Package org.sbml.jsbml.ext.qual

Examples of org.sbml.jsbml.ext.qual.QualitativeModel

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  private void setMissingQSpeciesBoundingBoxes(){
    Map<String, BoundingBox> boxes = speciesBoundingBoxes;
    BoundingBox genericBox = createGenericBoundingBox();
    String key;
    Model model = document.getModel();
    QualitativeModel qModel = (QualitativeModel) model.getExtension(QualConstant.namespaceURI);
    if (qModel != null){
      for (QualitativeSpecies qspecies : qModel.getListOfQualitativeSpecies()){
        key = qspecies.getId();
        if (!boxes.containsKey(key)){
          boxes.put(key, genericBox);
        }
      }
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  private void setMissingQTransitionBoundingBoxes(){
    Map<String, BoundingBox> boxes = reactionBoundingBoxes;
    BoundingBox genericBox = createGenericBoundingBox();
    String key;
    Model model = document.getModel();
    QualitativeModel qModel = (QualitativeModel) model.getExtension(QualConstant.namespaceURI);
    if (qModel != null){
      for (Transition qtransition : qModel.getListOfTransitions()){
        key = qtransition.getId();
        if (!boxes.containsKey(key)){
          boxes.put(key, genericBox);
        }
      }
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  public void addQualitativeModelEdges() {
    Model model = document.getModel();
    if (model == null) {
      return;
    }
    QualitativeModel qModel = (QualitativeModel) model.getExtension(QualConstant.namespaceURI);
    if (qModel == null){
      return;
    }
       
    for (ReactionGlyph rGlyph : layout.getListOfReactionGlyphs()) {
      CyNode rNode = Cytoscape.getCyNode(rGlyph.getId(), false);
      if (rGlyph.isSetListOfSpeciesReferencesGlyphs()) {
       
        if (rGlyph.isSetReaction()) {
          String reactionId = rGlyph.getReaction();
          Transition transition = (Transition) qModel.getTransition(reactionId);
          if (transition != null){
            for (SpeciesReferenceGlyph sRefGlyph: rGlyph.getListOfSpeciesReferenceGlyphs()){
              String sGlyphId = sRefGlyph.getSpeciesGlyph();
              SpeciesGlyph sGlyph = layout.getSpeciesGlyph(sGlyphId);
             
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    DefaultMutableTreeNode top = new DefaultMutableTreeNode(modelName);
    treeModel = new DefaultTreeModel(top);
    addListOfCompartmentsToTreeModel(top, model.getListOfCompartments());
    addListOfSpeciesToTreeModel(top, model.getListOfSpecies());
    addListOfReactionsToTreeModel(top, model.getListOfReactions());
        QualitativeModel qModel = (QualitativeModel) model.getExtension(QualConstant.namespaceURI);
    if (qModel != null){
      addListOfQualitativeSpeciesToTreeModel(top, qModel.getListOfQualitativeSpecies());
      addListOfTransitionsToTreeModel(top, qModel.getListOfTransitions());
    }
  }
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      }
    }
   
    ////////////// QUALITATIVE SBML MODEL ////////////////////////////////////////////
    //Must the network be generated again for the qual model ??
     QualitativeModel qModel = (QualitativeModel) model.getExtension(QualConstant.namespaceURI);
     if (qModel != null){
      
     //QualSpecies
     String qsid;
     for (QualitativeSpecies qSpecies : qModel.getListOfQualitativeSpecies()){ 
       qsid = qSpecies.getId();
         CyNode node = Cytoscape.getCyNode(qsid, true);
       nodeAttributes.setAttribute(qsid, CySBMLConstants.ATT_ID, qsid);
       nodeAttributes.setAttribute(qsid, CySBMLConstants.ATT_TYPE, CySBMLConstants.NODETYPE_QUAL_SPECIES);
      
       if (qSpecies.isSetName()){
         nodeAttributes.setAttribute(qsid, CySBMLConstants.ATT_NAME, qSpecies.getName());
       } else {
         nodeAttributes.setAttribute(qsid, CySBMLConstants.ATT_NAME, qsid);
       }
     
       if (qSpecies.isSetInitialLevel()){
         nodeAttributes.setAttribute(qsid,
             CySBMLConstants.ATT_INITIAL_LEVEL, new Integer(qSpecies.getInitialLevel())); 
       }
       if (qSpecies.isSetMaxLevel()){
         nodeAttributes.setAttribute(qsid,
             CySBMLConstants.ATT_MAX_LEVEL, new Double(qSpecies.getMaxLevel())); 
       }
       if (qSpecies.isSetSBOTerm()){
         nodeAttributes.setAttribute(qsid,
             CySBMLConstants.ATT_SBOTERM, qSpecies.getSBOTermID());
       }
       if (qSpecies.isSetCompartment()){
         nodeAttributes.setAttribute(qsid,
             CySBMLConstants.ATT_COMPARTMENT, qSpecies.getCompartment());
       }
       if (qSpecies.isSetConstant()){
         nodeAttributes.setAttribute(qsid,
             CySBMLConstants.ATT_CONSTANT, new Boolean(qSpecies.getConstant()));
       }
       if (qSpecies.isSetMetaId()){
         nodeAttributes.setAttribute(qsid, CySBMLConstants.ATT_METAID, qSpecies.getMetaId());
       }
       nodeIds.add(node.getRootGraphIndex());
    }
     
