A C D E F G H I R S U V

A

AuditPackageMapper - Class in uk.ac.ebi.intenz.mapper

Provides methods for audit package access.

AuditPackageMapper() - Constructor for class uk.ac.ebi.intenz.mapper.AuditPackageMapper

C

classExists(String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeClassMapper

Checks if the given class number is valid.

cloneExists(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Checks if a clone of an enzyme already exists.

close() - Method in class uk.ac.ebi.intenz.mapper.EnzymeCofactorMapper

close() - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

close() - Method in class uk.ac.ebi.intenz.mapper.EnzymeReactionMapper

CommonProceduresMapper - Class in uk.ac.ebi.intenz.mapper

Provides methods for access to procedures not related to a specific package.

CommonProceduresMapper() - Constructor for class uk.ac.ebi.intenz.mapper.CommonProceduresMapper

createClone(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.CommonProceduresMapper

Creates a clone of an enzyme by using its enzyme ID.

D

delete(Long, EnzymeLink, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeLinkMapper

deleteAll(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCofactorMapper

Deletes all cofactors related to one enzyme instance.

deleteAll(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCommentMapper

Deletes all comments related to an enzyme instance.

deleteAll(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeLinkMapper

deleteAll(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeReferenceMapper

deleteAllXref(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeLinkMapper

deleteByCodeXref(Long, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeLinkMapper

deleteByName(Long, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeLinkMapper

deleteCitations(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeReferenceMapper

deleteCitations(List<Long>, Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeReferenceMapper

Deletes enzyme relations to publications (internally called citations).

deleteCompound(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCofactorMapper

Deletes a cofactor from the COMPOUND_DATA table.

deleteNames(Long, EnzymeNameTypeConstant, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeNameMapper

deleteOtherLinks(List<EnzymeLink>, Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeLinkMapper

deletePublication(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeReferenceMapper

deleteXref(Long, EnzymeLink, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeLinkMapper

E

ecExists(EnzymeCommissionNumber, Connection) - Static method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Checks whether a given EC number already exists in the database.

EnzymeClassMapper - Class in uk.ac.ebi.intenz.mapper

Maps enzyme class information to the corresponding database tables.

EnzymeClassMapper() - Constructor for class uk.ac.ebi.intenz.mapper.EnzymeClassMapper

EnzymeCofactorMapper - Class in uk.ac.ebi.intenz.mapper

Maps reaction information to the corresponding database tables.

EnzymeCofactorMapper() - Constructor for class uk.ac.ebi.intenz.mapper.EnzymeCofactorMapper

EnzymeCommentMapper - Class in uk.ac.ebi.intenz.mapper

Maps link information to the corresponding database tables.

EnzymeCommentMapper() - Constructor for class uk.ac.ebi.intenz.mapper.EnzymeCommentMapper

EnzymeEntryMapper - Class in uk.ac.ebi.intenz.mapper

Maps enzyme entry information to the corresponding database tables.

EnzymeEntryMapper() - Constructor for class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

EnzymeEntryMapper(EnzymeReactionMapper) - Constructor for class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

EnzymeFutureMapper - Class in uk.ac.ebi.intenz.mapper

Maps future event information to the corresponding database tables.

EnzymeFutureMapper() - Constructor for class uk.ac.ebi.intenz.mapper.EnzymeFutureMapper

EnzymeHistoryMapper - Class in uk.ac.ebi.intenz.mapper

Maps history event information to the corresponding database tables.

EnzymeHistoryMapper() - Constructor for class uk.ac.ebi.intenz.mapper.EnzymeHistoryMapper

EnzymeLinkMapper - Class in uk.ac.ebi.intenz.mapper

Maps link information to the corresponding database tables.

EnzymeLinkMapper() - Constructor for class uk.ac.ebi.intenz.mapper.EnzymeLinkMapper

EnzymeNameMapper - Class in uk.ac.ebi.intenz.mapper

Maps enzyme names information to the corresponding database tables.

EnzymeNameMapper() - Constructor for class uk.ac.ebi.intenz.mapper.EnzymeNameMapper

EnzymeReactionMapper - Class in uk.ac.ebi.intenz.mapper

Maps reaction information to the corresponding database table.

EnzymeReactionMapper() - Constructor for class uk.ac.ebi.intenz.mapper.EnzymeReactionMapper

EnzymeReferenceMapper - Class in uk.ac.ebi.intenz.mapper

Maps reference information to the corresponding database tables.

EnzymeReferenceMapper() - Constructor for class uk.ac.ebi.intenz.mapper.EnzymeReferenceMapper

EnzymeSubclassMapper - Class in uk.ac.ebi.intenz.mapper

Maps enzyme subclass information to the corresponding database tables.

EnzymeSubclassMapper() - Constructor for class uk.ac.ebi.intenz.mapper.EnzymeSubclassMapper

EnzymeSubSubclassMapper - Class in uk.ac.ebi.intenz.mapper

Maps enzyme Sub-subclass information to the corresponding database tables.

