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

Packages that use EnzymeEntry

uk.ac.ebi.intenz.biopax.level2
uk.ac.ebi.intenz.domain.enzyme	The core enzyme information is held in these classes.
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.mapper	O/R mapping layer classes.
uk.ac.ebi.intenz.tools.export
uk.ac.ebi.intenz.tools.release.helper
uk.ac.ebi.intenz.tools.sib.helper
uk.ac.ebi.intenz.webapp.controller	All front controller related classes are stored here.
uk.ac.ebi.intenz.webapp.helper

Uses of EnzymeEntry in uk.ac.ebi.intenz.biopax.level2

Methods in uk.ac.ebi.intenz.biopax.level2 that return EnzymeEntry

EnzymeEntry

BiopaxCatalysis.getIntEnzEnzyme()

Method parameters in uk.ac.ebi.intenz.biopax.level2 with type arguments of type EnzymeEntry

static void

Biopax.write(Collection<EnzymeEntry> enzymes, OutputStream os) Writes a collection of enzyme entries to an output stream.

Constructors in uk.ac.ebi.intenz.biopax.level2 with parameters of type EnzymeEntry

BiopaxCatalysis(EnzymeEntry enzymeEntry, org.biopax.paxtools.model.Model model)
Constructor from an IntEnz EnzymeEntry.

Uses of EnzymeEntry in uk.ac.ebi.intenz.domain.enzyme

Methods in uk.ac.ebi.intenz.domain.enzyme that return types with arguments of type EnzymeEntry

List<EnzymeEntry>

EnzymeSubSubclass.getEntries()

Methods in uk.ac.ebi.intenz.domain.enzyme with parameters of type EnzymeEntry

int	EnzymeEntryNameComparator.compare(EnzymeEntry o1, EnzymeEntry o2)
int	EnzymeEntryEcComparator.compare(EnzymeEntry o1, EnzymeEntry o2)

Constructor parameters in uk.ac.ebi.intenz.domain.enzyme with type arguments of type EnzymeEntry

EnzymeSubSubclass(EnzymeCommissionNumber ec, String className, String subclassName, String name, String description, List<EnzymeEntry> entries)
Returns an EnzymeSubSubclass instance.

Uses of EnzymeEntry in uk.ac.ebi.intenz.domain.history

Methods in uk.ac.ebi.intenz.domain.history that return EnzymeEntry

EnzymeEntry

HistoryNode.getEnzymeEntry()

Methods in uk.ac.ebi.intenz.domain.history with parameters of type EnzymeEntry

void	HistoryNode.setEnzymeEntry(EnzymeEntry enzymeEntry)

Uses of EnzymeEntry in uk.ac.ebi.intenz.mapper

Methods in uk.ac.ebi.intenz.mapper that return EnzymeEntry

EnzymeEntry	EnzymeEntryMapper.findByEc(int ec1, int ec2, int ec3, int ec4, Status status, Connection con) Tries to find entry information about an enzyme.
EnzymeEntry	EnzymeEntryMapper.findByEc(String ecString, Status status, Connection con) Finds an enzyme by EC number (as String) and status.
EnzymeEntry	EnzymeEntryMapper.findById(long id, Connection con) Loads a complete version of the enzyme with the given ID.
EnzymeEntry	EnzymeEntryMapper.findById(Long id, Connection con, boolean ghost) Tries to find entry information about an enzyme.
EnzymeEntry	EnzymeEntryMapper.findGhostById(int id, Connection con) Loads a ghost version of the enzyme with the given ID.

Methods in uk.ac.ebi.intenz.mapper that return types with arguments of type EnzymeEntry

List<EnzymeEntry>	EnzymeEntryMapper.exportAllEntries(Connection con) Exports every piece of data for publicly available entries.
List<EnzymeEntry>	EnzymeEntryMapper.exportApprovedSibEntries(Connection con) Tries to export all approved entries containing only ENZYME relevant information.
List<EnzymeEntry>	EnzymeEntryMapper.findAll(Connection con) Tries to find all public entries but loads the entries only with minimum information.
List<EnzymeEntry>	EnzymeEntryMapper.findAllByEc(int ec1, int ec2, int ec3, int ec4, Boolean preliminary, Connection con)
List<EnzymeEntry>	EnzymeEntryMapper.findAllByEc(int ec1, int ec2, int ec3, int ec4, Connection con) Tries to find entry information about all enzymes specified by the given EC.
List<EnzymeEntry>	EnzymeEntryMapper.findAllSubSubclassEntriesByEc(int ec1, int ec2, int ec3, Connection con)
List<EnzymeEntry>	EnzymeEntryMapper.findByStatus(Connection con, Status status) Retrieves the list of enzymes with a given status.
List<EnzymeEntry>	EnzymeEntryMapper.findFullProposedList(Connection con) Tries to find all proposed entries with all information.
List<EnzymeEntry>	EnzymeEntryMapper.findFullSuggestedList(Connection con) Tries to find all suggested entries with all information.
List<EnzymeEntry>	EnzymeEntryMapper.findList(String ec1, String ec2, String ec3, Connection con) Tries to find all entries requested but loads the entries only with minimum information.
List<EnzymeEntry>	EnzymeEntryMapper.findPreliminaryEcsList(Connection con) Gets the list of preliminary EC numbers issued by UniProt.
List<EnzymeEntry>	EnzymeEntryMapper.findProposedList(Connection con) Tries to find all proposed entries but loads the entries only with minimum information.
List<EnzymeEntry>	EnzymeEntryMapper.findSuggestedList(Connection con) Tries to find all suggested entries but loads the entries only with minimum information.

