/** * Collect all DbReference under an xref. * * @param names aliases holder. * * @return a non null collection. */ @Deprecated public static Collection<Alias> getAllAliases( Names names ) { ArrayList<Alias> aliases = new ArrayList<Alias>( names.getAliases().size() ); for ( Alias alias : names.getAliases() ) { aliases.add( alias ); } return aliases; } }
public psidev.psi.mi.xml253.jaxb.NamesType toJaxb( psidev.psi.mi.xml.model.Names mNames ) { if ( mNames == null ) { throw new IllegalArgumentException( "You must give a non null model Names." ); } psidev.psi.mi.xml253.jaxb.NamesType jNames = new psidev.psi.mi.xml253.jaxb.NamesType(); // Initialise the JAXB object reading the model // 1. set attributes // shortlabel jNames.setShortLabel( mNames.getShortLabel() ); // fullname jNames.setFullName( mNames.getFullName() ); // 2. set encapsulated objects // aliases for ( psidev.psi.mi.xml.model.Alias mAlias : mNames.getAliases() ) { jNames.getAlias().add( aliasConverter.toJaxb( mAlias ) ); } return jNames; } }
public psidev.psi.mi.xml.model.Names fromJaxb( psidev.psi.mi.xml253.jaxb.NamesType jNames ) { if ( jNames == null ) { throw new IllegalArgumentException( "You must give a non null JAXB Names." ); } psidev.psi.mi.xml.model.Names mNames = new psidev.psi.mi.xml.model.Names(); // Initialise the model reading the Jaxb object // 1. set attributes // shortlabel mNames.setShortLabel( jNames.getShortLabel() ); // fullname mNames.setFullName( jNames.getFullName() ); // 2. set encapsulated objects // aliases for ( NamesType.Alias jAlias : jNames.getAlias() ) { mNames.getAliases().add( aliasConverter.fromJaxb( jAlias ) ); } return mNames; }
public psidev.psi.mi.xml.model.Names fromJaxb( psidev.psi.mi.xml254.jaxb.Names jNames ) { if ( jNames == null ) { throw new IllegalArgumentException( "You must give a non null JAXB Names." ); } psidev.psi.mi.xml.model.Names mNames = new psidev.psi.mi.xml.model.Names(); // Initialise the model reading the Jaxb object // 1. set attributes // shortlabel mNames.setShortLabel( jNames.getShortLabel() ); // fullname mNames.setFullName( jNames.getFullName() ); // 2. set encapsulated objects // aliases for ( Alias jAlias : jNames.getAlias() ) { mNames.getAliases().add( aliasConverter.fromJaxb( jAlias ) ); } return mNames; }
public psidev.psi.mi.xml254.jaxb.Names toJaxb( psidev.psi.mi.xml.model.Names mNames ) { if ( mNames == null ) { throw new IllegalArgumentException( "You must give a non null model Names." ); } psidev.psi.mi.xml254.jaxb.Names jNames = new psidev.psi.mi.xml254.jaxb.Names(); // Initialise the JAXB object reading the model // 1. set attributes // shortlabel jNames.setShortLabel( mNames.getShortLabel() ); // fullname jNames.setFullName( mNames.getFullName() ); // 2. set encapsulated objects // aliases for ( psidev.psi.mi.xml.model.Alias mAlias : mNames.getAliases() ) { jNames.getAlias().add( aliasConverter.toJaxb( mAlias ) ); } return jNames; } }
interactorName.getAliases().addAll(aliases);
public static void populateNames(Names names, AnnotatedObject<?, ?> annotatedObject, AliasConverter aliasConverter) { String shortLabel = getShortLabelFromNames(names); if (names == null && (annotatedObject instanceof Experiment) ) { shortLabel = createExperimentTempShortLabel(); } if ( ! ( annotatedObject instanceof Institution ) ) { if ( shortLabel != null ) { shortLabel = shortLabel.toLowerCase(); } } annotatedObject.setShortLabel(shortLabel); if (names != null) { annotatedObject.setFullName(names.getFullName()); if (aliasConverter == null){ Class<?> aliasClass = AnnotatedObjectUtils.getAliasClassType(annotatedObject.getClass()); aliasConverter = new AliasConverter(getInstitution(annotatedObject), aliasClass); } populateAliases(names.getAliases(), annotatedObject, aliasConverter); } }
