reaction from the list of reactions.

Parameters:

equation - The reaction to be removed.

Throws:

NullPointerException - if equation is null.

removeEnzymaticReaction

public void removeEnzymaticReaction(uk.ac.ebi.rhea.domain.Reaction reaction)

removeCofactor

public void removeCofactor(String cofactorString)

Deprecated. use removeCofactor(Object) instead

Removes a cofactor from the list of cofactors.

Parameters:

cofactorString - The cofactor string to be removed.

Throws:

NullPointerException - if cofactorString is null.

removeCofactor

public void removeCofactor(Cofactor cofactor)

Deprecated. use removeCofactor(Object) instead

Removes a cofactor from the list of cofactors.

Parameters:

cofactor -

removeCofactor

public void removeCofactor(Object cofactor)

Removes a cofactor from the list of cofactors.

Parameters:

cofactor -

addSynonym

public void addSynonym(EnzymeName synonym)

Adds a synonsm to the list of synonyms.

Parameters:

synonym - The synonym to be added.

Throws:

NullPointerException - if synonym is null.

removeSynonym

public void removeSynonym(String synonym)

Removes a synonsm from the list of synonyms.

Parameters:

synonym - The synonym to be removed.

Throws:

NullPointerException - if synonym is null.

addLink

public void addLink(EnzymeLink link)

Adds a link to the list of additional links.

Duplicates are not stored.

Parameters:

link - The link to be added.

Throws:

NullPointerException - if link is null.

removeLink

public void removeLink(EnzymeLink link)

Removes a link from the list of additional links.

Parameters:

link - The link to be removed.

Throws:

NullPointerException - if link is null.

addReference

public void addReference(Reference reference)

Adds a reference to the list of references.

Parameters:

reference - The reference to be added.

Throws:

NullPointerException - if reference is null.

removeReference

public void removeReference(Reference reference)

Removes a reference from the list of references.

Parameters:

reference - The reference to be removed.

Throws:

NullPointerException - if reference is null.

equals

public boolean equals(Object o)

Standard equals method.

Overrides:

equals in class Object

Parameters:

o - Object to be compared to this one.

Returns:

true if the objects are equal.

hashCode

public int hashCode()

Returns the hash code of this object.

Overrides:

hashCode in class Object

Returns:

the hash code of this object.

getId

public Long getId()

setId

public void setId(Long id)

getEc

public EnzymeCommissionNumber getEc()

setEc

public void setEc(EnzymeCommissionNumber ec)

Sets the EC number.

Parameters:

ec - The new EC number.

Throws:

NullPointerException - if ec is null.

getClassName

public String getClassName()

setClassName

public void setClassName(String className)

Sets the class name.

Parameters:

className - The class name.

Throws:

NullPointerException - if className is null

IllegalArgumentException - if className is empty.

getSubclassName

public String getSubclassName()

setSubclassName

public void setSubclassName(String subclassName)

Sets the subclass name.

Parameters:

subclassName - The subclass name.

Throws:

NullPointerException - if subclassName is null

IllegalArgumentException - if subclassName is empty.

getSubSubclassName

public String getSubSubclassName()

setSubSubclassName

public void setSubSubclassName(String subSubclassName)

Sets the sub-subclass name.

Parameters:

subSubclassName - The sub-subclass name.

Throws:

NullPointerException - if subSubclassName is null.

getCommonNames

public List<EnzymeName> getCommonNames()

getCommonName

public EnzymeName getCommonName()

Returns:

the IntEnz common name.

getCommonName

public EnzymeName getCommonName(EnzymeViewConstant view)

Returns the first common name which view value matches the parameter's view value.

Parameters:

view - web view (defaults to INTENZ)

Returns:

the common name.

Throws:

IllegalArgumentException - if view is not either uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.INTENZ, uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.IUBMB or uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.SIB .

setCommonNames

public void setCommonNames(List<EnzymeName> commonNames)
                    throws EnzymeNameException

Sets the list of common names.

An enzyme must have at least one or at most two common names. Empty strings will be omitted.

Parameters:

commonNames - List of common names.

Throws:

NullPointerException - if commonNames is null.

EnzymeNameException - if the list of common names does contain less than 1 or more than 2 common names or if the type of a name in the list is not defined as EnzymeNameTypeConstant.COMMON_NAME.

addCommonName

public void addCommonName(EnzymeName commonName)
                   throws EnzymeNameException

Adds a common name to the list of common names.

If the list already contains two elements an uk.ac.ebi.intenz.webapp.exceptions.EnzymeNameException is thrown. Empty strings will be omitted.

Parameters:

commonName - The common name to be added.

Throws:

EnzymeNameException - if the list of common names already contains two elements.

getSystematicName

public EnzymeName getSystematicName()

setSystematicName

public void setSystematicName(EnzymeName systematicName)

Sets the systematic name of the enzyme.

Parameters:

systematicName - The systematic name.

Throws:

NullPointerException - if systematicName is null.

getReactions

public List<uk.ac.ebi.rhea.domain.Reaction> getReactions()

Deprecated. use getEnzymaticReactions instead

getReactions

public List<uk.ac.ebi.rhea.domain.Reaction> getReactions(EnzymeViewConstant view)

Deprecated. use getReactions(View) or getReactions(String) instead.

