Examples with PhysicalEntity org.vcell.pathway.PhysicalEntity used on opensource projects

Example 6 with PhysicalEntity

use of org.vcell.pathway.PhysicalEntity in project vcell by virtualcell.

the class BioPaxObjectPropertiesPanel method refreshInterface.

protected void refreshInterface() {
    if (bioPaxObject == null) {
        // sanity check
        return;
    }
    ArrayList<BioPaxObjectProperty> propertyList = new ArrayList<BioPaxObjectProperty>();
    if (!(bioPaxObject instanceof SBEntity)) {
        tableModel.setData(propertyList);
        return;
    }
    SBEntity sbEntity = (SBEntity) bioPaxObject;
    if (!(sbEntity instanceof Entity)) {
        tableModel.setData(propertyList);
        return;
    }
    Entity entity = (Entity) sbEntity;
    // entity::type
    propertyList.add(new BioPaxObjectProperty("Type", bioPaxObject.getTypeLabel()));
    if (lookupContains(entity)) {
        propertyList.add(new BioPaxObjectProperty("Name", entity.getName().get(0) + " (looking...)"));
    } else if (entity.getFormalNames() != null && entity.getFormalNames().size() != 0) {
        propertyList.add(new BioPaxObjectProperty("Name", entity.getName().get(0) + " (" + entity.getFormalNames().get(0) + ")"));
    } else if (entity.getName() != null && entity.getName().size() > 0) {
        String displayName = entity.getName().get(0);
        if (entity.getxRef() != null && entity.getxRef().size() > 0) {
            displayName = displayName + " (double-click lookup)";
        }
        // entity::name
        propertyList.add(new BioPaxObjectProperty("Name", displayName));
    }
    // entity::Link
    for (RelationshipObject rObject : bioModel.getRelationshipModel().getRelationshipObjects(bioPaxObject)) {
        BioModelEntityObject beObject = rObject.getBioModelEntityObject();
        String sType = beObject.getDisplayType();
        propertyList.add(new BioPaxObjectProperty("Linked physiology object (" + sType + ")", beObject.getName(), beObject));
    }
    if (entity instanceof PhysicalEntity) {
        // ------------------------ PHYSICAL ENTITY -----------------------
        PhysicalEntity physicalEntity = (PhysicalEntity) entity;
        // physicalEntity::feature (***ignored***)
        // physicalEntity::memberPhysicalEntity (***ignored***)
        // physicalEntity::notFeature (***ignored***)
        // TODO:  extract the kinetic law, then the SBEntities, then the measurables, units, aso
        boolean isReactionParticipant = BioPAXUtil.isReactionParticipant(physicalEntity, bioModel.getPathwayModel());
        String role = "";
        if (BioPAXUtil.isController(physicalEntity, bioModel.getPathwayModel())) {
            role += "Controller";
            if (isReactionParticipant) {
                role += ", Participant";
            }
        } else if (isReactionParticipant) {
            role += "Participant";
        }
        if (!role.isEmpty()) {
            propertyList.add(new BioPaxObjectProperty("Role(s)", role));
        }
        if (!(physicalEntity instanceof SmallMolecule)) {
            // physicalEntity::cellular location
            CellularLocationVocabulary cellularLocation = physicalEntity.getCellularLocation();
            if (cellularLocation != null && cellularLocation.getTerm() != null && cellularLocation.getTerm().size() > 0) {
                propertyList.add(new BioPaxObjectProperty("Cellular Location", cellularLocation.getTerm().get(0), cellularLocation));
            } else if (entity.getName() != null && entity.getName().size() > 1) {
                String location = entity.getName().get(1);
                if (location.contains("[") && location.contains("]")) {
                    location = location.substring(location.indexOf("[") + 1, location.indexOf("]"));
                    propertyList.add(new BioPaxObjectProperty("Cellular Location", location));
                }
            }
        }
        if (physicalEntity instanceof Complex) {
            Complex complex = (Complex) physicalEntity;
            // complex::components
            for (PhysicalEntity pe : complex.getComponents()) {
                propertyList.add(new BioPaxObjectProperty("Component", getEntityName(pe), pe));
            }
        } else if (physicalEntity instanceof Protein) {
        // Protein protein = (Protein)entity;
        // protein::entity reference (***ignored***)
        } else if (physicalEntity instanceof SmallMolecule) {
            SmallMolecule sm = (SmallMolecule) physicalEntity;
            EntityReference er = sm.getEntityReference();
            if (er != null && !er.getName().isEmpty() && er.getName().get(0) != null && !er.getName().get(0).isEmpty()) {
                propertyList.add(new BioPaxObjectProperty("Entity Reference", er.getName().get(0)));
                ArrayList<Xref> xrefList = er.getxRef();
                for (Xref xref : xrefList) {
                    propertyList.add(new BioPaxObjectProperty("   Xref", xref.getDb() + ":" + xref.getId(), xref));
                }
            }
        } else if (physicalEntity instanceof Dna) {
        // dna::entityReference (***ignored***)
        } else if (physicalEntity instanceof DnaRegion) {
        // dnaRegion::entityReference (***ignored***)
        } else if (physicalEntity instanceof Rna) {
        // rna::entityReference (***ignored***)
        } else if (physicalEntity instanceof RnaRegion) {
        // rnaRegion::entityReference (***ignored***)
        }
    } else if (entity instanceof Interaction) {
        // --------------------------- INTERACTION -------------------
        Interaction interaction = (Interaction) entity;
        // interaction::interactionType
        for (InteractionVocabulary interactionVocabulary : interaction.getInteractionTypes()) {
            if (interactionVocabulary.getTerm().size() > 0) {
                propertyList.add(new BioPaxObjectProperty("Interaction Type", interactionVocabulary.getTerm().get(0), interactionVocabulary));
            }
        }
        // interaction::participants
        for (InteractionParticipant interactionParticipant : interaction.getParticipants()) {
            PhysicalEntity physicalEntity = interactionParticipant.getPhysicalEntity();
            String physicalEntityName = physicalEntity.getName().size() > 0 ? physicalEntity.getName().get(0) : physicalEntity.getIDShort();
            String cellularLocation = "";
            if (physicalEntity.getCellularLocation() != null) {
                cellularLocation = physicalEntity.getCellularLocation().getTerm().size() > 0 ? " [" + physicalEntity.getCellularLocation().getTerm().get(0) + "]" : "";
            }
            propertyList.add(new BioPaxObjectProperty(interactionParticipant.getLevel3PropertyName(), physicalEntityName + cellularLocation, physicalEntity));
        }
        // get the controllers for interactions
        // we always need this because there's no guarantee we'll have kinetic laws
