Examples of cytoscape.CyNode

cytoscape.CyNode

    setCyNodeAttributesForMap(nodeAttributes, reactionGlyphBoundingBoxes);    
  }
  
  private void setCyNodeAttributesForMap(CyAttributes attrs, Map<String, BoundingBox> map){
    for (String id : map.keySet()) {
      CyNode node = Cytoscape.getCyNode(id, false);
      if (node != null){
        BoundingBox box = map.get(id);
        attrs.setAttribute(id, ATT_LAYOUT_HEIGHT,
            new Double(box.getDimensions().getHeight()));
        attrs.setAttribute(id, ATT_LAYOUT_WIDTH,

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    }
    
    // Species
    for (Species species : model.getListOfSpecies()) {
      id = species.getId();
      CyNode node = Cytoscape.getCyNode(id, true);
      
      nodeAttributes.setAttribute(id, CySBMLConstants.ATT_ID, id);
      nodeAttributes.setAttribute(id, CySBMLConstants.ATT_TYPE, CySBMLConstants.NODETYPE_SPECIES);
      if (species.isSetName()){
        nodeAttributes.setAttribute(id, CySBMLConstants.ATT_NAME, species.getName());
      } else {
        nodeAttributes.setAttribute(id, CySBMLConstants.ATT_NAME, id);
      }
      if (species.isSetInitialConcentration()){
        nodeAttributes.setAttribute(id, CySBMLConstants.ATT_INITIAL_CONCENTRATION,
            new Double(species.getInitialConcentration()));
      }
      if (species.isSetInitialAmount()){
        nodeAttributes.setAttribute(id, CySBMLConstants.ATT_INITIAL_AMOUNT,
            new Double(species.getInitialAmount()));
      }
      if (species.isSetSBOTerm()){
          nodeAttributes.setAttribute(id, CySBMLConstants.ATT_SBOTERM,
            species.getSBOTermID());
      }
      if (species.isSetCompartment()){
        nodeAttributes.setAttribute(id, 
            CySBMLConstants.ATT_COMPARTMENT, species.getCompartment());
      }
      if (species.isSetBoundaryCondition()){
        nodeAttributes.setAttribute(id, CySBMLConstants.ATT_BOUNDARY_CONDITION, 
            new Boolean(species.getBoundaryCondition()));
      }
      if (species.isSetConstant()){
        nodeAttributes.setAttribute(id, CySBMLConstants.ATT_CONSTANT, 
            new Boolean(species.getConstant()));
      }
      if (species.isSetMetaId()){
        nodeAttributes.setAttribute(id, CySBMLConstants.ATT_METAID, species.getMetaId());
      }
      if (species.isSetHasOnlySubstanceUnits()){
        nodeAttributes.setAttribute(id, CySBMLConstants.ATT_HAS_ONLY_SUBSTANCE_UNITS, 
            new Boolean(species.getHasOnlySubstanceUnits()));
      }
      nodeIds.add(node.getRootGraphIndex());
    }


    // Reactions
    String rid;
    for (Reaction reaction : model.getListOfReactions()) {
      rid = reaction.getId();
      CyNode node = Cytoscape.getCyNode(rid, true);
      nodeAttributes.setAttribute(rid, CySBMLConstants.ATT_TYPE, CySBMLConstants.NODETYPE_REACTION);
      nodeAttributes.setAttribute(rid, CySBMLConstants.ATT_ID, reaction.getId());
      
      if (reaction.isSetSBOTerm()){
        nodeAttributes.setAttribute(rid, CySBMLConstants.ATT_SBOTERM, reaction.getSBOTermID());
      }
      if (reaction.isSetName()){
        nodeAttributes.setAttribute(rid, CySBMLConstants.ATT_NAME, reaction.getName());
      } else {
        nodeAttributes.setAttribute(rid, CySBMLConstants.ATT_NAME, rid);
      }
    
      if (reaction.isSetCompartment()){
        nodeAttributes.setAttribute(rid, CySBMLConstants.ATT_COMPARTMENT, reaction.getCompartment());
      } else {
        nodeAttributes.setAttribute(rid, CySBMLConstants.ATT_COMPARTMENT, "-");
      }
      // Reactions are reversible by default
      if (reaction.isSetReversible()){
        nodeAttributes.setAttribute(rid, CySBMLConstants.ATT_REVERSIBLE, 
            new Boolean(reaction.getReversible()));
      } else {
        nodeAttributes.setAttribute(rid, CySBMLConstants.ATT_REVERSIBLE, 
            new Boolean(true));
      }
      if (reaction.isSetMetaId()){
        nodeAttributes.setAttribute(rid, CySBMLConstants.ATT_METAID, reaction.getMetaId());
      }
      nodeIds.add(node.getRootGraphIndex());


