Index (IntEnz core module 4.3.3 API)

A B C D E F G H I J K L M N O P R S T U V W X

A

add(Reaction, String, boolean) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions: Adds a reaction to the list.
add(EnzymaticReactions) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions: Adds several reactions to the list in one go.
add(EnzymaticReactions.VisibleReaction) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
addAll(Collection<? extends EnzymaticReactions.VisibleReaction>) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
addCofactor(Cofactor) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Deprecated.
use EnzymeEntry.addCofactor(Object) instead
addCofactor(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Adds a cofactor to the list of cofactors.
addCommonName(EnzymeName) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Adds a common name to the list of common names.
addEnzymaticReaction(Reaction, String, boolean) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Adds a reaction to the list of alternative reactions.
addLink(EnzymeLink) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Adds a link to the list of additional links.
addReaction(Reaction) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Deprecated.
use addEnzymaticReaction instead
addReference(Reference) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Adds a reference to the list of references.
addSynonym(EnzymeName) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Adds a synonsm to the list of synonyms.
afterNode - Variable in class uk.ac.ebi.intenz.domain.history.HistoryEvent
AMBIGUOUS - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant
APPROVED - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeStatusConstant: Deprecated.

B

beforeNode - Variable in class uk.ac.ebi.intenz.domain.history.HistoryEvent
Book - Class in uk.ac.ebi.intenz.domain.reference: This class stores additional information about a book.
Book(Long, String, String, String, String, String, String, String, String, String, String, String, EnzymeViewConstant, EnzymeSourceConstant) - Constructor for class uk.ac.ebi.intenz.domain.reference.Book: Returns a Book instance.
BRENDA - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant
BRENDA - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: BRENDA collects functional data about enzymes.
BRENDA - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Static link to the BRENDA database.

C

CAS - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: CAS is commercial and cannot be linked to.
checkForDeletion() - Method in class uk.ac.ebi.intenz.domain.history.HistoryNode: Checks all events of this node for DELETION events and returns the source node of this event.
clear() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
Cofactor - Class in uk.ac.ebi.intenz.domain.enzyme: Cofactors are compounds participating in the reaction and are represented by this class.
Cofactor(String, EnzymeSourceConstant, EnzymeViewConstant) - Constructor for class uk.ac.ebi.intenz.domain.enzyme.Cofactor: Deprecated.
use the valueOf method instead to call the private constructor
Cofactor.Operators - Enum in uk.ac.ebi.intenz.domain.enzyme
Commented - Interface in uk.ac.ebi.intenz.domain.enzyme: Interface for data objects to which a comment is applied.
COMMON_NAME - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeNameTypeConstant
compare(EnzymeEntry, EnzymeEntry) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntryEcComparator
compare(EnzymeEntry, EnzymeEntry) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntryNameComparator
compareTo(XrefDatabaseConstant) - Method in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant
compareTo(EnzymeClass) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeClass: Makes instances of this class comparable.
compareTo(EnzymeCommissionNumber) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Compares this EC number with another one.
compareTo(EnzymeLink) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Used for ordering links in a collection.
compareTo(EnzymeName) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeName
compareTo(EnzymeSubclass) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubclass: Makes instances of this class comparable.
compareTo(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubSubclass: Makes instances of this class comparable.
compareTo(HistoryEvent) - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent: Makes instances of this class comparable.
contains(String) - Static method in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: Checks if the given link source code exists in this enumeration.
contains(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
containsAll(Collection<?>) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
copy(EnzymeCommissionNumber) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Creates a copy of the given EnzymeCommissionNumber.
CREATION - Static variable in class uk.ac.ebi.intenz.domain.constants.EventConstant: Deprecated.
CSA - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: Catalytic Site Atlas provides catalytic residues details.
CSA - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Static link to the CSA database.

D

DataComment - Class in uk.ac.ebi.intenz.domain.enzyme: Deprecated.
use a plain String.
DataComment(Long, String) - Constructor for class uk.ac.ebi.intenz.domain.enzyme.DataComment: Deprecated.
DataComment(String) - Constructor for class uk.ac.ebi.intenz.domain.enzyme.DataComment: Deprecated.
date - Variable in class uk.ac.ebi.intenz.domain.history.HistoryEvent
DELETION - Static variable in class uk.ac.ebi.intenz.domain.constants.EventConstant: Deprecated.
DIAGRAM - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant
DomainException - Exception in uk.ac.ebi.intenz.domain.exceptions: This exception is the base exception for all domain exception and just acts as a wrapper.
DomainException() - Constructor for exception uk.ac.ebi.intenz.domain.exceptions.DomainException
DomainException(String) - Constructor for exception uk.ac.ebi.intenz.domain.exceptions.DomainException
DomainException(String, String) - Constructor for exception uk.ac.ebi.intenz.domain.exceptions.DomainException
DomainObject - Class in uk.ac.ebi.intenz.domain: This class is the base class of most of the domain classes.
DomainObject() - Constructor for class uk.ac.ebi.intenz.domain.DomainObject: The ID is initially set to 0.
DomainObject(Long) - Constructor for class uk.ac.ebi.intenz.domain.DomainObject: Initialises the ID.