        // for instance pathway commons doesn't have quantitative information
        Set<String> controllersNames = getControllersNames(interaction);
        if (controllersNames.size() > 0) {
            for (String str : controllersNames) {
                // String tooltip = "<html>how many of these 12 M <br>average size  1.12345*E12 nm <br>temperature 37 degrees Celsius</html>";
                String tooltip = "";
                propertyList.add(new BioPaxObjectProperty("Controlled by", str, interaction, tooltip));
            }
        }
        // get the kinetic laws (if any)
        Set<Control> controls = BioPAXUtil.getControlsOfInteraction(interaction, bioModel.getPathwayModel());
        for (Control control : controls) {
            ArrayList<SBEntity> sbEntities = control.getSBSubEntity();
            for (SBEntity sbE : sbEntities) {
                // the only SBSubEntities allowed in a control are kinetic laws
                if (sbE.getID().contains("kineticLaw")) {
                    String str = new String();
                    if (control.getPhysicalControllers() != null) {
                        str += " for Controller(s): ";
                        for (PhysicalEntity ep : control.getPhysicalControllers()) {
                            if (ep.getName().size() > 0) {
                                str += ep.getName().get(0);
                            } else {
                                str += ep.getIDShort();
                            }
                            str += " ";
                        }
                    }
                    String sDetails = "";
                    ArrayList<SBVocabulary> sbTerms = sbE.getSBTerm();
                    for (SBVocabulary sbv : sbTerms) {
                        // type of kinetic law
                        String str1 = sbv.getID();
                        str1 = str1.substring(str1.lastIndexOf('#') + 1);
                        System.out.println(str1);
                        SBOTerm sboT = SBOListEx.sboMap.get(str1);
                        sDetails += "<font color=\"#660000\"><b>" + sboT.getName() + "</b></font>" + "  " + "<font color=\"#006600\">" + sboT.getDescription() + "</font>";
                        sDetails += "<br>";
                    }
                    ArrayList<SBEntity> klProperties = sbE.getSBSubEntity();
                    for (SBEntity klProperty : klProperties) {
                        if (klProperty instanceof SBMeasurable) {
                            SBMeasurable m = (SBMeasurable) klProperty;
                            String str1 = "";
                            String str2 = "";
                            String str3 = "";
                            if (m.hasTerm()) {
                                str1 += m.extractSBOTermAsString();
                            }
                            if (m.hasNumber()) {
                                str2 += m.getNumber().get(0);
                            }
                            if (m.hasUnit()) {
                                str3 += m.extractSBOUnitAsString();
                            }
                            // str1 is an SBO id, for example "SBO:0000064"
                            SBOTerm sboT = SBOListEx.sboMap.get(str1);
                            sDetails += sboT.getSymbol() + "   (" + sboT.getName() + ")" + "<font color=\"#660000\"><b>" + str2 + str3 + "</b></font>" + "  " + "<font color=\"#006600\">" + sboT.getDescription() + "</font>";
                        } else {
                            sDetails = klProperty.getIDShort() + "  " + klProperty.getTypeLabel();
                        }
                        sDetails += "<br>";
                    }
                    // String tooltip = "<html>how many of these 12 M <br>average size  1.12345*E12 nm <br>temperature 37 degrees Celsius</html>";
                    String tooltip = "";
                    BioPaxObjectProperty bpop = new BioPaxObjectProperty("Kinetic Law" + str, sbE.getID(), sbE, tooltip);
                    bpop.setDetails(sDetails);
                    propertyList.add(bpop);
                }
            }
        }
        if (interaction instanceof Control) {
            // TODO: is this ever being called?
            Control c = (Control) interaction;
            // catalysis::controlled
            Interaction controlledInteraction = c.getControlledInteraction();
            if (controlledInteraction != null) {
                String controlledName = controlledInteraction.getIDShort();
                if (controlledInteraction.getName().size() > 0) {
                    controlledName = controlledInteraction.getName().get(0);
                }
                propertyList.add(new BioPaxObjectProperty("Controlled Interaction", controlledName, controlledInteraction));
            }
        }
    } else if (entity instanceof GroupObject) {
        // ---------------------- GROUP OBJECT ------------------
        GroupObject groupObject = (GroupObject) entity;
        for (BioPaxObject bpo : groupObject.getGroupedObjects()) {
            propertyList.add(new BioPaxObjectProperty("Element::" + bpo.getTypeLabel(), getEntityName((Entity) bpo), bpo));
        }
    }
    // entity::comments
    for (String comment : entity.getComments()) {
        propertyList.add(new BioPaxObjectProperty("Comment", comment));
    }
    // entity::xRef
    ArrayList<Xref> xrefList = ((Entity) bioPaxObject).getxRef();
    for (Xref xref : xrefList) {
        if (xref instanceof UnificationXref) {
            propertyList.add(new BioPaxObjectProperty("Xref", xref.getDb() + ":" + xref.getId(), xref));
        }
    }
    for (Xref xref : xrefList) {
        if (xref instanceof RelationshipXref) {
            propertyList.add(new BioPaxObjectProperty("Xref (related)", xref.getDb() + ":" + xref.getId(), xref));
        }
    }
    for (Xref xref : xrefList) {
        if (xref instanceof PublicationXref) {
            propertyList.add(new BioPaxObjectProperty("Publication", xref.getDb() + ":" + xref.getId(), xref));
        }
    }
    // for(SBVocabulary sbVocab : sbEntity.getSBTerm()) {
    // propertyList.add(new BioPaxObjectProperty("SBO Term", SBPAXLabelUtil.makeLabel(sbVocab)));
    // }
    // if(sbEntity instanceof Interaction) {
    // // TODO: this goes away
    // Interaction interaction = (Interaction) sbEntity;
    // Set<SBEntity> subEntities = new HashSet<SBEntity>();
    // subEntities.add(interaction);
    // Set<Control> controls = BioPAXUtil.findAllControls(interaction, bioModel.getPathwayModel());
    // subEntities.addAll(controls);
    // subEntities = SBPAX3Util.extractAllEntities(subEntities);
    // for(SBEntity subEntity : subEntities) {
    // if(subEntity instanceof SBMeasurable) {
    // propertyList.add(new BioPaxObjectProperty("Measured quantity", SBPAXLabelUtil.makeLabel(subEntity)));
    // }
    // }
    // }
    tableModel.setData(propertyList);
}

