private void updateAlias(Collection<Alias> psiAlias, Map<String, List<String>> encoreOtherInteractor) { for(String db:encoreOtherInteractor.keySet()){ List<String> accs = encoreOtherInteractor.get(db); for(String acc:accs){ Alias pA = new AliasImpl(db,acc); psiAlias.add(pA); } } } }
public AliasImpl( String dbSource, String name, String aliasType ) { this.dbSource = dbSource; setName( name ); this.aliasType = aliasType; }
public List<Alias> createAliasRandom( int aliasCount, String db ) { List<Alias> aliases = new ArrayList<Alias>( aliasCount ); for ( int i = 0; i < aliasCount; i++ ) { aliases.add( new AliasImpl( db, randomString() ) ); } return aliases; }
@Override protected void processAliases(Interactor mitabInteractor, Collection<InteractorAlias> aliases) { for (InteractorAlias alias : aliases){ psidev.psi.mi.tab.model.Alias aliasField = aliasConverter.intactToMitab(alias); if (aliasField != null){ mitabInteractor.getAliases().add(aliasField); // create display short which should be gene name or gene name synonym if (CvAliasType.GENE_NAME.equals(aliasField.getAliasType())){ psidev.psi.mi.tab.model.Alias displayShort = new AliasImpl( CvDatabase.PSI_MI, aliasField.getName(),InteractorConverter.DISPLAY_SHORT ); mitabInteractor.getAliases().add(displayShort); hasFoundDisplayShort = true; } } } }
@Override protected void processAliases(Interactor mitabInteractor, Collection<InteractorAlias> aliases) { for (InteractorAlias alias : aliases){ psidev.psi.mi.tab.model.Alias aliasField = aliasConverter.intactToMitab(alias); if (aliasField != null){ mitabInteractor.getAliases().add(aliasField); // create display short which should be gene name or gene name synonym if (CvAliasType.GENE_NAME.equals(aliasField.getAliasType())){ hasFoundDisplayShort = true; psidev.psi.mi.tab.model.Alias displayShort = new AliasImpl( CvDatabase.PSI_MI, aliasField.getName(),InteractorConverter.DISPLAY_SHORT ); mitabInteractor.getAliases().add(displayShort); } } } } }
psidev.psi.mi.tab.model.Alias displayShort = new AliasImpl( CvDatabase.PSI_MI, mol.getShortLabel(), InteractorConverter.DISPLAY_SHORT ); mitabInteractor.getAliases().add(displayShort); psidev.psi.mi.tab.model.Alias displayLong = new AliasImpl( CvDatabase.PSI_MI, mitabInteractor.getIdentifiers().iterator().next().getIdentifier(), InteractorConverter.DISPLAY_LONG ); mitabInteractor.getAliases().add(displayLong); psidev.psi.mi.tab.model.Alias displayShort = new AliasImpl( CvDatabase.PSI_MI, mol.getShortLabel(), InteractorConverter.DISPLAY_SHORT ); mitabInteractor.getAliases().add(displayShort); psidev.psi.mi.tab.model.Alias displayLong = new AliasImpl( CvDatabase.PSI_MI, mol.getAc(), InteractorConverter.DISPLAY_LONG ); mitabInteractor.getAliases().add(displayLong); psidev.psi.mi.tab.model.Alias displayShort = new AliasImpl( CvDatabase.PSI_MI, mol.getShortLabel(), InteractorConverter.DISPLAY_SHORT ); mitabInteractor.getAliases().add(displayShort); psidev.psi.mi.tab.model.Alias displayLong = new AliasImpl( CvDatabase.PSI_MI, mol.getShortLabel(), InteractorConverter.DISPLAY_LONG ); mitabInteractor.getAliases().add(displayLong);
psidev.psi.mi.tab.model.Alias displayShort = new AliasImpl( CvDatabase.PSI_MI, mol.getShortLabel(), InteractorConverter.DISPLAY_SHORT ); mitabInteractor.getAliases().add(displayShort); psidev.psi.mi.tab.model.Alias displayLong = new AliasImpl( CvDatabase.PSI_MI, identifier, InteractorConverter.DISPLAY_LONG ); mitabInteractor.getAliases().add(displayLong); psidev.psi.mi.tab.model.Alias displayLong = new AliasImpl( CvDatabase.PSI_MI, mol.getAc(), InteractorConverter.DISPLAY_LONG ); mitabInteractor.getAliases().add(displayLong); psidev.psi.mi.tab.model.Alias displayLong = new AliasImpl( CvDatabase.PSI_MI, mol.getShortLabel(), InteractorConverter.DISPLAY_LONG ); mitabInteractor.getAliases().add(displayLong);