E

EcException - Exception in uk.ac.ebi.intenz.domain.exceptions: This exception is thrown when a EC number is not valid (e.g.
EcException() - Constructor for exception uk.ac.ebi.intenz.domain.exceptions.EcException
EcException(String) - Constructor for exception uk.ac.ebi.intenz.domain.exceptions.EcException
EnzymaticReactions - Class in uk.ac.ebi.intenz.domain.enzyme: A collection of alternative reactions catalysed by one enzyme entry.
EnzymaticReactions() - Constructor for class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
EnzymaticReactions.VisibleReaction - Class in uk.ac.ebi.intenz.domain.enzyme: Utility class to wrap a Reaction with the views where it is available and the IUBMB flag.
ENZYME - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: ENZYME is the EXPASY version of the NC-IUBMB Nomenclature containing some additional information (cofactors, improved comments and additional links).
EnzymeClass - Class in uk.ac.ebi.intenz.domain.enzyme: This class represents an enzyme class of the Enzyme Nomenclature.
EnzymeComment - Class in uk.ac.ebi.intenz.domain.enzyme: This class represents a comment of an enzyme entry.
EnzymeComment(String, EnzymeSourceConstant, EnzymeViewConstant) - Constructor for class uk.ac.ebi.intenz.domain.enzyme.EnzymeComment: Returns a EnzymeComment instance.
EnzymeCommissionNumber - Class in uk.ac.ebi.intenz.domain.enzyme: This class represents an Enzyme Commission (EC) number.
EnzymeCommissionNumber.Type - Enum in uk.ac.ebi.intenz.domain.enzyme: Type of EC number.
EnzymeEntry - Class in uk.ac.ebi.intenz.domain.enzyme: This class stores the information of an IntEnz enzyme.
EnzymeEntry() - Constructor for class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: The default source is INTENZ.
EnzymeEntryEcComparator - Class in uk.ac.ebi.intenz.domain.enzyme: Compares enzyme entries according to their EC number.
EnzymeEntryEcComparator() - Constructor for class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntryEcComparator
EnzymeEntryNameComparator - Class in uk.ac.ebi.intenz.domain.enzyme: Compares enzyme entries according to their common name (SwissProt - ASCII - encoding).
EnzymeEntryNameComparator() - Constructor for class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntryNameComparator
EnzymeLink - Class in uk.ac.ebi.intenz.domain.enzyme: An enzyme link is used to store cross-reference information.
EnzymeName - Class in uk.ac.ebi.intenz.domain.enzyme: This class stores a name related to an enzyme.
EnzymeNameException - Exception in uk.ac.ebi.intenz.domain.exceptions: If an error regarding an enzyme name occurs this exception should be thrown.
EnzymeNameException() - Constructor for exception uk.ac.ebi.intenz.domain.exceptions.EnzymeNameException
EnzymeNameException(String) - Constructor for exception uk.ac.ebi.intenz.domain.exceptions.EnzymeNameException
EnzymeNameQualifierConstant - Class in uk.ac.ebi.intenz.domain.constants: This class represents an enumeration of all supported name qualifiers.
EnzymeNameTypeConstant - Class in uk.ac.ebi.intenz.domain.constants: This class represents an enumeration of all database source types.
EnzymeReactionException - Exception in uk.ac.ebi.intenz.domain.exceptions: If an error regarding an enzyme reaction occurs this exception should be thrown.
EnzymeReactionException() - Constructor for exception uk.ac.ebi.intenz.domain.exceptions.EnzymeReactionException
EnzymeReactionException(String) - Constructor for exception uk.ac.ebi.intenz.domain.exceptions.EnzymeReactionException
EnzymeReferenceException - Exception in uk.ac.ebi.intenz.domain.exceptions: If an error regarding an enzyme reference occurs this exception should be thrown.
EnzymeReferenceException() - Constructor for exception uk.ac.ebi.intenz.domain.exceptions.EnzymeReferenceException
EnzymeReferenceException(String) - Constructor for exception uk.ac.ebi.intenz.domain.exceptions.EnzymeReferenceException
EnzymeSourceConstant - Class in uk.ac.ebi.intenz.domain.constants: This class represents an enumeration of all database source types.
EnzymeStatistics - Class in uk.ac.ebi.intenz.domain.stats: This class ...
EnzymeStatistics() - Constructor for class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
EnzymeStatusConstant - Class in uk.ac.ebi.intenz.domain.constants: Deprecated.
use enumeration Status instead.
EnzymeSubclass - Class in uk.ac.ebi.intenz.domain.enzyme: This class represents an enzyme subclass of the Enzyme Nomenclature.
EnzymeSubclass(EnzymeCommissionNumber, String, String, String, List<EnzymeSubSubclass>) - Constructor for class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubclass: Returns an EnzymeSubclass instance.
EnzymeSubSubclass - Class in uk.ac.ebi.intenz.domain.enzyme: This class represents an enzyme sub-subclass of the Enzyme Nomenclature.
EnzymeSubSubclass(EnzymeCommissionNumber, String, String, String, String, List<EnzymeEntry>) - Constructor for class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubSubclass: Returns an EnzymeSubSubclass instance.
EnzymeViewConstant - Class in uk.ac.ebi.intenz.domain.constants: Deprecated.
use enumeration View instead.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant: Standard equals method.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeNameTypeConstant: Standard equals method.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant: Standard equals method.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeStatusConstant: Deprecated.

