private Boolean isIntraMolecular(BinaryInteraction<?> binaryInteraction) { Interactor A = binaryInteraction.getInteractorA(); Interactor B = binaryInteraction.getInteractorB(); if ((A == null && B != null && !B.isEmpty())) { //We have only one participant in mitab so we don't need to check the stoichiometry. return true; } else if (B == null && A != null && !A.isEmpty()) { return true; } return false; }
public AliasImpl( String dbSource, String name, String aliasType ) { this.dbSource = dbSource; setName( name ); this.aliasType = aliasType; }
/** * Create a new ChecksumImpl object. * * @param methodName String with the PSI-MI name of the CVTerm * @param checksum String with the value generated by the method */ public ChecksumImpl(String methodName, String checksum) { setMethodName(methodName); setChecksum(checksum); }
private void invertInteractors(BinaryInteraction binaryInteraction) { Interactor a = binaryInteraction.getInteractorA(); Interactor b = binaryInteraction.getInteractorB(); binaryInteraction.setInteractorA(b); binaryInteraction.setInteractorB(a); }
public Interactor createInteractor( int taxid, String db, String id, String txt ) { CrossReference cr = new CrossReferenceImpl( db, id, txt ); final Interactor interactor = buildInteractor(); interactor.setIdentifiers( createList( cr ) ); Organism o = new OrganismImpl( taxid ); interactor.setOrganism( o ); return interactor; }
private void clearExperimentDetails(){ if (this.binaryTemplate != null){ this.binaryTemplate.setDetectionMethods(new ArrayList<CrossReference>()); this.binaryTemplate.setHostOrganism(new OrganismImpl()); } } }
protected CrossReference createCrossReferenceFromAc(uk.ac.ebi.intact.model.Interactor mol) { CrossReference acField = new CrossReferenceImpl(); String db = defaultInstitution; acField.setDatabase(db); acField.setIdentifier(mol.getAc()); return acField; }
public void flip() { T interactorA = getInteractorA(); T interactorB = getInteractorB(); setInteractorA(interactorB); setInteractorB(interactorA); }
protected BinaryInteraction buildInteraction(Interactor a, Interactor b) { return new BinaryInteractionImpl( a, b ); }
public OrganismImpl( int taxid ) { addIdentifier( new CrossReferenceImpl( DEFAULT_DATABASE, String.valueOf( taxid ) ) ); }
public Interactor newInteractor(List<CrossReference> identifiers) { return new Interactor(identifiers); } }
/** * Construct a FeatureImpl object * * @param featureType String with the PSI-MI name of the CVTerm for the feature * @param range Range where appears of the feature. See more information in: * @param text optional information like features type names, interpro cross references, etc. * @link https://docs.google.com/spreadsheet/ccc?key=0AhnBwV7LOdY_dE1xbDVSYkpoa3ptZ3NRbzNmdWpySXc&hl=en_GB#gid=0 */ public FeatureImpl(String featureType, List<String> range, String text) { setFeatureType(featureType); setRange(range); setText(text); }
public CrossReference createCrossReference( String db, String id, String text ) { return new CrossReferenceImpl( db, id, text ); }
public AbstractBinaryInteraction(T interactorA, T interactorB) { setInteractorA(interactorA); setInteractorB(interactorB); }
public CrossReferenceImpl(String database, String identifier) { setIdentifier(identifier); setDatabase(database); }
public ConfidenceImpl( String type, String value, String text ) { this.type = type; setValue( value ); this.text = text; }
public CrossReferenceImpl(String database, String identifier, String text) { this(database, identifier); setText(text); }
public OrganismImpl( List<CrossReference> identifiers ) { setIdentifiers( identifiers ); }
protected T newInteractor(List<CrossReference> identifiers) { return (T) new psidev.psi.mi.tab.model.Interactor(identifiers); }