EnzymeSubSubclassMapper() - Constructor for class uk.ac.ebi.intenz.mapper.EnzymeSubSubclassMapper

EventPackageMapper - Class in uk.ac.ebi.intenz.mapper

Deprecated.

use HistoryEventMapper instead.

EventPackageMapper() - Constructor for class uk.ac.ebi.intenz.mapper.EventPackageMapper

Deprecated.

exportAllEntries(Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Exports every piece of data for publicly available entries.

exportApprovedSibEntries(Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Tries to export all approved entries containing only ENZYME relevant information.

exportSibCofactors(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCofactorMapper

Exports all cofactors which are displayed in the ENZYME view.

exportSibComments(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCommentMapper

Exports all comments which are displayed in the ENZYME view.

exportSibLinks(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeLinkMapper

Exports all links which are displayed in the ENZYME view.

exportSibNames(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeNameMapper

Exports all names which are displayed in the ENZYME view.

exportSibReactions(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeReactionMapper

Exports all reactions which are displayed in the ENZYME view.

F

finalize() - Method in class uk.ac.ebi.intenz.mapper.EnzymeCofactorMapper

finalize() - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

finalize() - Method in class uk.ac.ebi.intenz.mapper.EnzymeReactionMapper

find(String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeClassMapper

Tries to find Class information about an enzyme.

find(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCofactorMapper

Tries to find cofactor information about an enzyme.

find(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCommentMapper

Tries to find comment information about an enzyme.

find(EnzymeEntry, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeFutureMapper

find(EnzymeEntry, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeHistoryMapper

find(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeLinkMapper

Tries to find link information about an enzyme in tables LINKS and XREFS.

find(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeNameMapper

Tries to find name information about an enzyme.

find(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeReactionMapper

Tries to find reaction information about an enzyme.

find(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeReferenceMapper

Tries to find comment information about an enzyme.

find(String, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeSubclassMapper

Tries to find Subclass information about an enzyme.

find(int, int, int, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeSubSubclassMapper

Tries to find Sub-subclass information about an enzyme.

findAll(Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeClassMapper

findAll(Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCofactorMapper

Retrieves a list of compounds acting as cofactors in the database, along with the identifiers for the enzymes they appear in.

findAll(Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Tries to find all public entries but loads the entries only with minimum information.

findAll(Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeSubclassMapper

findAll(Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeSubSubclassMapper

findAllByEc(int, int, int, int, Boolean, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

findAllByEc(int, int, int, int, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Tries to find entry information about all enzymes specified by the given EC.

findAllSubSubclassEntriesByEc(int, int, int, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

findByChebiId(String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCofactorMapper

Retrieves one cofactor from the IntEnz database by its ChEBI ID.

findByEc(int, int, int, int, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Tries to find entry information about an enzyme.

findByEc(String, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Finds an enzyme by EC number (as String) and status.

findById(Long, Connection, boolean) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Tries to find entry information about an enzyme.

findById(long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Loads a complete version of the enzyme with the given ID.

findByStatus(Connection, Status) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Retrieves the list of enzymes with a given status.

findCommonNames(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeNameMapper

Finds only the common name of an entry.

findEC(String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Returns the EC number of the given enzyme ID.

findFullProposedList(Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Tries to find all proposed entries with all information.

findFullSuggestedList(Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Tries to find all suggested entries with all information.

findGhostById(int, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Loads a ghost version of the enzyme with the given ID.

findHistoryLine(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Returns the history line of the enzyme with the given ID.

findIDInMappingTable(String, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

findList(String, String, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Tries to find all entries requested but loads the entries only with minimum information.

findList(String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeSubclassMapper

Tries to find all Subclasses requested.

findList(String, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeSubSubclassMapper

Tries to find all Sub-subclasses requested.

findNextEnzymeId(Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Returns the next available enzyme ID.

findNote(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Returns the note of the enzyme with the given ID.

findNumberOfClasses(Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeClassMapper

Finds the number of classes.

findPreliminaryEcsList(Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Gets the list of preliminary EC numbers issued by UniProt.

findProposedList(Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Tries to find all proposed entries but loads the entries only with minimum information.

findPubIds(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeReferenceMapper

findSibXrefs(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeLinkMapper

Finds all xrefs which are displayed in the ENZYME view.

findStats(Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

findSuggestedList(Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Tries to find all suggested entries but loads the entries only with minimum information.

findSystematicName(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeNameMapper

Finds only the systematic name of an entry.

findXrefs(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeLinkMapper

Tries to find SwissProt xref information about an enzyme.

futureEventExists(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeFutureMapper

Checks whether an entry in this table exists containing the given enzyme_id.

G

getCompound(Connection, Long) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCofactorMapper

Retrieves a compound (cofactor) from the database.