    // QualTransitions
    String qtid;
    for (Transition qTransition : qModel.getListOfTransitions()){
      qtid = qTransition.getId();
      CyNode tNode = Cytoscape.getCyNode(qtid, true);
   
      nodeAttributes.setAttribute(qtid, CySBMLConstants.ATT_TYPE, CySBMLConstants.NODETYPE_QUAL_TRANSITION);
      nodeAttributes.setAttribute(qtid, CySBMLConstants.ATT_ID, qtid);
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    }

    List<Object> listOfElementsToWrite = new ArrayList<Object>();

    if (sbase instanceof Model) {
      QualitativeModel modelGE = (QualitativeModel) ((Model) sbase).getExtension(QualConstants.namespaceURI);

      Enumeration<TreeNode> children = modelGE.children();

      while (children.hasMoreElements()) {
        listOfElementsToWrite.add(children.nextElement());
      }
    }
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    boolean hasAttributes, boolean hasNamespaces, Object contextObject) {
    // logger.debug("processStartElement: elementName = " + elementName + " (" + contextObject.getClass().getSimpleName() + ")");

    if (contextObject instanceof Model) {
      Model model = (Model) contextObject;
      QualitativeModel qualModel = null;

      if (model.getExtension(QualConstants.namespaceURI) != null) {
        qualModel = (QualitativeModel) model.getExtension(QualConstants.namespaceURI);
      } else {
        qualModel = new QualitativeModel(model);
        model.addExtension(QualConstants.namespaceURI, qualModel);
      }

      if (elementName.equals("listOfQualitativeSpecies")) {

        ListOf<QualitativeSpecies> listOfQualitativeSpecies = qualModel.getListOfQualitativeSpecies();
        groupList = QualList.listOfQualitativeSpecies;
        return listOfQualitativeSpecies;
      }
      else if (elementName.equals("listOfTransitions")) {

        ListOf<Transition> listOfObjectives = qualModel.getListOfTransitions();
        groupList = QualList.listOfTransitions;
        return listOfObjectives;
      }
    } else if (contextObject instanceof Transition) {
      Transition transition = (Transition) contextObject;

      if (elementName.equals("listOfInputs")) {
        ListOf<Input> listOfInputs = transition.getListOfInputs();
        groupList = QualList.listOfInputs;
        return listOfInputs;
      } else if (elementName.equals("listOfOutputs")) {
        ListOf<Output> listOfOutputs = transition.getListOfOutputs();
        groupList = QualList.listOfOutputs;
        return listOfOutputs;
      } else if (elementName.equals("listOfFunctionTerms")) {
        ListOf<FunctionTerm> listOfFunctionTerms = transition.getListOfFunctionTerms();
        groupList = QualList.listOfFunctionTerms;
        return listOfFunctionTerms;
      }
    }
    else if (contextObject instanceof ListOf<?>) {
      ListOf<SBase> listOf = (ListOf<SBase>) contextObject;

      if (elementName.equals("transition") && groupList.equals(QualList.listOfTransitions)) {
        Model model = (Model) listOf.getParentSBMLObject();
        QualitativeModel extendeModel = (QualitativeModel) model.getExtension(QualConstants.namespaceURI);

        Transition transition = new Transition();
        extendeModel.addTransition(transition);
        return transition;

      } else if ((elementName.equals("qualitativeSpecies")) && groupList.equals(QualList.listOfQualitativeSpecies)) {
        Model model = (Model) listOf.getParentSBMLObject();
        QualitativeModel extendeModel = (QualitativeModel) model.getExtension(QualConstants.namespaceURI);

        QualitativeSpecies qualSpecies = new QualitativeSpecies();
        extendeModel.addQualitativeSpecies(qualSpecies);
        return qualSpecies;

      } else if (elementName.equals("input") && groupList.equals(QualList.listOfInputs)) {
        Transition transition = (Transition) listOf.getParentSBMLObject();
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  @Override
  public SBasePlugin createPluginFor(SBase sbase) {

    if (sbase != null) {
      if (sbase instanceof Model) {
        return new QualitativeModel((Model) sbase);
      }
    }

    return null;
  }
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Related Classes of org.sbml.jsbml.ext.qual.QualitativeModel

  • cysbml.layout.NetworkLayout
  • cysbml.mapping.NavigationTree
  • cysbml.SBMLGraphReader
  • cysbml.SBMLLayoutGraphReader
  • org.sbml.jsbml.Model
  • org.sbml.jsbml.util.filters.NameFilter
  • org.sbml.jsbml.xml.parsers.QualParser
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