Example 7 with PhysicalEntity

use of org.vcell.pathway.PhysicalEntity in project vcell by virtualcell.

the class PathwayGraphModel method removeEdgeShape.

private void removeEdgeShape(EdgeShape shape) {
    PhysicalEntity physicalEntity = null;
    if (shape instanceof BioPaxInteractionParticipantShape) {
        BioPaxInteractionParticipantShape edgeShape = (BioPaxInteractionParticipantShape) shape;
        physicalEntity = ((InteractionParticipant) edgeShape.getModelObject()).getPhysicalEntity();
    } else if (shape instanceof BioPaxGroupNeighborShape) {
        BioPaxGroupNeighborShape edgeShape = (BioPaxGroupNeighborShape) shape;
        BioPaxObject bpObject = ((GroupNeighbor) edgeShape.getModelObject()).getNeighbor();
        if (bpObject instanceof PhysicalEntity) {
            physicalEntity = (PhysicalEntity) bpObject;
        }
    }
    if (physicalEntity == null)
        return;
    if (!pathwayModel.getDisplayableBioPaxObjectList().contains(physicalEntity)) {
        removeShape(shape);
    }
}

Example 8 with PhysicalEntity

use of org.vcell.pathway.PhysicalEntity in project vcell by virtualcell.

the class PathwayReader method addContentConversion.

private boolean addContentConversion(Conversion conversion, Element element, Element childElement) {
    if (addContentInteraction(conversion, element, childElement)) {
        return true;
    }
    /**
     * String getConversionDirection();
     * ArrayList<PhysicalEntity> getLeftSide();
     * ArrayList<Stoichiometry> getParticipantStoichiometry();
     * ArrayList<PhysicalEntity> getRightSide();
     * Boolean getSpontaneous();
     */
    if (childElement.getName().equals("LEFT") || childElement.getName().equals("RIGHT")) {
        Element physicalEntityParticipantElement = childElement.getChild("physicalEntityParticipant", bp);
        if (physicalEntityParticipantElement != null) {
            boolean found = false;
            PhysicalEntity thePhysicalEntity = null;
            Element physicalEntityPropertyElement = physicalEntityParticipantElement.getChild("PHYSICAL-ENTITY", bp);
            // always create a proxy, the real PhysicalEntity (if present) is not ready to be inserted as is because it is incomplete
            // the reason is that PhysicalEntity object is a "species" in v2 but becomes a "species context" in v3
            PhysicalEntityProxy physicalEntityProxy = null;
            if (physicalEntityPropertyElement != null) {
                found = true;
                physicalEntityProxy = new PhysicalEntityProxy();
                addAttributes(physicalEntityProxy, physicalEntityPropertyElement);
                pathwayModel.add(physicalEntityProxy);
                if (childElement.getName().equals("LEFT")) {
                    conversion.addLeft(physicalEntityProxy);
                } else {
                    conversion.addRight(physicalEntityProxy);
                }
                if (physicalEntityPropertyElement.getChildren().size() > 0) {
                    thePhysicalEntity = addObjectPhysicalEntity(physicalEntityPropertyElement);
                }
            }
            Element cellularLocationElement = physicalEntityParticipantElement.getChild("CELLULAR-LOCATION", bp);
            if (cellularLocationElement != null && found == true) {
                Element controlledVocabularyElement = cellularLocationElement.getChild("openControlledVocabulary", bp);
                if (controlledVocabularyElement != null) {
                    CellularLocationVocabularyProxy cellularLocationVocabularyProxy = new CellularLocationVocabularyProxy();
                    addAttributes(cellularLocationVocabularyProxy, controlledVocabularyElement);
                    pathwayModel.add(cellularLocationVocabularyProxy);
                    if (controlledVocabularyElement.getChildren().size() == 0) {
                        physicalEntityProxy.setCellularLocation(cellularLocationVocabularyProxy);
                    } else {
                        physicalEntityProxy.setCellularLocation(addObjectCellularLocationVocabulary(controlledVocabularyElement));
                    }
                // System.out.println(" -          " + controlledVocabularyElement.getName());
                // we'll use the extra info in this proxy during reconciliation phase to reconstruct a complete PhysicalEntity
                }
            }
            Element stoichiometricCoefficientElement = physicalEntityParticipantElement.getChild("STOICHIOMETRIC-COEFFICIENT", bp);
            if (stoichiometricCoefficientElement != null && found == true) {
                // System.out.println(" -          " + stoichiometricCoefficientElement.getTextTrim());
