public Alias( Institution anOwner, AnnotatedObject annotatedObject, CvAliasType cvAliasType, String name ) { this(annotatedObject, cvAliasType, name); setOwner(anOwner); }
public Alias( Institution anOwner, AnnotatedObject annotatedObject, CvAliasType cvAliasType, String name ) { this(annotatedObject, cvAliasType, name); setOwner(anOwner); }
public static <A extends Alias> A createAlias(AnnotatedObject<?,A> parent, String name, CvAliasType aliasType) { A alias = (A) newAliasInstanceFor(parent.getClass()); alias.setOwner(parent.getOwner()); alias.setParent(parent); alias.setCvAliasType(aliasType); alias.setName(name); return alias; }
public static <A extends Alias> A createAlias(AnnotatedObject<?, A> parent, String name, CvAliasType aliasType) { A alias = (A) newAliasInstanceFor(parent.getClass()); alias.setOwner(parent.getOwner()); alias.setParent(parent); alias.setCvAliasType(aliasType); alias.setName(name); return alias; }
public static <A extends Alias> A createAlias(AnnotatedObject<?, A> parent, String name, CvAliasType aliasType) { A alias = (A) newAliasInstanceFor(parent.getClass()); alias.setOwner(parent.getOwner()); alias.setParent(parent); alias.setCvAliasType(aliasType); alias.setName(name); return alias; }
public static <A extends Alias> void populateAliases(Collection<psidev.psi.mi.xml.model.Alias> psiAliases, AnnotatedObject<?, A> annotatedObject, AliasConverter<A> aliasConverter) { if (psiAliases == null) { return; } for (psidev.psi.mi.xml.model.Alias psiAlias : psiAliases) { if (psiAlias.hasValue()) { A alias = aliasConverter.psiToIntact(psiAlias); annotatedObject.addAlias(alias); if (annotatedObject instanceof Institution) { alias.setOwner((Institution) annotatedObject); } } else { if (log.isWarnEnabled()) log.warn("Alias without value in location: "+ ConverterContext.getInstance().getLocation().getCurrentLocation().pathFromRootAsString()); } } }
/** * Create a new Alias for the given Annotated object * * @param anOwner The institution owning this Alias * @param annotatedObject the object to which we'll add a new Alias * @param cvAliasType the CvAliasType (may be null) * @param name the name of the alias (namy be null) * * @see uk.ac.ebi.intact.model.CvAliasType * @see uk.ac.ebi.intact.model.AnnotatedObject */ public Alias( Institution anOwner, AnnotatedObject annotatedObject, CvAliasType cvAliasType, String name ) { setOwner( anOwner ); setParentAc( annotatedObject.getAc() ); setCvAliasType( cvAliasType ); setName( name ); }
public A psiToIntact(psidev.psi.mi.xml.model.Alias psiObject) { psiStartConversion(psiObject); String name = psiObject.getValue(); String aliasType = psiObject.getType(); String aliasTypeAc = psiObject.getTypeAc(); if (name.length() == 0) { throw new PsiConversionException("Value in Alias is empty: "+psiObject); } CvAliasType cvAliasType = null; // a type ac must always be a mi term if (aliasType != null) { cvAliasType = new CvAliasType(getInstitution(), aliasType); if( aliasTypeAc != null ) { cvAliasType.setIdentifier(aliasTypeAc); psiMiPopulator.populateWithPsiMi(cvAliasType, aliasTypeAc); } else { if ( log.isWarnEnabled() ) log.warn( "Attempting to build an Alias ("+ aliasType + ") without nameAc, this will result in a CvTopic without Xref" ); } } A alias = newAliasInstance(aliasClass, cvAliasType, name); alias.setOwner(getInstitution()); psiEndConversion(psiObject); return alias; }
alias.setOwner(institutionPersister.syncIfTransient(alias.getOwner()));