Standard equals method.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.

Standard equals method.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.constants.EventConstant: Deprecated.

Standard equals method.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: Standard equals method.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.DomainObject
equals(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.Cofactor: Standard equals method.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.DataComment: Deprecated.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
equals(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions.VisibleReaction
equals(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeClass: Standard equals method.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeComment: Standard equals method.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber
equals(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Standard equals method.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Checks for equality.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeName: Standard equals method omitting 'orderIn' attribute, which is irrelevant for this check.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubclass: Standard equals method.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubSubclass: Standard equals method.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.history.FutureEvent: Checks if two FutureEvent objects are equal.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent: Checks if two HistoryEvent objects are equal.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.history.Timeout
equals(Object) - Method in class uk.ac.ebi.intenz.domain.reference.Book: Standard equals() method.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.reference.Journal: Standard equals() method.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.reference.Patent: Standard equals() method.
equals(Object) - Method in class uk.ac.ebi.intenz.domain.reference.Reference: Standard equals() method.
ERGO - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: Deprecated.
This website does not work any more (if it ever did).
ERGO - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Deprecated.
the ERGO website is not working any more.
Event - Enum in uk.ac.ebi.intenz.domain.constants: Events for enzyme entries.
eventClass - Variable in class uk.ac.ebi.intenz.domain.history.HistoryEvent
EventConstant - Class in uk.ac.ebi.intenz.domain.constants: Deprecated.
use enumeration Event instead.
eventId - Variable in class uk.ac.ebi.intenz.domain.history.HistoryEvent
EXPASY - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Static link to the ENZYME database at expasy.org.
EXPLORENZ - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: Link to ExplorEnz (Dublin's MySQL implementation of NC-IUBMB).
EXPLORENZ - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink

F

forView(View) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions: Filters this collection of reactions for a given view.
fromCode(String) - Method in enum uk.ac.ebi.intenz.domain.constants.Event
fromCode(String) - Static method in enum uk.ac.ebi.intenz.domain.constants.Status
FutureEvent - Class in uk.ac.ebi.intenz.domain.history: A future event adds some information to a history event as it has a status and a timeout associated.
FutureEvent() - Constructor for class uk.ac.ebi.intenz.domain.history.FutureEvent: Nothing special here.

G

getAccession() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink
getAfterNode() - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent
getAllEnzymes() - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
getApprovedDeletedEnzymes() - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
getApprovedEnzymes() - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
getAttribute() - Method in enum uk.ac.ebi.intenz.domain.constants.Event
getAuthors() - Method in class uk.ac.ebi.intenz.domain.reference.Reference
getBeforeNode() - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent
getCasNumbers() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: CAS numbers for IntEnz and IUBMB views.
getClasses() - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
getClassName() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getClassName() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubclass
getClassName() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubSubclass
getCode() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeStatusConstant: Deprecated.

Returns the status code.
getCode() - Method in enum uk.ac.ebi.intenz.domain.constants.Event
getCode() - Method in class uk.ac.ebi.intenz.domain.constants.EventConstant: Deprecated.