      //products
      Double stoichiometry;
      for (SpeciesReference speciesRef : reaction.getListOfProducts()) {
        CyNode product = Cytoscape.getCyNode(speciesRef.getSpecies(), false);
        CyEdge edge = Cytoscape.getCyEdge(node, product, Semantics.INTERACTION,
            CySBMLConstants.EDGETYPE_REACTION_PRODUCT, true);
        if (speciesRef.isSetStoichiometry()){
          stoichiometry = speciesRef.getStoichiometry();
        } else {
          stoichiometry = 1.0;
        }
        edgeAttributes.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_STOICHIOMETRY, stoichiometry);
        if (speciesRef.isSetSBOTerm()){
          edgeAttributes.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_SBOTERM, speciesRef.getSBOTermID());
        }
        if (speciesRef.isSetMetaId()){
          edgeAttributes.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_METAID, speciesRef.getMetaId());
        }
        edgeIds.add(edge.getRootGraphIndex());
      }


      //reactants
      for (SpeciesReference speciesRef : reaction.getListOfReactants()) {
        CyNode reactant = Cytoscape.getCyNode(speciesRef.getSpecies(), false);
        CyEdge edge = Cytoscape.getCyEdge(node, reactant, Semantics.INTERACTION,
            CySBMLConstants.EDGETYPE_REACTION_REACTANT, true);
        if (speciesRef.isSetStoichiometry()){
          stoichiometry = speciesRef.getStoichiometry();
        } else {
          stoichiometry = 1.0;
        }
        edgeAttributes.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_STOICHIOMETRY, stoichiometry);
        if (speciesRef.isSetSBOTerm()){
          edgeAttributes.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_SBOTERM, speciesRef.getSBOTermID());
        }
        if (speciesRef.isSetMetaId()){
          edgeAttributes.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_METAID, speciesRef.getMetaId());
        }
        edgeIds.add(edge.getRootGraphIndex());
      }
      
      //modifier
      for (ModifierSpeciesReference msref : reaction.getListOfModifiers()) {
        CyNode modifier = Cytoscape.getCyNode(msref.getSpecies(), false);
        CyEdge edge = Cytoscape.getCyEdge(modifier, node, Semantics.INTERACTION,
            CySBMLConstants.EDGETYPE_REACTION_MODIFIER, true);
        stoichiometry = 1.0;
        edgeAttributes.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_STOICHIOMETRY, stoichiometry);
        if (msref.isSetSBOTerm()){
          edgeAttributes.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_SBOTERM, msref.getSBOTermID());
        }
        if (msref.isSetMetaId()){
          edgeAttributes.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_METAID, msref.getMetaId());
        }
        edgeIds.add(edge.getRootGraphIndex());
      }
      
      //parse the parameters from the kinetic laws
      //TODO: better handling of the kinetic information
      if (reaction.isSetKineticLaw()){
        KineticLaw law = reaction.getKineticLaw();
        if (law.isSetListOfLocalParameters()){
          for (LocalParameter parameter: law.getListOfLocalParameters()){
            String attName = "kineticLaw-" + parameter.getId();
            String attUnitsName = "kineticLaw-" + parameter.getId() + "-units";
            if (parameter.isSetValue()){
              nodeAttributes.setAttribute(rid, attName, parameter.getValue());
            }
            if (parameter.isSetUnits()){
              nodeAttributes.setAttribute(rid, attUnitsName, parameter.getValue());
            }
          }
        }
      }
    }
    
    ////////////// 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);
      nodeAttributes.setAttribute(qtid,  CySBMLConstants.ATT_COMPARTMENT, "-");
      if (qTransition.isSetSBOTerm()){
        nodeAttributes.setAttribute(qtid, CySBMLConstants.ATT_SBOTERM, qTransition.getSBOTermID());
      }
      if (qTransition.isSetName()){
        nodeAttributes.setAttribute(qtid, CySBMLConstants.ATT_NAME, qTransition.getName());
      } else {
        nodeAttributes.setAttribute(qtid, CySBMLConstants.ATT_NAME, qtid);
      }  
      if (qTransition.isSetMetaId()){
        nodeAttributes.setAttribute(qtid,  CySBMLConstants.ATT_METAID, qTransition.getMetaId());
      }
      nodeIds.add(tNode.getRootGraphIndex());
      
