@Override public boolean accepts(Object o) { if (o instanceof SBase) { SBase sbase = (SBase) o; if (sbase.isSetMetaId() && (metaid != null) && sbase.getMetaId().equals(metaid)) { return true; } } return false; }
/** * Sets the value of metaIdRef, using the metaid defined in the given {@link SBase} * * @param sbase the {@link SBase} that contain the metaid to be set. * */ public void setMetaIdRef(SBase sbase) { setMetaIdRef(sbase != null ? sbase.getMetaId() : null); }
@Override public boolean check(ValidationContext ctx, SBase sb) { if (sb.isSetMetaId()) { return SyntaxChecker.isValidMetaId(sb.getMetaId()); } return true; } };
@SuppressWarnings("unchecked") @Override public boolean check(ValidationContext ctx, SBase sb) { if (sb.isSetMetaId()) { Object o = ctx.getHashMap().get(ValidationTools.KEY_META_ID_SET); Set<String> metaIds; if (o != null && o instanceof Set) { metaIds = (Set<String>) o; } else { metaIds = new HashSet<String>(); ctx.getHashMap().put(ValidationTools.KEY_META_ID_SET, metaIds); } boolean added = metaIds.add(sb.getMetaId()); return added; } return true; } };
/** * This updates the metaid of an SBase. * * @param doc * @param arraysPlugin * @param sbase * @param index */ private static void updateSBase(SBMLDocument doc, ArraysSBasePlugin arraysPlugin, SBase sbase, int index) { //TODO check if unique if (sbase.isSetMetaId()) { String metaId = sbase.getMetaId(); String appendId = "_" + index; while(doc.findSBase(metaId + appendId) != null) { appendId = "_" + appendId; } sbase.setMetaId(metaId+appendId); } }
private void flattenSBaseList(Model modelOfSubmodel, ListOf listOfSBase){ ListOf<SBase> list = (ListOf<SBase>) listOfSBase; for(SBase sBase : list){ if (!sBase.getId().equals("")) { sBase.setId(modelOfSubmodel.getId() + sBase.getId()); } if (!sBase.getMetaId().equals("")) { sBase.setMetaId(modelOfSubmodel.getId() + sBase.getMetaId()); } if(sBase.isPackageEnabled(CompConstants.shortLabel)){ CompSBasePlugin compSBasePlugin = (CompSBasePlugin) sBase.getExtension(CompConstants.shortLabel); CompModelPlugin compModelPlugin = (CompModelPlugin) modelOfSubmodel.getExtension(CompConstants.shortLabel); replaceElementsInModelDefinition(compModelPlugin,compSBasePlugin); } //sBase.unsetPlugin(CompConstants.shortLabel); } }
elementId = "id[" + ((NamedSBase) getExtendedSBase()).getId() + "]"; } else if (getExtendedSBase().isSetMetaId()) { elementId = "metaid[" + getExtendedSBase().getMetaId() + "]";
elementId = "id[" + ((NamedSBase) getExtendedSBase()).getId() + "]"; } else if (getExtendedSBase().isSetMetaId()) { elementId = "metaid[" + getExtendedSBase().getMetaId() + "]";
messageBuilder.append('\n').append(MessageFormat.format(postMessageI18n, sbase.getElementName(), sbase.getMetaId()));
/** * @param id * the identifier to be set for the new {@link Member}, can be * {@code null}. * @param sbase * the element that should be referenced as a new member of this * {@link Group}. * @return the newly created {@link Member} or {@code null} if the given * {@link SBase} neither has a metaId nor an id. */ public Member createMember(String id, SBase sbase) { if (sbase.isSetId()) { return createMemberWithIdRef(id, sbase.getId()); } if (sbase.isSetMetaId()) { return createMemberWithMetaIdRef(id, sbase.getMetaId()); } return null; }
metaId = new String(sb.getMetaId());
private ConceptClass determineCC(SBase element, TypeOfConcept type) throws PluginConfigurationException { if (element.isSetSBOTerm()) { ConceptClass cc = ccLookup.get(element.getSBOTermID()); if (cc != null) { return cc; } else { log("No translation entry found for: " + element.getSBOTermID()); } } else { log("Element " +element.getMetaId() + "named: \""+ element.getElementName() + "\" is missing an SBO term"); } SBase parent = element.getParentSBMLObject(); ConceptClass parentCC = null; if (parent != null && (parent.isSetSBOTerm())) { parentCC = determineCC(parent, type); } return mdu.safeFetchConceptClass(type.getId(), type.getDescription(), parentCC); }
equals &= sbase.isSetMetaId() == isSetMetaId(); if (equals && sbase.isSetMetaId()) { equals &= sbase.getMetaId().equals(getMetaId());