Package cytoscape

Examples of cytoscape.CyEdge

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  private void createSpeciesEdgesInNetworkForReaction(CyNetwork net, CyNode reaction){
    int[] inEdgeInds = network.getAdjacentEdgeIndicesArray(reaction.getRootGraphIndex(), false, true, false);
    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);
         
          // Set reversibility from reaction
          eAtts.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_REVERSIBLE,
              (String) nAtts.getAttribute(reaction.getIdentifier(), CySBMLConstants.ATT_REVERSIBLE));
         
          net.addEdge(edge);
        } 
      }
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  private void createReactionEdgesInNetworkForSpecies(CyNetwork net, CyNode reaction){
    int[] inEdgeInds = network.getAdjacentEdgeIndicesArray(reaction.getRootGraphIndex(), false, true, false);
    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);
          net.addEdge(edge);
        } 
      }
    } 
  }
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        // 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 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);
             
              edgeIds.add(edge.getRootGraphIndex());
            }
          }
        }
      }
    }
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  private void addEdgesToGRNForReaction(CyNode reaction){
    int[] inEdgeInds = sbmlNetwork.getAdjacentEdgeIndicesArray(reaction.getRootGraphIndex(), false, true, false);
    int[] outEdgeInds = sbmlNetwork.getAdjacentEdgeIndicesArray(reaction.getRootGraphIndex(), false, false, true);
   
    for (int in: inEdgeInds){
      CyEdge inEdge  = (CyEdge) sbmlNetwork.getEdge(in);
      String inEdgeSBO = (String) eAtts.getAttribute(inEdge.getIdentifier(), CySBMLConstants.ATT_SBOTERM);
      CyNode n1 = (CyNode) inEdge.getSource();
      if (inEdgeSBO == null){
        continue;
      }
      for (int out: outEdgeInds){
        // Get the two edges and end nodes;  n1 --inEdge-> reaction --outEdge-> n2
        CyEdge outEdge = (CyEdge) sbmlNetwork.getEdge(out);
        String outEdgeSBO = (String) eAtts.getAttribute(outEdge.getIdentifier(), CySBMLConstants.ATT_SBOTERM);
        System.out.println("OUT edge: " + outEdge.getIdentifier());
       
        CyNode n2 = (CyNode) outEdge.getTarget();       
        if (outEdgeSBO == null){
          continue;
        }
        // Edges to add
        if (GeneRegulatoryNetwork.productSBOforGRN.contains(outEdgeSBO) &&
          GeneRegulatoryNetwork.modifierSBOforGRN.contains(inEdgeSBO)){
            CyEdge edge = Cytoscape.getCyEdge(n1, n2, Semantics.INTERACTION, inEdgeSBO, true);
            edgeIds.add(edge.getRootGraphIndex());
         
            // Set reversibility from reaction
            eAtts.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_SBOTERM, inEdgeSBO);
        } 
      } 
    }
  } 
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      //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());
        }
        if (input.isSetMetaId()){
          edgeAttributes.setAttribute(edge.getIdentifier(), CySBMLConstants.ATT_METAID, input.getMetaId());
        }
        edgeIds.add(edge.getRootGraphIndex());
      }
    }
     }
  }
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Related Classes of cytoscape.CyEdge

  • cysbml.grn.GRNGraphReader
  • cysbml.grn.NetworkTransformation
  • cysbml.SBMLGraphReader
  • cysbml.SBMLLayoutGraphReader
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