Deprecated API

Contents

• Deprecated Classes
• Deprecated Methods
• Deprecated Constructors

Deprecated Classes

uk.ac.ebi.intenz.domain.enzyme.DataComment
use a plain String.

uk.ac.ebi.intenz.webapp.dtos.DataCommentDTO

uk.ac.ebi.intenz.tools.release.helper.EnzymeEntryHelper

uk.ac.ebi.intenz.webapp.helper.EnzymeEntryHelper
PLEASE PLEASE TAKE ALL THIS ******* HTML OUT OF HERE!

uk.ac.ebi.intenz.tools.sib.helper.EnzymeHelper
Use the new class uk.ac.ebi.intenz.webapp.helper.SibEntryHelper

uk.ac.ebi.intenz.webapp.helper.EnzymeLinksHelper
this class is an aberration. Its name should have been EnzymeLinksHell. Please, use HTML somewhere else.

uk.ac.ebi.intenz.webapp.helper.EnzymeReactionHelper

uk.ac.ebi.intenz.domain.constants.EnzymeStatusConstant
use enumeration Status instead.

uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant
use enumeration View instead.

uk.ac.ebi.intenz.domain.constants.EventConstant
use enumeration Event instead.

uk.ac.ebi.intenz.mapper.EventPackageMapper
use HistoryEventMapper instead.

uk.ac.ebi.intenz.tools.sib.helper.FFWriterHelper
this is a view-tier task, use the IntEnzUtilities class instead (public webapp)

Deprecated Methods

uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry.addCofactor(Cofactor)
use EnzymeEntry.addCofactor(Object) instead

uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry.addReaction(Reaction)
use addEnzymaticReaction instead

uk.ac.ebi.intenz.webapp.IntEnzUtilities.cleanInternalLinks(String, boolean)
use IntEnzUtilities.cleanLinks(String) and IntEnzUtilities.firstLetterToUppercase(String)

uk.ac.ebi.intenz.webapp.IntEnzUtilities.firstLetterToUppercase(String)
use JSTL's fn:toUpperCase and fn:substring instead

uk.ac.ebi.intenz.domain.enzyme.Cofactor.getCofactorValue()
use Cofactor.getCompound().getName() or Cofactor.toString() instead

uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry.getComments(EnzymeViewConstant)
use EnzymeEntry.getComments(String) instead

uk.ac.ebi.intenz.domain.enzyme.DataComment.getId()

uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry.getLinks(EnzymeViewConstant)
use EnzymeEntry.getLinks(String) instead

uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry.getReactions()
use getEnzymaticReactions instead

uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry.getReactions(EnzymeViewConstant)
use EnzymeEntry.getReactions(View) or EnzymeEntry.getReactions(String) instead.

uk.ac.ebi.intenz.tools.sib.helper.EnzymeHelper.getSibEnzymeEntry(EnzymeEntry, SpecialCharacters, EncodingType, boolean)
Use uk.ac.ebi.intenz.webapp.helper.SibEntryHelper

uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry.getSynonyms(EnzymeViewConstant)
use EnzymeEntry.getSynonyms(String) or EnzymeEntry.getSynonyms(View) instead.

uk.ac.ebi.intenz.webapp.IntEnzUtilities.linkEcNumber(String, boolean)
use IntEnzUtilities.linkEcNumbers(String) instead and - if needed - IntEnzUtilities.firstLetterToUppercase(String)

uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry.removeCofactor(Cofactor)
use EnzymeEntry.removeCofactor(Object) instead

uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry.removeCofactor(String)
use removeCofactor(Object) instead

uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry.removeReaction(String)
use removeEnzymaticReaction instead

uk.ac.ebi.intenz.webapp.util.EnzymeEntryMapperPool.setFactory(PoolableObjectFactory)

uk.ac.ebi.intenz.webapp.util.XmlExporterPool.setFactory(PoolableObjectFactory)

uk.ac.ebi.intenz.domain.enzyme.DataComment.setId(long)

uk.ac.ebi.intenz.webapp.helper.EnzymeReactionHelper.textualRepresentationToHTML(Reaction, SpecialCharacters, EncodingType)
MVC sin

uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant.toASCII(EnzymeNameQualifierConstant)

uk.ac.ebi.intenz.tools.sib.translator.XCharsASCIITranslator.toASCII(String, boolean)
Use toAscii(String text, boolean useReactionRules, boolean useDeLineRules)

uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.toDisplayImage()
MVC sin

uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.toDisplayImage(String)
MVC sin

uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.toDisplayString()

uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant.toDisplayString()

uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.toDisplayString(String)

uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant.toDisplayString(String)

uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant.toEditableHTML()
MVC sin

uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant.toHTML(String)
MVC sin

uk.ac.ebi.intenz.domain.enzyme.DataComment.valueOf(String, String)

Deprecated Constructors

uk.ac.ebi.intenz.domain.enzyme.Cofactor(String, EnzymeSourceConstant, EnzymeViewConstant)
use the valueOf method instead to call the private constructor

uk.ac.ebi.intenz.domain.enzyme.DataComment(Long, String)

uk.ac.ebi.intenz.webapp.utilities.UnitOfWork()