Returns the code of this event.
getCode() - Method in enum uk.ac.ebi.intenz.domain.constants.Status
getCode() - Method in enum uk.ac.ebi.intenz.domain.enzyme.Cofactor.Operators
getCodes() - Static method in enum uk.ac.ebi.intenz.domain.enzyme.Cofactor.Operators
getCofactors() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getCofactorValue() - Method in class uk.ac.ebi.intenz.domain.enzyme.Cofactor: Deprecated.
use Cofactor.getCompound().getName() or Cofactor.toString() instead
getComment() - Method in class uk.ac.ebi.intenz.domain.enzyme.DataComment: Deprecated.
getComments() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getComments(String) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getComments(View) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getComments(EnzymeViewConstant) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Deprecated.
use EnzymeEntry.getComments(String) instead
getCommentText() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeComment
getCommonName() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getCommonName(EnzymeViewConstant) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Returns the first common name which view value matches the parameter's view value.
getCommonNameInstance(String, EnzymeSourceConstant, EnzymeViewConstant) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeName: Returns an EnzymeName instance representing an enzyme's common (recommended) name.
getCommonNames() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getCompound() - Method in class uk.ac.ebi.intenz.domain.enzyme.Cofactor
getDatabaseCode() - Method in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant
getDatabaseCodeOf(String) - Static method in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant
getDataComment() - Method in interface uk.ac.ebi.intenz.domain.enzyme.Commented
getDataComment() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink
getDate() - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent
getDescription() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeClass
getDescription() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubclass
getDescription() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubSubclass
getDisplayName() - Method in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant
getDisplayNameOf(String) - Static method in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: Returns the display name of the source defined by databaseCode.
getDueDate() - Method in class uk.ac.ebi.intenz.domain.history.Timeout
getEc() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeClass: Returns the hash code of this object.
getEc() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getEc() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubclass
getEc() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubSubclass
getEc1() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Returns the enzyme's class number.
getEc2() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Returns the enzyme's subclass number.
getEc3() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Returns the enzyme's sub-subclass number.
getEc4() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Returns the enzyme's number.
getEdges() - Method in class uk.ac.ebi.intenz.domain.history.HistoryGraph
getEdges() - Method in class uk.ac.ebi.intenz.domain.history.HistoryNode
getEdition(boolean) - Method in class uk.ac.ebi.intenz.domain.reference.Book: Returns the edition string as it is stored in the database or formatted.
getEdition() - Method in class uk.ac.ebi.intenz.domain.reference.Book
getEditor(boolean) - Method in class uk.ac.ebi.intenz.domain.reference.Book: Returns the editor string as it is stored in the database or formatted.
getEditor() - Method in class uk.ac.ebi.intenz.domain.reference.Book
getEntries() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubSubclass
getEnzymaticReactions(View) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Gets a collection of enzymatic reactions for the given view.
getEnzymaticReactions() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getEnzymeEntry() - Method in class uk.ac.ebi.intenz.domain.history.HistoryNode
getEnzymeId() - Method in class uk.ac.ebi.intenz.domain.history.Timeout
getEventClass() - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent
getEventId() - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent
getFirstPage() - Method in class uk.ac.ebi.intenz.domain.reference.Book
getFirstPage() - Method in class uk.ac.ebi.intenz.domain.reference.Journal
getFullUrl(String) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Links with the EC number as identifier need to call this method to get the correct URL.
getGroupId() - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent
getHistory() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getHistoryLine() - Method in class uk.ac.ebi.intenz.domain.history.HistoryNode
getId() - Method in class uk.ac.ebi.intenz.domain.DomainObject
getId() - Method in class uk.ac.ebi.intenz.domain.enzyme.DataComment: Deprecated.
getId() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getLabel() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant
getLabel() - Method in enum uk.ac.ebi.intenz.domain.constants.View
getLastPage() - Method in class uk.ac.ebi.intenz.domain.reference.Book
getLastPage() - Method in class uk.ac.ebi.intenz.domain.reference.Journal
getLatestHistoryEventOfAll() - Method in class uk.ac.ebi.intenz.domain.history.HistoryGraph: Returns the most recent event of the WHOLE graph.
getLatestHistoryEventOfRoot() - Method in class uk.ac.ebi.intenz.domain.history.HistoryGraph: Returns the most recent event of the root node only.
getLatestRelevantHistoryEventOfRoot() - Method in class uk.ac.ebi.intenz.domain.history.HistoryGraph: Returns the most recent event of the root node only.
getLinks() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getLinks(String) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getLinks(View) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Return the links to entries in external databases.
getLinks(EnzymeViewConstant) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Deprecated.
use EnzymeEntry.getLinks(String) instead
getListOrderCriterion() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Creates a unique name for this link.
getMedlineId() - Method in class uk.ac.ebi.intenz.domain.reference.Journal
getMessageKey() - Method in exception uk.ac.ebi.intenz.domain.exceptions.DomainException
getName() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeClass
getName() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink
getName() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeName: Returns the name.
getName() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubclass
getName() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubSubclass
getNote() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getNote() - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent
getPatentNumber() - Method in class uk.ac.ebi.intenz.domain.reference.Patent
getProperty() - Method in exception uk.ac.ebi.intenz.domain.exceptions.DomainException
getProposedDeletedEnzymes() - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
getProposedEnzymes() - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
getPubId() - Method in class uk.ac.ebi.intenz.domain.reference.Reference
getPublisher() - Method in class uk.ac.ebi.intenz.domain.reference.Book
getPublisherPlace() - Method in class uk.ac.ebi.intenz.domain.reference.Book
getPubMedId() - Method in class uk.ac.ebi.intenz.domain.reference.Journal
getPubName() - Method in class uk.ac.ebi.intenz.domain.reference.Book
getPubName() - Method in class uk.ac.ebi.intenz.domain.reference.Journal
getQualifier() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeName: Returns the name's qualifier.
getReaction(int) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
getReaction() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions.VisibleReaction
getReactionIubmbFlag(int) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions: Has a reaction the IUBMB flag set?
getReactions(View) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
getReactions() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Deprecated.
use getEnzymaticReactions instead
getReactions(EnzymeViewConstant) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Deprecated.
use EnzymeEntry.getReactions(View) or EnzymeEntry.getReactions(String) instead.
getReactions(String) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getReactions(View) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getReactionView(int) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
getReferences() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getRelative(HistoryNode) - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent: Returns the relative node of the given node.
getRootNode() - Method in class uk.ac.ebi.intenz.domain.history.HistoryGraph
getSource() - Method in class uk.ac.ebi.intenz.domain.enzyme.Cofactor
getSource() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeComment
getSource() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getSource() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink
getSource() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeName: Returns the name's source.
getSource() - Method in class uk.ac.ebi.intenz.domain.reference.Reference
getSpecificUrl() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink
getStartDate() - Method in class uk.ac.ebi.intenz.domain.history.Timeout
getStaticLink(XrefDatabaseConstant) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink
getStatus() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getStatus() - Method in class uk.ac.ebi.intenz.domain.history.FutureEvent
getSubclasses() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeClass
getSubclasses() - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
getSubclassName() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getSubclassName() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubSubclass
getSubSubclasses() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubclass
getSubsubclasses() - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
getSubSubclassName() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getSuggestedDeletedEnzymes() - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
getSuggestedEnzymes() - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
getSynonymInstance(String, EnzymeNameQualifierConstant, EnzymeSourceConstant, EnzymeViewConstant) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeName: Returns an EnzymeName instance representing an enzyme's synonym.
getSynonyms() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getSynonyms(String) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getSynonyms(View) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getSynonyms(EnzymeViewConstant) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Deprecated.
use EnzymeEntry.getSynonyms(String) or EnzymeEntry.getSynonyms(View) instead.
getSystematicName() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getSystematicNameInstance(String, EnzymeSourceConstant, EnzymeViewConstant) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeName: Returns an EnzymeName instance representing an enzyme's systematic name.
getTimeout() - Method in class uk.ac.ebi.intenz.domain.history.FutureEvent
getTimeoutId() - Method in class uk.ac.ebi.intenz.domain.history.Timeout
getTitle() - Method in class uk.ac.ebi.intenz.domain.reference.Reference
getType() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Returns the type of this EC number.
getType() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeName: Returns the name's type.
getUniProtLinks() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
getUrl() - Method in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant
getUrlOf(String) - Static method in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: Returns the URL of the given source code.
getView() - Method in class uk.ac.ebi.intenz.domain.enzyme.Cofactor
getView() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions.VisibleReaction
getView() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeComment
getView() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink
getView() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeName: Returns the name's view code.
getView() - Method in interface uk.ac.ebi.intenz.domain.enzyme.Viewable
getView() - Method in class uk.ac.ebi.intenz.domain.reference.Reference
getVolume() - Method in class uk.ac.ebi.intenz.domain.reference.Book
getVolume() - Method in class uk.ac.ebi.intenz.domain.reference.Journal
getXrefDatabaseConstant() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink
getYear() - Method in class uk.ac.ebi.intenz.domain.reference.Reference
GO - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: GO is the Gene Ontology database.
GO - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Static link to the Gene Ontology database.
groupId - Variable in class uk.ac.ebi.intenz.domain.history.HistoryEvent