@Override protected void processAccessionAndDisplay(uk.ac.ebi.intact.model.Interactor mol, Interactor mitabInteractor, boolean hasFoundEMBLIdentity) { psidev.psi.mi.tab.model.Alias displayShort = new AliasImpl( CvDatabase.PSI_MI, mol.getShortLabel(), InteractorConverter.DISPLAY_SHORT ); mitabInteractor.getAliases().add(displayShort); psidev.psi.mi.tab.model.Alias displayLong = new AliasImpl( CvDatabase.PSI_MI, identifier, InteractorConverter.DISPLAY_LONG ); mitabInteractor.getAliases().add(displayLong); psidev.psi.mi.tab.model.Alias displayLong = new AliasImpl( CvDatabase.PSI_MI, mol.getAc(), InteractorConverter.DISPLAY_LONG ); mitabInteractor.getAliases().add(displayLong); psidev.psi.mi.tab.model.Alias displayLong = new AliasImpl( CvDatabase.PSI_MI, mol.getShortLabel(), InteractorConverter.DISPLAY_LONG ); mitabInteractor.getAliases().add(displayLong);
psidev.psi.mi.tab.model.Alias displayLong = new AliasImpl( CvDatabase.PSI_MI, mol.getShortLabel(), InteractorConverter.DISPLAY_SHORT ); mitabInteractor.getAliases().add(displayLong); psidev.psi.mi.tab.model.Alias shortLabel = new AliasImpl( CvDatabase.ENSEMBL, mol.getShortLabel(), InteractorConverter.SHORTLABEL ); mitabInteractor.getAliases().add(shortLabel); psidev.psi.mi.tab.model.Alias displayLong = new AliasImpl( CvDatabase.PSI_MI, identifier, InteractorConverter.DISPLAY_LONG ); mitabInteractor.getAliases().add(displayLong); psidev.psi.mi.tab.model.Alias altId = new AliasImpl( defaultInstitution, mol.getShortLabel(), InteractorConverter.SHORTLABEL ); mitabInteractor.getAliases().add(altId); psidev.psi.mi.tab.model.Alias displayLong = new AliasImpl( CvDatabase.PSI_MI, mol.getAc(), InteractorConverter.DISPLAY_LONG ); mitabInteractor.getAliases().add(displayLong); psidev.psi.mi.tab.model.Alias displayLong = new AliasImpl( CvDatabase.PSI_MI, mol.getShortLabel(), InteractorConverter.DISPLAY_LONG ); mitabInteractor.getAliases().add(displayLong);
psidev.psi.mi.tab.model.Alias displayLong = new AliasImpl( CvDatabase.PSI_MI, polymer.getShortLabel(), InteractorConverter.DISPLAY_LONG ); mitabInteractor.getAliases().add(displayLong); if (!hasFoundDisplayShort){ psidev.psi.mi.tab.model.Alias altId = new AliasImpl( CvDatabase.PSI_MI, polymer.getShortLabel(),InteractorConverter.DISPLAY_SHORT ); mitabInteractor.getAliases().add(altId); psidev.psi.mi.tab.model.Alias displayLong = new AliasImpl( CvDatabase.PSI_MI, polymer.getAc(),InteractorConverter.DISPLAY_LONG ); mitabInteractor.getAliases().add(displayLong); psidev.psi.mi.tab.model.Alias altId = new AliasImpl( CvDatabase.PSI_MI, polymer.getShortLabel(),InteractorConverter.DISPLAY_SHORT ); mitabInteractor.getAliases().add(altId); psidev.psi.mi.tab.model.Alias displayLong = new AliasImpl( CvDatabase.PSI_MI, polymer.getShortLabel(),InteractorConverter.DISPLAY_LONG ); mitabInteractor.getAliases().add(displayLong);
db = UNKNOWN; psidev.psi.mi.tab.model.Alias a = new psidev.psi.mi.tab.model.AliasImpl(db, aliasValue); a.setAliasType(alias.getType()); tabAliases.add(a); psidev.psi.mi.tab.model.Alias a = new psidev.psi.mi.tab.model.AliasImpl(UNKNOWN, shortLabel); a.setAliasType(SHORT_LABEL); tabAliases.add(a); psidev.psi.mi.tab.model.Alias a = new psidev.psi.mi.tab.model.AliasImpl(UNKNOWN, fullName); a.setAliasType(FULL_NAME); tabAliases.add(a);
Alias alias = new AliasImpl();