EnzymeEntry (IntEnz core module 4.3.3 API)

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

Constructors
Constructor and Description

EnzymeEntry()
The default source is INTENZ.

Constructors
Constructor and Description
`EnzymeEntry()` The default source is `INTENZ`.

Method Summary

Methods
Modifier and Type	Method and Description
`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()
```

Class EnzymeEntry

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

EnzymeEntry

Method Detail

addReaction

addEnzymaticReaction

addCofactor

addCofactor

removeReaction

removeEnzymaticReaction

removeCofactor

removeCofactor

removeCofactor

addSynonym

removeSynonym

addLink

removeLink

addReference

removeReference

equals

hashCode

getId

setId

getEc

setEc

getClassName

setClassName

getSubclassName

setSubclassName

getSubSubclassName

setSubSubclassName

getCommonNames

getCommonName

getCommonName

setCommonNames

addCommonName

getSystematicName

setSystematicName

getReactions

getReactions

getReactions

getReactions

getEnzymaticReactions

setReactions

getEnzymaticReactions

setEnzymaticReactions

getCofactors

setCofactors

getSynonyms

getSynonyms

getSynonyms

getSynonyms

setSynonyms

getComments

getComments

getComments

getComments

setComments

getLinks

getLinks

getCasNumbers

getUniProtLinks

getLinks

getLinks

setLinks

getReferences

setReferences

getNote

setNote

getHistory

setHistory

getStatus

setStatus

getSource

setSource

isActive

setActive