      //outputs
      for (Output output : qTransition.getListOfOutputs()) {
        CyNode outNode = Cytoscape.getCyNode(output.getQualitativeSpecies(), false);
        CyEdge edge = Cytoscape.getCyEdge(tNode, outNode, Semantics.INTERACTION,
            CySBMLConstants.EDGETYPE_TRANSITION_OUTPUT, true);
        edgeAttributes.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_STOICHIOMETRY, new Double(1.0));
        if (output.isSetSBOTerm()){
          edgeAttributes.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_SBOTERM, output.getSBOTermID());
        }
        if (output.isSetMetaId()){
          edgeAttributes.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_METAID, output.getMetaId());
        }
        edgeIds.add(edge.getRootGraphIndex());
      }
      //inputs
      for (Input input : qTransition.getListOfInputs()) {
        CyNode inNode = Cytoscape.getCyNode(input.getQualitativeSpecies(), false);
        CyEdge edge = Cytoscape.getCyEdge(tNode, inNode, Semantics.INTERACTION,
            CySBMLConstants.EDGETYPE_TRANSITION_INPUT, true);
        edgeAttributes.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_STOICHIOMETRY, new Double(1.0));
        if (input.isSetSBOTerm()){
          edgeAttributes.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_SBOTERM, input.getSBOTermID());

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  /** Get all nodes with the type from the origin network */
  private List<CyNode> getNodesOfType(String nodeType){
    List<CyNode> netNodes = new LinkedList<CyNode>();
    for (Object obj: network.nodesList()){
      CyNode node = (CyNode) obj;
      String type = (String) nAtts.getAttribute(node.getIdentifier(), CySBMLConstants.ATT_TYPE);
      if (type.equals(nodeType)){
        netNodes.add(node);
      }
    }
    return netNodes;

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    int[] outEdgeInds = network.getAdjacentEdgeIndicesArray(reaction.getRootGraphIndex(), false, false, true);
    for (int in: inEdgeInds){
      // Get the two edges and end nodes;  n1 --inEdge-> reaction --outEdge-> n2 
      CyEdge inEdge  = (CyEdge) network.getEdge(in);
      String inEdgeType = (String) eAtts.getAttribute(inEdge.getIdentifier(), Semantics.INTERACTION);
      CyNode n1 = (CyNode) inEdge.getSource();
      
      for (int out: outEdgeInds){
        CyEdge outEdge = (CyEdge) network.getEdge(out);
        String outEdgeType = (String) eAtts.getAttribute(outEdge.getIdentifier(), Semantics.INTERACTION);  
        // only certain combination will be converted to edges in the compound network
        // TODO: better a strict positive list what to take
        if (   inEdgeType.equals(CySBMLConstants.EDGETYPE_REACTION_ACTIVATOR)
          || inEdgeType.equals(CySBMLConstants.EDGETYPE_REACTION_INHIBITOR)
          || inEdgeType.equals(CySBMLConstants.EDGETYPE_REACTION_MODIFIER)){
          // ignore the modifier edges
          continue;
        }
        CyNode n2 = (CyNode) outEdge.getTarget();
        
        // source and target node are in the network, add the respective edge between these nodes
        if (net.containsNode(n1) && net.containsNode(n2)){
          String type = inEdgeType + "2" + outEdgeType;
          CyEdge edge = Cytoscape.getCyEdge(n1, n2, Semantics.INTERACTION, type, true);

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    int[] outEdgeInds = network.getAdjacentEdgeIndicesArray(reaction.getRootGraphIndex(), false, false, true);
    for (int in: inEdgeInds){
      // Get the two edges and end nodes;  n1 --inEdge-> reaction --outEdge-> n2 
      CyEdge inEdge  = (CyEdge) network.getEdge(in);
      String inEdgeType = (String) eAtts.getAttribute(inEdge.getIdentifier(), Semantics.INTERACTION);
      CyNode n1 = (CyNode) inEdge.getSource();
      
      for (int out: outEdgeInds){
        CyEdge outEdge = (CyEdge) network.getEdge(out);
        String outEdgeType = (String) eAtts.getAttribute(outEdge.getIdentifier(), Semantics.INTERACTION);
        // only certain combination will be converted to edges in the compound network
        if (   outEdgeType.equals(CySBMLConstants.EDGETYPE_REACTION_ACTIVATOR)
          || outEdgeType.equals(CySBMLConstants.EDGETYPE_REACTION_INHIBITOR)
          || outEdgeType.equals(CySBMLConstants.EDGETYPE_REACTION_MODIFIER)){
          
          // ignore the modifier edges
          continue;
        }
        CyNode n2 = (CyNode) outEdge.getTarget();
        
        // source and target node are in the network, add the respective edge between these nodes
        if (net.containsNode(n1) && net.containsNode(n2)){
          String type = inEdgeType + "2" + outEdgeType;
          CyEdge edge = Cytoscape.getCyEdge(n1, n2, Semantics.INTERACTION, type, true);

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    assertEquals(2, network.getEdgeCount());
  }
  
  @Test
  public void nodeTest() throws IOException {
    CyNode s1 = Cytoscape.getCyNode("s1");
    CyNode s2 = Cytoscape.getCyNode("s2");
    CyNode r1 = Cytoscape.getCyNode("r1");
    assertNotNull(s1);
    assertNotNull(s2);
    assertNotNull(r1);  
  }