                // Create a Stoichiometry object from the stoichiometricCoefficient and from PhysicalEntity object
                Stoichiometry stoichiometry = new Stoichiometry();
                stoichiometry.setID(generateInstanceID());
                stoichiometry.setStoichiometricCoefficient(Double.valueOf(stoichiometricCoefficientElement.getTextTrim()));
                if (physicalEntityProxy == null) {
                    // reuse the proxy if we created one already
                    physicalEntityProxy = new PhysicalEntityProxy();
                    String uri = context.unRelativizeURI(physicalEntityPropertyElement, generateResourceID(physicalEntityPropertyElement));
                    physicalEntityProxy.setID(uri);
                    pathwayModel.add(physicalEntityProxy);
                }
                stoichiometry.setPhysicalEntity(physicalEntityProxy);
                // Add the Stoichiometry object to the participantStoichiometry property of the conversion
                conversion.getParticipantStoichiometry().add(stoichiometry);
                // add the Stoichiometry object to the pathway model
                pathwayModel.add(stoichiometry);
                found = true;
            }
            return found;
        }
        Element sequenceParticipantElement = childElement.getChild("sequenceParticipant", bp);
        if (sequenceParticipantElement != null) {
            boolean found = false;
            PhysicalEntity thePhysicalEntity = null;
            Element physicalEntityPropertyElement = sequenceParticipantElement.getChild("PHYSICAL-ENTITY", bp);
            PhysicalEntityProxy physicalEntityProxy = null;
            if (physicalEntityPropertyElement != null) {
                found = true;
                if (physicalEntityPropertyElement.getChildren().size() == 0) {
                    physicalEntityProxy = new PhysicalEntityProxy();
                    addAttributes(physicalEntityProxy, physicalEntityPropertyElement);
                    pathwayModel.add(physicalEntityProxy);
                    if (childElement.getName().equals("LEFT")) {
                        conversion.addLeft(physicalEntityProxy);
                    } else {
                        conversion.addRight(physicalEntityProxy);
                    }
                // return true;
                } else {
                    thePhysicalEntity = addObjectPhysicalEntity(physicalEntityPropertyElement);
                }
                Element cellularLocationElement = sequenceParticipantElement.getChild("CELLULAR-LOCATION", bp);
                if (cellularLocationElement != null && found == true) {
                    Element controlledVocabularyElement = cellularLocationElement.getChild("openControlledVocabulary", bp);
                    if (controlledVocabularyElement != null) {
                        CellularLocationVocabularyProxy cellularLocationVocabularyProxy = new CellularLocationVocabularyProxy();
                        addAttributes(cellularLocationVocabularyProxy, controlledVocabularyElement);
                        pathwayModel.add(cellularLocationVocabularyProxy);
                        if (controlledVocabularyElement.getChildren().size() == 0) {
                            physicalEntityProxy.setCellularLocation(cellularLocationVocabularyProxy);
                        } else {
                            physicalEntityProxy.setCellularLocation(addObjectCellularLocationVocabulary(controlledVocabularyElement));
                        }
                    // System.out.println(" -          " + controlledVocabularyElement.getName());
                    // we'll use the extra info in this proxy during reconciliation phase to reconstruct a complete PhysicalEntity
                    }
                }
            }
            return found;
        }
        if (childElement.getChildren().size() == 0) {
            // PhysicalEntityProxy physicalEntityProxy = new PhysicalEntityProxy();
            // addAttributes(physicalEntityProxy, childElement);
            // pathwayModel.add(physicalEntityProxy);
            // if (childElement.getName().equals("LEFT")){
            // conversion.getLeftSide().add(physicalEntityProxy);
            // }else{
            // conversion.getRightSide().add(physicalEntityProxy);
            // }
            showIgnored(childElement, "conversion/LEFT or conversion/RIGHT assuming redundant sequenceParticipant or physicalEntityParticipant", conversion);
            return true;
        }
        return false;
    // }else if(childElement.getName().equals("participantStoichiometry")) {
    // conversion.getParticipantStoichiometry().add(addObjectStoichiometry(childElement));
    // return true;
    } else {
        return false;
    }
}