Methods in uk.ac.ebi.intenz.mapper with parameters of type EnzymeEntry

HistoryGraph	EnzymeHistoryMapper.find(EnzymeEntry enzymeEntry, Connection con)
HistoryGraph	EnzymeFutureMapper.find(EnzymeEntry enzymeEntry, Connection con)

Uses of EnzymeEntry in uk.ac.ebi.intenz.tools.export

Methods in uk.ac.ebi.intenz.tools.export that return types with arguments of type EnzymeEntry

protected Collection<EnzymeEntry>

ExporterApp.getEnzymeList(String ecString) Gets the list of enzymes to be exported.

Methods in uk.ac.ebi.intenz.tools.export with parameters of type EnzymeEntry

void	XmlExporter.export(EnzymeEntry entry, String release, String relDate, OutputStream os) Exports one enzyme entry as IntEnzXML.

Method parameters in uk.ac.ebi.intenz.tools.export with type arguments of type EnzymeEntry

void	KeggExporter.export(Collection<EnzymeEntry> enzymes, OutputStream os)
void	XmlExporter.export(List<EnzymeEntry> entries, String release, String relDate, OutputStream os) Exports a list of enzymes as IntEnzXML.
protected void	ExporterApp.exportBiopax(Collection<EnzymeEntry> enzymeList, String biopaxFile)
protected void	ExporterApp.exportKegg(Collection<EnzymeEntry> enzymes, String keggFile)
protected void	ExporterApp.exportSitemap(Collection<EnzymeEntry> enzymeList, Map<String,Object> descriptions, String sitemapFile)
protected void	ExporterApp.exportXML(Collection<EnzymeEntry> enzymeList, Map<String,Object> descriptions, String toDir) Exports data in XML format.

Uses of EnzymeEntry in uk.ac.ebi.intenz.tools.release.helper

Methods in uk.ac.ebi.intenz.tools.release.helper with parameters of type EnzymeEntry

static String

EnzymeEntryHelper.toXML(EnzymeEntry enzymeEntry, uk.ac.ebi.xchars.SpecialCharacters encoding, EnzymeViewConstant view, boolean intenzTextXML) Deprecated.

Uses of EnzymeEntry in uk.ac.ebi.intenz.tools.sib.helper

Methods in uk.ac.ebi.intenz.tools.sib.helper with parameters of type EnzymeEntry

static EnzymeEntryImpl	SibEntryHelper.getSibEnzymeEntry(EnzymeEntry enzymeEntry, uk.ac.ebi.xchars.SpecialCharacters encoding, uk.ac.ebi.xchars.domain.EncodingType encodingType)
static EnzymeEntryImpl	EnzymeHelper.getSibEnzymeEntry(EnzymeEntry enzymeEntry, uk.ac.ebi.xchars.SpecialCharacters encoding, uk.ac.ebi.xchars.domain.EncodingType encodingType, boolean translate) Deprecated. Use uk.ac.ebi.intenz.webapp.helper.SibEntryHelper

Uses of EnzymeEntry in uk.ac.ebi.intenz.webapp.controller

Methods in uk.ac.ebi.intenz.webapp.controller that return EnzymeEntry

protected EnzymeEntry	SearchECCommand.findEnzymeEntry(EnzymeCommissionNumber ec, Status status) Calls the according find() method and handles empty results and SQL exceptions.
protected EnzymeEntry	SearchIDCommand.findEnzymeEntry(Long id) Calls the according find() method and handles empty results and SQL exceptions.

Uses of EnzymeEntry in uk.ac.ebi.intenz.webapp.helper

Methods in uk.ac.ebi.intenz.webapp.helper with parameters of type EnzymeEntry

static String	EnzymeEntryHelper.getSibView(EnzymeEntry enzymeEntry, uk.ac.ebi.xchars.SpecialCharacters encoding, uk.ac.ebi.xchars.domain.EncodingType encodingType) Deprecated.
static String	EnzymeEntryHelper.toHTML(EnzymeEntry enzymeEntry, uk.ac.ebi.xchars.SpecialCharacters encoding, uk.ac.ebi.xchars.domain.EncodingType encodingType, EnzymeViewConstant view) Deprecated.