public static Bibref createBibref(String publicationId, String dbAc, String dbName) { DbReference dbReference = createDbReference(publicationId, dbAc, dbName, "MI:0358", "primary-reference"); Xref xref = new Xref(dbReference); return new Bibref(xref); }
public static Range createRangeCertain(long startPosition, long endPosition) { Position start = new Position(startPosition); Position end = new Position(endPosition); return new Range(createRangeStatusCertain(), start, createRangeStatusCertain(), end); }
public static <C extends CvType> C createCvType(Class<C> cvTypeClass, String miRef, String label) { C cv = createCvType(cvTypeClass, label); cv.setXref(createXrefPsiMi(miRef)); return cv; }
protected Object psiElementKey(Source psiObject) { String key; if (psiObject.getNames() != null) { key = "source:"+psiObject.getNames().getShortLabel(); } else if (psiObject.getXref() != null) { key = "source:xref:"+psiObject.getXref().getPrimaryRef().getId(); } else if (psiObject.getBibref() != null) { key = "source:bibref:"+psiObject.getBibref().getXref().getPrimaryRef().getId(); } else { throw new PsiConversionException("Could not create key to cache the source: "+psiObject); } return key; } }
public static Interactor createInteractor(String primaryId, String dbMi, InteractorType interactorType, Organism organism) { Interactor interactor = new Interactor(); assignNextId(interactor); interactor.setNames(createNames(primaryId, null)); interactor.setInteractorType(interactorType); interactor.setOrganism(organism); interactor.setXref(createXrefIdentity(primaryId, dbMi, dbMi)); return interactor; }
/** * Get the interactor's shortlabel. * @param interactor * @return the name of null of no shortlabel available. */ private String getName(Interactor interactor) { if( interactor.getNames() != null ) { if ( interactor.getNames().hasShortLabel() ) { return interactor.getNames().getShortLabel(); } } return null; } }
public Range( RangeStatus startStatus, Position begin, RangeStatus endStatus, Position end ) { setStartStatus( startStatus ); setBegin( begin ); setEndStatus( endStatus ); setEnd( end ); }
public static Source createSource(String name, String description, String sourcePublicationId, String miId) { Source source = new Source(); Names names = createNames(name, description); source.setNames(names); if (miId != null) { Xref miRef = createXrefPsiMi(miId); source.setXref(miRef); } if (sourcePublicationId != null) { source.setBibref(createBibrefPubmed(sourcePublicationId)); } return source; }
public static Organism createOrganism(int taxid, String name) { Organism organism = new Organism(); organism.setNames(createNames(name, null)); organism.setNcbiTaxId(taxid); return organism; }
/** * Retrieve an experiment description in an interaction using an experiment ref * @param eref : the experiment reference * @param i : the interaction to look into * @return the experiment which has been found */ private ExperimentDescription findExperimentDescriptionInInteraction(ExperimentRef eref, Interaction i){ for ( ExperimentDescription ed : i.getExperiments() ) { if( ed.getId() == eref.getRef() ) { return ed; } } return null; }
public static Xref createXrefIdentity(String primaryId, String dbMi, String dbName) { Xref xref = new Xref(); xref.setPrimaryRef(createDbReference(primaryId, dbMi, dbName, "MI:0356", "identity")); return xref; }
public static DbReference createDbReferencePsiMi(String psiMiRef) { DbReference ref = createDbReferenceIdentity(psiMiRef, "MI:0488", "psi-mi"); ref.setId(psiMiRef); return ref; }
public static InteractorType createInteractorType(String mi, String name) { InteractorType intType = createCvType(InteractorType.class, name); intType.setXref(createXrefPsiMi(mi)); return intType; }
public static Confidence createConfidence(String value, String unitMi, String unitName){ Unit unit = createCvType( Unit.class, unitMi, unitName); return new Confidence(unit, value); }
@Override public int hashCode() { int result = 31; //result = (names != null ? names.hashCode() : 0); result = 31 * result + ( xref != null ? xref.hashCode() : 0 ); result = 31 * result + ( interactorType != null ? interactorType.hashCode() : 0 ); result = 31 * result + ( organism != null ? organism.hashCode() : 0 ); result = 31 * result + ( sequence != null ? sequence.hashCode() : 0 ); return result; } }
public static Xref createXref(String primaryId, String dbMi, String dbName, String qualifierMi, String qualifierName) { Xref xref = new Xref(); xref.setPrimaryRef(createDbReference(primaryId, dbMi, dbName, qualifierMi, qualifierName)); return xref; }