H

hashCode() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant: Returns the hash code of this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeNameTypeConstant: Returns the hash code of this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant: Returns the hash code of this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeStatusConstant: Deprecated.

Returns the hash code of this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.

Returns the hash code of this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.constants.EventConstant: Deprecated.

Returns the hash code of this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: Returns the hash code of this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.DomainObject
hashCode() - Method in class uk.ac.ebi.intenz.domain.enzyme.Cofactor: Returns the hash code of this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.enzyme.DataComment: Deprecated.
hashCode() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
hashCode() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions.VisibleReaction
hashCode() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeClass
hashCode() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeComment: Returns the hash code of this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber
hashCode() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Returns the hash code of this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Generates a hash code for this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeName: Returns the hash code of this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubclass: Returns the hash code of this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeSubSubclass: Returns the hash code of this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.history.FutureEvent: Calculates a unique hash code.
hashCode() - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent: Calculates a unique hash code.
hashCode() - Method in class uk.ac.ebi.intenz.domain.history.Timeout
hashCode() - Method in class uk.ac.ebi.intenz.domain.reference.Book: Generates a hash code for this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.reference.Journal: Generates a hash code for this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.reference.Patent: Generates a hash code for this object.
hashCode() - Method in class uk.ac.ebi.intenz.domain.reference.Reference: Generates a hash code for this object.
hasNames() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
HistoryEvent - Class in uk.ac.ebi.intenz.domain.history: The history event is a structural copy of the corresponding database table, that is attributes of this class correspond to the table's columns.
HistoryEvent() - Constructor for class uk.ac.ebi.intenz.domain.history.HistoryEvent: Nothing special.
HistoryGraph - Class in uk.ac.ebi.intenz.domain.history: The directed acyclic history graph stores all events related to an enzyme.
HistoryGraph(HistoryNode) - Constructor for class uk.ac.ebi.intenz.domain.history.HistoryGraph: Returns a HistoryGraph instance.
HistoryNode - Class in uk.ac.ebi.intenz.domain.history: This node represents an enzyme within the history graph of an enzyme.
HistoryNode() - Constructor for class uk.ac.ebi.intenz.domain.history.HistoryNode: Nothing special.

