public static Names createNames(String name, String description) { Names names = new Names(); names.setShortLabel(name); names.setFullName(description); return names; }
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; }
private static <T extends CvType> T createUnspecifiedRole( Class<T> roleClass ) { T role; try { role = roleClass.newInstance(); } catch ( Exception e ) { throw new RuntimeException( e ); } Names names = new Names(); names.setShortLabel(CvExperimentalRole.UNSPECIFIED); names.setFullName(CvExperimentalRole.UNSPECIFIED); role.setNames( names ); Xref xref = new Xref(); String unspecifiedRoleMiRef = CvExperimentalRole.UNSPECIFIED_PSI_REF; DbReference dbRef = new DbReference( unspecifiedRoleMiRef, CvDatabase.PSI_MI ); dbRef.setRefType( CvXrefQualifier.IDENTITY ); dbRef.setRefTypeAc( CvXrefQualifier.IDENTITY_MI_REF ); dbRef.setDbAc( CvDatabase.PSI_MI_MI_REF ); xref.setPrimaryRef( dbRef ); role.setXref( xref ); return role; }
names.setFullName(IntactConverterUtils.AUTH_CONF); names.setShortLabel(IntactConverterUtils.AUTH_CONF_MI);
names.setFullName("range"); names.setFullName("greater-than"); names.setFullName("less-than"); names.setFullName("n-terminal range"); names.setFullName("c-terminal range"); names.setFullName("undetermined sequence position"); names.setFullName("certain sequence position");
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 ); }
names.setFullName(crossReference.getText());
interactorTypeName.setFullName("protein"); } else if (id.equals("MI:0328")) { interactorTypeName.setShortLabel("small molecule"); interactorTypeName.setFullName("small molecule"); } else if (id.equals("MI:0317")) { interactorTypeName.setShortLabel("interaction"); interactorTypeName.setFullName("interaction"); } else if (id.equals("MI:0329")) { interactorTypeName.setShortLabel("unknown participant"); interactorTypeName.setFullName("unknown participant"); } else { interactorTypeName.setShortLabel(id); interactorTypeName.setFullName(id); interactorTypeName.setFullName("protein"); interactorTypeName.setFullName("small molecule"); interactorTypeName.setFullName("unknown participant"); interactorTypeName.setFullName("unknown participant");
unit.setNames(new Names()); unit.getNames().setShortLabel(tabConfidence.getType()); if (tabConfidence.getText() != null) unit.getNames().setFullName(tabConfidence.getText());
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 ); }
names.setFullName("unspecified role"); names.setFullName("unspecified role"); featureTypeNames.setFullName(mitabFeature.getFeatureType()); names.setFullName(participantIdentificationMethod.getText());