Returns a list of reactions which view values match the parameter's view value.

Returns:

the ArrayList of reactions.

Throws:

NullPointerException - if view is null.

IllegalArgumentException - if view is not either uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.INTENZ, uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.IUBMB or uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.SIB .

getReactions

public List<uk.ac.ebi.rhea.domain.Reaction> getReactions(String view)

getReactions

public List<uk.ac.ebi.rhea.domain.Reaction> getReactions(View view)

getEnzymaticReactions

public EnzymaticReactions getEnzymaticReactions(View view)

Gets a collection of enzymatic reactions for the given view.

Parameters:

view - a web view.

Returns:

an EnzymaticReactions object containing only reactions in the given view.

Since:

4.3.0

setReactions

public void setReactions(List<uk.ac.ebi.rhea.domain.Reaction> reactions)
                  throws EnzymeReactionException

Sets the list of reactions.

Empty reaction strings will be omitted.

Parameters:

reactions - The list of reactions.

Throws:

EnzymeReactionException - if the list of reactions is empty.

getEnzymaticReactions

public EnzymaticReactions getEnzymaticReactions()

setEnzymaticReactions

public void setEnzymaticReactions(EnzymaticReactions enzymaticReactions)

getCofactors

public Set<Object> getCofactors()

setCofactors

public void setCofactors(Set<Object> cofactors)

getSynonyms

public List<EnzymeName> getSynonyms()

getSynonyms

public List<EnzymeName> getSynonyms(String view)

getSynonyms

public List<EnzymeName> getSynonyms(View theView)

getSynonyms

public List<EnzymeName> getSynonyms(EnzymeViewConstant view)

Deprecated. use getSynonyms(String) or getSynonyms(View) instead.

Returns a list of synonyms which view values match the parameter's view value.

Returns:

the ArrayList of synonyms.

Throws:

NullPointerException - if view is null.

IllegalArgumentException - if view is not either uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.INTENZ, uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.IUBMB or uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.SIB .

setSynonyms

public void setSynonyms(List<EnzymeName> synonyms)

Sets the list of synonyms.

Parameters:

synonyms - The list of synonyms.

Throws:

NullPointerException - if synonyms is null.

getComments

public List<EnzymeComment> getComments()

getComments

public List<EnzymeComment> getComments(String view)

getComments

public List<EnzymeComment> getComments(View theView)

getComments

public List<EnzymeComment> getComments(EnzymeViewConstant view)

Deprecated. use getComments(String) instead

Returns a list of comments which view values match the parameter's view value.

Returns:

the ArrayList of comments.

Throws:

NullPointerException - if view is null.

IllegalArgumentException - if view is not either uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.INTENZ, uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.IUBMB or uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.SIB .

setComments

public void setComments(List<EnzymeComment> comments)

Sets the list of comments.

Parameters:

comments - The list of comments.

Throws:

NullPointerException - if comments is null.

getLinks

public SortedSet<EnzymeLink> getLinks()

getLinks

public SortedSet<EnzymeLink> getLinks(String view)

getCasNumbers

public SortedSet<EnzymeLink> getCasNumbers()

CAS numbers for IntEnz and IUBMB views.

Returns:

getUniProtLinks

public SortedSet<EnzymeLink> getUniProtLinks()

getLinks

public SortedSet<EnzymeLink> getLinks(View theView)

Return the links to entries in external databases. These exclude:

• CAS numbers (they are just identifiers, without any URL to go to). Use getCasNumbers.
• UniProt links. Use getUniProtLinks.

Parameters:

theView -

Returns:

getLinks

public SortedSet<EnzymeLink> getLinks(EnzymeViewConstant view)

Deprecated. use getLinks(String) instead

Parameters:

view -

Returns:

setLinks

public void setLinks(SortedSet<EnzymeLink> links)

Sets the list of links.

Parameters:

links - The list of links.

Throws:

NullPointerException - if links is null.

getReferences

public List<Reference> getReferences()

setReferences

public void setReferences(List<Reference> references)
                   throws EnzymeReferenceException

Sets the list of refernces.

Parameters:

references - The list of references.

Throws:

EnzymeReferenceException - if references is null.

getNote

public String getNote()

setNote

public void setNote(String note)

Sets the note.

Parameters:

note - the note.

Throws:

NullPointerException - if note is null.

getHistory

public HistoryGraph getHistory()

setHistory

public void setHistory(HistoryGraph historyGraph)

Sets the history graph.

Parameters:

historyGraph - the history graph.

Throws:

NullPointerException - if historyGraph is null.

getStatus

public Status getStatus()

setStatus

public void setStatus(Status status)

Sets the enzyme's status.

Parameters:

status - The enzyme's status.

Throws:

NullPointerException - if status is null.

getSource

public EnzymeSourceConstant getSource()

setSource

public void setSource(EnzymeSourceConstant source)

Sets the enzyme's source.

Parameters:

source - The enzyme's source.

Throws:

NullPointerException - if source is null.

isActive

public boolean isActive()

setActive

public void setActive(boolean active)

isGhost

public boolean isGhost()

setGhost

public void setGhost(boolean ghost)

hasNames

public boolean hasNames()