I

id - Variable in class uk.ac.ebi.intenz.domain.DomainObject: IDs can be long, therefore this data type.
INCORRECT - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant
INTENZ - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant
INTENZ - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
isActive() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
isDeletedRootNode() - Method in class uk.ac.ebi.intenz.domain.history.HistoryGraph: Returns true if this node's event is a DELETION event.
isEmpty() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
isGhost() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
isInIntEnzView() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
isInIntEnzView(String) - Static method in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
isInIUBMBView() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
isInIUBMBView(String) - Static method in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
isInSIBView() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
isInSIBView(String) - Static method in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
isInView(EnzymeViewConstant, Object) - Static method in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
isIubmb() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions.VisibleReaction
isPreliminary(String) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Checks lazily if the given EC number is preliminary (according to UniProt format of preliminary EC numbers, see EnzymeCommissionNumber.PRELIMINARY_PREFIX).
isRoot() - Method in class uk.ac.ebi.intenz.domain.history.HistoryNode
isStaticLink(XrefDatabaseConstant) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Checks if the given link is a static link.
isSuccessor(HistoryNode) - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent: Returns true if the given node is the successor of this node.
isTransferredRootNode() - Method in class uk.ac.ebi.intenz.domain.history.HistoryGraph: Returns true if this node's event is a TRANSFER event.
isUniqueXrefDatabaseCode(String) - Static method in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant
isUniqueXrefDatabaseName(String) - Static method in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant
isValid(String) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Checks whether a given EC number is valid.
isXref(String) - Static method in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: Returns true if this link belongs to the XREFS table.
isXref() - Method in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant
iterator() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
IUBMB - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant
IUBMB - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
IUBMB_INTENZ - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
IUBMB_SIB - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.

J

Journal - Class in uk.ac.ebi.intenz.domain.reference: This class stores additional information about a journal.
Journal(Long, String, String, String, String, String, String, String, String, String, EnzymeViewConstant, EnzymeSourceConstant) - Constructor for class uk.ac.ebi.intenz.domain.reference.Journal: Returns a Journal instance.

K

KEGG - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: KEGG comprises several databases storing information especially related to enzymes (e.g.
KEGG - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Static link to the KEGG database.

L

LINK_SOURCE_CONSTANTS - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: All link sources ordered alphabetically.

M

MEROPS - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: MEROPS is a resource for peptidases.
METACYC - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant
METACYC - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Link to MetaCyc.
MIM - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: OMIM stores information about human genetic diseases.
MISLEADING - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant
MISPRINT - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant
MODIFICATION - Static variable in class uk.ac.ebi.intenz.domain.constants.EventConstant: Deprecated.

N

NC_IUBMB - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: Gerry Moss' web pages (Nomenclature Comitee of the IUBMB).
NC_IUBMB - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Static link to the GM pages (NC-IUBMB).
NIST74 - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: NIST74 provides further information about the catalytic activity.
NIST74 - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Static link to the NIST 74 database.
note - Variable in class uk.ac.ebi.intenz.domain.history.HistoryEvent

O

OBSOLETE - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant
OTHER_NAME - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeNameTypeConstant

P

Patent - Class in uk.ac.ebi.intenz.domain.reference: This class stores additional information about patents.
Patent(Long, String, String, String, String, EnzymeViewConstant, EnzymeSourceConstant) - Constructor for class uk.ac.ebi.intenz.domain.reference.Patent: Returns a Patent instance.
PDB - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: Link to the Protein Data Bank (PDB).
PDB - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Static link to the PDB database.
PRELIMINARY_PREFIX - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: The character prefixing the fourth digit in preliminary EC numbers.
PROPOSED - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeStatusConstant: Deprecated.
PROSITE - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: PROSITE is located at the SIB and contains information about protein families and domains.

R

Reference - Class in uk.ac.ebi.intenz.domain.reference: This class represents a reference and serves as the super class for all types of references.
remove(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
removeAll(Collection<?>) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
removeCofactor(String) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Deprecated.
use removeCofactor(Object) instead
removeCofactor(Cofactor) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Deprecated.
use EnzymeEntry.removeCofactor(Object) instead
removeCofactor(Object) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Removes a cofactor from the list of cofactors.
removeEnzymaticReaction(Reaction) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
removeLink(EnzymeLink) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Removes a link from the list of additional links.
removeReaction(Reaction) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions: Removes a reaction from the list, no matter its view.
removeReaction(String) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Deprecated.
use removeEnzymaticReaction instead
removeReference(Reference) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Removes a reference from the list of references.
removeSynonym(String) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Removes a synonsm from the list of synonyms.
retainAll(Collection<?>) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions