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  }
  
  public void addSpeciesGlyphNodes() {
    for (SpeciesGlyph glyph : layout.getListOfSpeciesGlyphs()) {
      String id = glyph.getId();
      CyNode node = Cytoscape.getCyNode(id, true);
      if (glyph.isSetSpecies()){
        CyNode sNode = Cytoscape.getCyNode(glyph.getSpecies(), false);
        copyNodeInformation(sNode, node);
      } else {
        nodeAttributes.setAttribute(id, CySBMLConstants.ATT_ID, id);
        nodeAttributes.setAttribute(id, CySBMLConstants.ATT_TYPE, "SpeciesGlyph");
      }

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  }
  
  public void addReactionGlyphNodes(){
    for (ReactionGlyph glyph: layout.getListOfReactionGlyphs()){
      String id = glyph.getId();
      CyNode node = Cytoscape.getCyNode(id, true);
      if (glyph.isSetReaction()){
        CyNode rNode = Cytoscape.getCyNode(glyph.getReaction(), false);
        copyNodeInformation(rNode, node);
      } else {
        nodeAttributes.setAttribute(id, CySBMLConstants.ATT_ID, id);
        nodeAttributes.setAttribute(id, CySBMLConstants.ATT_TYPE, "ReactionGlyph");
      }

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    Model model = document.getModel();
    if (model == null) {
      return;
    }
    for (ReactionGlyph rGlyph : layout.getListOfReactionGlyphs()) {
      CyNode rNode = Cytoscape.getCyNode(rGlyph.getId(), false);
      if (rGlyph.isSetListOfSpeciesReferencesGlyphs()) {
        
        // if the reaction is not set
        if (!rGlyph.isSetReaction()) {
          for (SpeciesReferenceGlyph sRefGlyph : rGlyph.getListOfSpeciesReferenceGlyphs()) {
            String sGlyphId = sRefGlyph.getSpeciesGlyph();
            CyNode sNode = Cytoscape.getCyNode(sGlyphId, false);
            CyEdge edge = Cytoscape.getCyEdge(rNode, sNode, Semantics.INTERACTION,
                              CySBMLConstants.EDGETYPE_UNDEFINED, true);
            readEdgeAttributesFromSpeciesReferenceGlyph(edge, sRefGlyph);
            edgeIds.add(edge.getRootGraphIndex());
          }
        }


        // if the reaction is set
        if (rGlyph.isSetReaction()) {
          String reactionId = rGlyph.getReaction();
          Reaction reaction = model.getReaction(reactionId);
          if (reaction == null) {
            System.err.println("reactionId in in ReactionGlyph is not in SBML model: " + reactionId);
            continue;
          }
          for (SpeciesReferenceGlyph sRefGlyph : rGlyph.getListOfSpeciesReferenceGlyphs()) {
            String sGlyphId = sRefGlyph.getSpeciesGlyph();
            SpeciesGlyph sGlyph = layout.getSpeciesGlyph(sGlyphId);
            
            String edgeType = getEdgeTypeFromSpeciesReferenceGlyphRole(sRefGlyph);
            // if not found try via SBML model
            if (edgeType.equals(CySBMLConstants.EDGETYPE_UNDEFINED)){
              edgeType = getEdgeTypeFromSBMLModel(reaction, sGlyph);
            }
            
            CyNode sNode = Cytoscape.getCyNode(sGlyphId, false);
            CyEdge edge = Cytoscape.getCyEdge(rNode, sNode, Semantics.INTERACTION, edgeType, true);
            
            // Read additional edge information
            readEdgeAttributesFromSpeciesReferenceGlyph(edge, sRefGlyph);
            edgeIds.add(edge.getRootGraphIndex());

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    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);
              
              String edgeType = getEdgeTypeFromSpeciesReferenceGlyphRole(sRefGlyph);
              // if not found try via SBML model
              if (edgeType.equals(CySBMLConstants.EDGETYPE_UNDEFINED)){
                edgeType = getEdgeTypeFromQualModel(transition, sGlyph);
              }
              CyNode sNode = Cytoscape.getCyNode(sGlyphId, false);
              CyEdge edge = Cytoscape.getCyEdge(rNode, sNode, Semantics.INTERACTION, edgeType, true);
        
              // Read additional edge information
              readEdgeAttributesFromSpeciesReferenceGlyph(edge, sRefGlyph);

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cysbml.grn.GRNGraphReader

cysbml.grn.NetworkTransformation

cysbml.layout.NetworkLayout

cysbml.SBMLGraphReader

cysbml.SBMLGraphReaderTest

cysbml.SBMLLayoutGraphReader

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