@Override public List<Object> getListOfSBMLElementsToWrite(Object sbase) { logger.debug("getListOfSBMLElementsToWrite: " + sbase.getClass().getCanonicalName()); List<Object> listOfElementsToWrite = new ArrayList<Object>(); if (sbase instanceof Model) { SBasePlugin modelPlugin = ((Model) sbase).getExtension(getNamespaceURI()); if (modelPlugin != null) { listOfElementsToWrite = super.getListOfSBMLElementsToWrite(modelPlugin); } } else { listOfElementsToWrite = super.getListOfSBMLElementsToWrite(sbase); } return listOfElementsToWrite; }
@SuppressWarnings("unchecked") @Override public List<Object> getListOfSBMLElementsToWrite(Object sbase) { if (logger.isDebugEnabled()) { logger.debug("getListOfSBMLElementsToWrite: " + sbase.getClass().getCanonicalName()); } List<Object> listOfElementsToWrite = new ArrayList<Object>(); if (sbase instanceof Model) { QualModelPlugin modelGE = (QualModelPlugin) ((Model) sbase).getExtension(QualConstants.namespaceURI); Enumeration<TreeNode> children = modelGE.children(); while (children.hasMoreElements()) { listOfElementsToWrite.add(children.nextElement()); } } else if (sbase instanceof TreeNode) { Enumeration<? extends TreeNode> children = ((TreeNode) sbase).children(); while (children.hasMoreElements()) { listOfElementsToWrite.add(children.nextElement()); } } if (listOfElementsToWrite.isEmpty()) { listOfElementsToWrite = null; } else if (logger.isDebugEnabled()) { logger.debug("getListOfSBMLElementsToWrite size = " + listOfElementsToWrite.size()); } return listOfElementsToWrite; }
/** * Returns the {@link Geometry} instance. * * @return the {@link Geometry} instance. */ public Geometry getGeometryInstance() { Model model = getModel(); SpatialModelPlugin m = (SpatialModelPlugin) model.getExtension(SpatialConstants.shortLabel); return m.getGeometry(); }
/** * * @return the domainType instance of the {@link DomainType} class */ public DomainType getDomainTypeInstance() { Model m = getModel(); if (m!=null) { SpatialModelPlugin sm = (SpatialModelPlugin) m.getExtension(packageName); sm.getGeometry().getListOfDomainTypes().get(getDomainType()); } return null; }
@Override public List<Object> getListOfSBMLElementsToWrite(Object treeNode) { if (logger.isDebugEnabled()) { logger.debug("getListOfSBMLElementsToWrite: " + treeNode.getClass().getCanonicalName()); } List<Object> listOfElementsToWrite = new ArrayList<Object>(); // test if this treeNode is an extended SBase. if (treeNode instanceof SBase && ((SBase) treeNode).getExtension(shortLabel) != null) { SBasePlugin sbasePlugin = ((Model) treeNode).getExtension(shortLabel); if (sbasePlugin != null) { listOfElementsToWrite = super.getListOfSBMLElementsToWrite(sbasePlugin); logger.debug("getListOfSBMLElementsToWrite: nb children = " + sbasePlugin.getChildCount()); } } else { listOfElementsToWrite = super.getListOfSBMLElementsToWrite(treeNode); } // IntraSpeciesReaction children if (treeNode instanceof IntraSpeciesReaction) { String sbmlNamespace = JSBML.getNamespaceFrom(((IntraSpeciesReaction) treeNode).getLevel(), ((IntraSpeciesReaction) treeNode).getVersion()); for (Object child : listOfElementsToWrite) { if (child instanceof AbstractSBase && ((AbstractSBase) child).getNamespace() == null) { AbstractSBase sbase = (AbstractSBase) child; logger.debug("Found one suspect Model child: " + sbase.getElementName() + ". Setting the SBML namespace to it."); sbase.setNamespace(sbmlNamespace); } } } return listOfElementsToWrite; }
GroupsModelPlugin extendeModel = (GroupsModelPlugin) model.getExtension(GroupsConstants.namespaceURI);
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); } }
QualModelPlugin qualModel = null; if (model.getExtension(QualConstants.namespaceURI) != null) { qualModel = (QualModelPlugin) model.getExtension(QualConstants.namespaceURI); } else { qualModel = new QualModelPlugin(model); QualModelPlugin extendeModel = (QualModelPlugin) model.getExtension(QualConstants.namespaceURI); && groupList.equals(QualList.listOfQualitativeSpecies)) { Model model = (Model) listOf.getParentSBMLObject(); QualModelPlugin extendeModel = (QualModelPlugin) model.getExtension(QualConstants.namespaceURI);
CompModelPlugin compModel = null; if (model.getExtension(namespaceURI) != null) { compModel = (CompModelPlugin) model.getExtension(namespaceURI); } else { compModel = new CompModelPlugin(model);
this.externalModelDefinitionListOf = compSBMLDocumentPlugin.getListOfExternalModelDefinitions(); if (document.isSetModel() && document.getModel().getExtension(CompConstants.shortLabel) != null) { CompModelPlugin compModelPlugin = (CompModelPlugin) document.getModel().getExtension(CompConstants.shortLabel); handlePorts(compModelPlugin, compModelPlugin.getListOfPorts()); replaceElementsInModelDefinition(compModelPlugin, null);
SpatialModelPlugin spatialModel = null; if (model.getExtension(SpatialConstants.namespaceURI) != null) { spatialModel = (SpatialModelPlugin) model.getExtension(SpatialConstants.namespaceURI); } else { spatialModel = new SpatialModelPlugin(model);