S

setActive(boolean) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
setAfterNode(HistoryNode) - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent
setAllEnzymes(int) - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
setApprovedDeletedEnzymes(int) - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
setApprovedEnzymes(int) - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
setBeforeNode(HistoryNode) - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent
setClasses(int) - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
setClassName(String) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Sets the class name.
setCofactors(Set<Object>) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
setComments(List<EnzymeComment>) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Sets the list of comments.
setCommonNames(List<EnzymeName>) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Sets the list of common names.
setDataComment(String) - Method in interface uk.ac.ebi.intenz.domain.enzyme.Commented
setDataComment(String) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink
setDate(Date) - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent
setDueDate(Date) - Method in class uk.ac.ebi.intenz.domain.history.Timeout
setEc(EnzymeCommissionNumber) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Sets the EC number.
setEdges(List<HistoryEvent>) - Method in class uk.ac.ebi.intenz.domain.history.HistoryNode
setEnzymaticReactions(EnzymaticReactions) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
setEnzymeEntry(EnzymeEntry) - Method in class uk.ac.ebi.intenz.domain.history.HistoryNode
setEnzymeId(int) - Method in class uk.ac.ebi.intenz.domain.history.Timeout
setEventClass(EventConstant) - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent
setEventId(Long) - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent
setGhost(boolean) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
setGroupId(Long) - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent
setHistory(HistoryGraph) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Sets the history graph.
setHistoryLine(String) - Method in class uk.ac.ebi.intenz.domain.history.HistoryNode
setId(long) - Method in class uk.ac.ebi.intenz.domain.enzyme.DataComment: Deprecated.
setId(Long) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry
setLinks(SortedSet<EnzymeLink>) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Sets the list of links.
setMessageKey(String) - Method in exception uk.ac.ebi.intenz.domain.exceptions.DomainException
setNote(String) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Sets the note.
setNote(String) - Method in class uk.ac.ebi.intenz.domain.history.HistoryEvent
setProperty(String) - Method in exception uk.ac.ebi.intenz.domain.exceptions.DomainException
setProposedDeletedEnzymes(int) - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
setProposedEnzymes(int) - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
setReactions(LinkedHashSet<EnzymaticReactions.VisibleReaction>) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
setReactions(List<Reaction>) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Sets the list of reactions.
setReferences(List<Reference>) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Sets the list of refernces.
setRoot(boolean) - Method in class uk.ac.ebi.intenz.domain.history.HistoryNode
setSource(EnzymeSourceConstant) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Sets the enzyme's source.
setStartDate(Date) - Method in class uk.ac.ebi.intenz.domain.history.Timeout
setStatus(Status) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Sets the enzyme's status.
setStatus(Status) - Method in class uk.ac.ebi.intenz.domain.history.FutureEvent
setSubclasses(int) - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
setSubclassName(String) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Sets the subclass name.
setSubsubclasses(int) - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
setSubSubclassName(String) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Sets the sub-subclass name.
setSuggestedDeletedEnzymes(int) - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
setSuggestedEnzymes(int) - Method in class uk.ac.ebi.intenz.domain.stats.EnzymeStatistics
setSynonyms(List<EnzymeName>) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Sets the list of synonyms.
setSystematicName(EnzymeName) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry: Sets the systematic name of the enzyme.
setTimeout(Timeout) - Method in class uk.ac.ebi.intenz.domain.history.FutureEvent
setTimeoutId(int) - Method in class uk.ac.ebi.intenz.domain.history.Timeout
SIB - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant
SIB - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
SIB_INTENZ - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
size() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
Status - Enum in uk.ac.ebi.intenz.domain.constants: Enzyme entry status.
SUGGESTED - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeStatusConstant: Deprecated.
SWISSPROT - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: Swiss-Prot is THE protein sequence database.
SYSTEMATIC_NAME - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeNameTypeConstant

T

Timeout - Class in uk.ac.ebi.intenz.domain.history: This class stores information about the timeout related to a future event.
Timeout() - Constructor for class uk.ac.ebi.intenz.domain.history.Timeout
toArray() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
toArray(VisibleReaction[]) - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymaticReactions
toASCII(EnzymeNameQualifierConstant) - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant: Deprecated.
toDisplayImage(String) - Static method in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
MVC sin
toDisplayImage() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
MVC sin
toDisplayString(String) - Static method in class uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant: Deprecated.
toDisplayString() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant: Deprecated.
toDisplayString(String) - Static method in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
toDisplayString() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
toEditableHTML() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant: Deprecated.
MVC sin
toHTML(String) - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant: Deprecated.
MVC sin
toString() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant: Returns the name qualifier.
toString() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeNameTypeConstant: Returns the database code.
toString() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant: Returns the database code.
toString() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeStatusConstant: Deprecated.

Returns the status code's text.
toString() - Method in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.

Returns the database code.
toString() - Method in class uk.ac.ebi.intenz.domain.constants.EventConstant: Deprecated.

Returns the database code.
toString() - Method in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: Returns the display name.
toString() - Method in enum uk.ac.ebi.intenz.domain.enzyme.Cofactor.Operators
toString() - Method in class uk.ac.ebi.intenz.domain.enzyme.Cofactor
toString() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Returns a string representation of this EC number.
toString() - Method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Provides a string representation of an EnzymeLink.
toString() - Method in class uk.ac.ebi.intenz.domain.history.HistoryNode
toString() - Method in class uk.ac.ebi.intenz.domain.reference.Book: Returns a string representation of this book.
toString() - Method in class uk.ac.ebi.intenz.domain.reference.Journal: Returns a string representation of this book.
toString() - Method in class uk.ac.ebi.intenz.domain.reference.Patent: Returns a string representation of this patent.
toXML(int, boolean) - Method in class uk.ac.ebi.intenz.domain.reference.Book
toXML(int, boolean) - Method in class uk.ac.ebi.intenz.domain.reference.Journal
toXML(int, boolean) - Method in class uk.ac.ebi.intenz.domain.reference.Patent
toXML(int, boolean) - Method in class uk.ac.ebi.intenz.domain.reference.Reference
TRANSFER - Static variable in class uk.ac.ebi.intenz.domain.constants.EventConstant: Deprecated.