H

HistoryEventMapper - Class in uk.ac.ebi.intenz.mapper

HistoryEventMapper() - Constructor for class uk.ac.ebi.intenz.mapper.HistoryEventMapper

I

insert(Collection<Object>, Long, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCofactorMapper

Stores the given list of cofactors into the database.

insert(List<EnzymeComment>, Long, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCommentMapper

Stores the given comment into the database.

insert(Long, EnzymeCommissionNumber, Status, EnzymeSourceConstant, String, String, boolean, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Inserts the core data of a new enzyme entry.

insert(List<EnzymeLink>, Long, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeLinkMapper

Stores the given list of links into the database.

insert(EnzymeName, Long, Status, int, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeNameMapper

insert(EnzymaticReactions, Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeReactionMapper

Stores the given list of reactions into the database.

insert(Reference, Long, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeReferenceMapper

insert(List<Reference>, Long, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeReferenceMapper

Stores the given list of references into the database.

insertCompound(Compound, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCofactorMapper

Inserts one compound (cofactor) into the COMPOUND_DATA table.

insertEvent(Event, Long, Long, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.HistoryEventMapper

insertFutureCreationEvent(Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EventPackageMapper

Deprecated.

Inserts a new enzyme creation event into the FUTURE_EVENTS table.

insertFutureDeletionEvent(Long, Long, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EventPackageMapper

Deprecated.

Inserts a new deletion event into the FUTURE_EVENTS table.

insertFutureModificationEvent(Long, Long, Connection) - Method in class uk.ac.ebi.intenz.mapper.EventPackageMapper

Deprecated.

Inserts a new enzyme creation event into the FUTURE_EVENTS table.

insertFutureTransferEvent(Long, Long, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EventPackageMapper

Deprecated.

Inserts a new transfer event into the FUTURE_EVENTS table.

insertLink(EnzymeLink, Long, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeLinkMapper

insertMapping(Long, Long, EnzymeViewConstant, boolean, int, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeReactionMapper

Inserts a mapping reaction-enzyme into the database.

insertNames(List<EnzymeName>, Long, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeNameMapper

insertSubSubclass(EnzymeCommissionNumber, String, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeSubSubclassMapper

Creates a new row in the SUBSUBCLASSES table.

R

reload(Collection<Object>, Long, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCofactorMapper

Reloads the given list of cofactors into the database.

reload(List<EnzymeComment>, Long, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCommentMapper

reload(List<EnzymeName>, Long, EnzymeNameTypeConstant, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeNameMapper

reload(List<Reference>, Long, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeReferenceMapper

reloadLinks(List<EnzymeLink>, Long, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeLinkMapper

rheaReader - Variable in class uk.ac.ebi.intenz.mapper.EnzymeReactionMapper

S

setRemark(String, Connection) - Method in class uk.ac.ebi.intenz.mapper.AuditPackageMapper

Sets a remark in the audit tables.

STANDARD_REMARK - Static variable in class uk.ac.ebi.intenz.mapper.AuditPackageMapper

subclassExists(String, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeSubclassMapper

Checks if the given subclass numbers are valid.

subSubclassExists(String, String, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeSubSubclassMapper

Checks if the given sub-subclass numbers are valid.

U

uk.ac.ebi.intenz.mapper - package uk.ac.ebi.intenz.mapper

O/R mapping layer classes.

update(Compound, Compound, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCofactorMapper

Updates the ChEBI mapping of a cofactor, and the name if needed too.

update(EnzymeComment, Long, Status, int, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeCommentMapper

update(Long, EnzymeCommissionNumber, Status, EnzymeSourceConstant, String, String, boolean, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Updates the core data of an enzyme stored in the table ENZYMES.

update(EnzymeName, Long, Status, int, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeNameMapper

update(Long, EnzymaticReactions, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeReactionMapper

Replace the reactions in the database related to one enzyme with those passed as parameter.

update(Reference, Long, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeReferenceMapper

update(List<Reference>, Long, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeReferenceMapper

updateEc(Long, EnzymeCommissionNumber, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Updates the EC of the given enzyme.

updateEvent(int, int, String, Integer, Integer, Connection) - Method in class uk.ac.ebi.intenz.mapper.HistoryEventMapper

Modifies an event in the history.

updateEventNote(int, int, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.HistoryEventMapper

Updates the note for an event in the history.

updateFutureCreationEvent(int, int, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EventPackageMapper

Deprecated.

Updates a new enzyme creation event in the FUTURE_EVENTS table.

updateFutureDeletionEvent(int, int, String, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EventPackageMapper

Deprecated.

Updates a future deletion event.

updateFutureModificationEvent(int, int, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EventPackageMapper

Deprecated.

Updates a new enzyme creation event in the FUTURE_EVENTS table.

updateFutureTransferEvent(int, int, String, String, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EventPackageMapper

Deprecated.

Updates a transferred enzyme (target and origin) event in the FUTURE_EVENTS table.

updateHistoryLine(Long, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Updates the history line of the given enzyme.

updateLinkUrl(EnzymeLink, Long, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeLinkMapper

updateNote(Long, String, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Updates the notes of the given enzyme.

updateStatus(Long, Status, Connection) - Method in class uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

Updates the status of the given enzyme.

V

visitedNodes - Variable in class uk.ac.ebi.intenz.mapper.EnzymeHistoryMapper

A C D E F G H I R S U V