public static void populateNames(Names names, AnnotatedObject<?, ?> annotatedObject) { String shortLabel = getShortLabelFromNames(names); if (names == null && (annotatedObject instanceof Experiment) ) { shortLabel = createExperimentTempShortLabel(); } if ( ! ( annotatedObject instanceof Institution ) ) { if ( shortLabel != null ) { shortLabel = shortLabel.toLowerCase(); } } annotatedObject.setShortLabel(shortLabel); if (names != null) { annotatedObject.setFullName(names.getFullName()); Class<?> aliasClass = AnnotatedObjectUtils.getAliasClassType(annotatedObject.getClass()); AliasConverter aliasConverter = new AliasConverter(getInstitution(annotatedObject), aliasClass); populateAliases(names.getAliases(), annotatedObject, aliasConverter); } }
interactorName.getAliases().addAll( aliases );
if (names.getAliases().isEmpty()) { names.getAliases().add(alias); } else { if (!names.getAliases().contains(alias)) names.getAliases().add(alias);
protected static void populateNames( AnnotatedObject<?, ?> annotatedObject, NamesContainer namesContainer ) { Names names = namesContainer.getNames(); if ( names == null ) { names = new Names(); } String shortLabel = annotatedObject.getShortLabel(); String fullName = annotatedObject.getFullName(); names.setShortLabel( shortLabel ); names.setFullName( fullName ); if ( !ConverterContext.getInstance().getInteractorConfig().isExcludeInteractorAliases() ) { AliasConverter aliasConverter = new AliasConverter( annotatedObject.getOwner(), AnnotatedObjectUtils.getAliasClassType( annotatedObject.getClass() ) ); for ( Alias alias : IntactCore.ensureInitializedAliases(annotatedObject)) { names.getAliases().add( aliasConverter.intactToPsi( alias ) ); } } namesContainer.setNames( names ); }
if (names.getAliases().isEmpty()) { names.getAliases().add(alias); } else { if (!names.getAliases().contains(alias)) names.getAliases().add(alias);
Collection<Alias> aliases = xmlInteractor.getNames().getAliases();
shortName = (psiNames.hasShortLabel()) ? psiNames.getShortLabel() : null; if (psiNames.hasAliases()) { for (Alias alias : psiNames.getAliases()) { if (alias.hasValue()) { synonyms.add(alias.getValue());
public static void populateNames( AnnotatedObject<?, ?> annotatedObject, NamesContainer namesContainer, AliasConverter aliasConverter ) { Names names = namesContainer.getNames(); if ( names == null ) { names = new Names(); } String shortLabel = annotatedObject.getShortLabel(); String fullName = annotatedObject.getFullName(); names.setShortLabel( shortLabel ); names.setFullName( fullName ); if ( !ConverterContext.getInstance().getInteractorConfig().isExcludeInteractorAliases() ) { Collection<? extends Alias> aliases; if (aliasConverter.isCheckInitializedCollections()){ aliases = IntactCore.ensureInitializedAliases(annotatedObject); } else { aliases = annotatedObject.getAliases(); } for ( Alias alias : aliases) { names.getAliases().add( aliasConverter.intactToPsi( alias ) ); } } namesContainer.setNames( names ); }
if (names.getAliases().isEmpty()) { names.getAliases().add(alias); } else { if (!names.getAliases().contains(alias)) names.getAliases().add(alias);
final String shortNameLael; final String fullNameLabel; final Collection<Alias> aliases = names.getAliases();