U

uk.ac.ebi.intenz.domain - package uk.ac.ebi.intenz.domain: Contains the IntEnz domain packages and classes.
uk.ac.ebi.intenz.domain.constants - package uk.ac.ebi.intenz.domain.constants: The most commonly used constants are implemented as typesafe enums.
uk.ac.ebi.intenz.domain.enzyme - package uk.ac.ebi.intenz.domain.enzyme: The core enzyme information is held in these classes.
uk.ac.ebi.intenz.domain.exceptions - package uk.ac.ebi.intenz.domain.exceptions
uk.ac.ebi.intenz.domain.history - package uk.ac.ebi.intenz.domain.history: The classification classes will be used to represent the EC hierarchy and the enzyme history.
uk.ac.ebi.intenz.domain.reference - package uk.ac.ebi.intenz.domain.reference: Classes for storing publication data.
uk.ac.ebi.intenz.domain.stats - package uk.ac.ebi.intenz.domain.stats
UMBBD - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: UM-BBD is a comprehensive resource about enzymes also containing enzymes which haven't got an EC number yet.
UMBBD - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Static link to the UM-BBD database.
UNDEF - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant
UNDEF - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeNameTypeConstant
UNDEF - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant
UNDEF - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
UNDEF - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant
UNDEF - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Constant for an undefined EC which can be used for new enzyme suggestions where the EC number is not known (yet).
UNDEF - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeName
UNIPATHWAY - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant
UNIPATHWAY - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink
UNIQUE_LINK_SOURCES - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: This set contains all link which can only occur once in an enzyme entry.

V

valueOf(String) - Static method in class uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant: Returns an EnzymeNameQualifierConstant instance of the given qualifier string.
valueOf(String) - Static method in class uk.ac.ebi.intenz.domain.constants.EnzymeNameTypeConstant: Returns an EnzymeNameTypeConstant instance of the given type string.
valueOf(String) - Static method in class uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant: Returns the corresponding instance of the given source code.
valueOf(String) - Static method in class uk.ac.ebi.intenz.domain.constants.EnzymeStatusConstant: Deprecated.

Returns the corresponding instance of the given status code.
valueOf(String) - Static method in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.

Returns the corresponding instance of the given view code.
valueOf(String) - Static method in enum uk.ac.ebi.intenz.domain.constants.Event: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in class uk.ac.ebi.intenz.domain.constants.EventConstant: Deprecated.

Returns the corresponding instance of the given event code.
valueOf(String) - Static method in enum uk.ac.ebi.intenz.domain.constants.Status: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.intenz.domain.constants.View: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant
valueOf(String) - Static method in enum uk.ac.ebi.intenz.domain.enzyme.Cofactor.Operators: Returns the enum constant of this type with the specified name.
valueOf(Compound, EnzymeSourceConstant, EnzymeViewConstant) - Static method in class uk.ac.ebi.intenz.domain.enzyme.Cofactor: Builds a cofactor from the passed parameters.
valueOf(String, String) - Static method in class uk.ac.ebi.intenz.domain.enzyme.DataComment: Deprecated.
valueOf(EnzymeCommissionNumber, String, String, List<EnzymeSubclass>) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeClass: Returns an EnzymeClass instance.
valueOf(String) - Static method in enum uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber.Type: Returns the enum constant of this type with the specified name.
valueOf(int) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Returns an EnzymeCommissionNumber instance defined by the given integer.
valueOf(int, int) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Returns an EnzymeCommissionNumber instance defined by the given integers.
valueOf(int, int, int) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Returns an EnzymeCommissionNumber instance defined by the given integers.
valueOf(int, int, int, int) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Returns an EnzymeCommissionNumber instance defined by the given integers.
valueOf(int, int, int, int, boolean) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Constructor allowing preliminary EC numbers.
valueOf(String) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber: Returns an EnzymeCommissionNumber instance defined by the given string.
valueOf(XrefDatabaseConstant, String, String, String, EnzymeSourceConstant, EnzymeViewConstant) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Returns an EnzymeLink instance.
valueOf(XrefDatabaseConstant, String, String, String, EnzymeSourceConstant, EnzymeViewConstant, String) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Returns a commented EnzymeLink instance.
valueOf(String, EnzymeNameTypeConstant, EnzymeNameQualifierConstant, EnzymeSourceConstant, EnzymeViewConstant) - Static method in class uk.ac.ebi.intenz.domain.enzyme.EnzymeName
values() - Static method in enum uk.ac.ebi.intenz.domain.constants.Event: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.intenz.domain.constants.Status: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.intenz.domain.constants.View: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.intenz.domain.enzyme.Cofactor.Operators: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber.Type: Returns an array containing the constants of this enum type, in the order they are declared.
View - Enum in uk.ac.ebi.intenz.domain.constants: Enumeration for web views of IntEnz data.
VIEW_CONSTANTS - Static variable in class uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant: Deprecated.
Viewable - Interface in uk.ac.ebi.intenz.domain.enzyme: Interface for objects with a web view.

W

WIT - Static variable in class uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant: ERGO formerly WIT.
WIT - Static variable in class uk.ac.ebi.intenz.domain.enzyme.EnzymeLink: Static link to the ERGO (formerly WIT) database.

X

XrefDatabaseConstant - Class in uk.ac.ebi.intenz.domain.constants: This class represents an enumeration of all supported link source types.

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