Example 9 with PhysicalEntity

use of org.vcell.pathway.PhysicalEntity in project vcell by virtualcell.

the class PathwayProducerBiopax3 method addContentCatalysis.

// cofactor 			PhysicalEntity 	multiple
// catalysisDirection 	String 			single
private Element addContentCatalysis(BioPaxObject bpObject, Element element) {
    element = addContentControl(bpObject, element);
    Catalysis ob = (Catalysis) bpObject;
    Element tmpElement = null;
    if (ob.getCofactors() != null && ob.getCofactors().size() > 0) {
        List<PhysicalEntity> list = ob.getCofactors();
        for (PhysicalEntity item : list) {
            tmpElement = new Element("cofactor", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getCatalysisDirection() != null && ob.getCatalysisDirection().length() > 0) {
        tmpElement = new Element("catalysisDirection", bp);
        tmpElement.setAttribute("datatype", schemaString, rdf);
        tmpElement.setText(ob.getCatalysisDirection());
        element.addContent(tmpElement);
    }
    return element;
}

Example 10 with PhysicalEntity

use of org.vcell.pathway.PhysicalEntity in project vcell by virtualcell.

the class PathwayMapping method createReactionStepFromPathway.

/*
	 * for reaction:
	 * 1. annotate the selected vcell object using linked pathway conversion
	 * 2. add non-existing speciesContexts from linked pathway conversion
	 * 3. add links between relative vcell objects and pathway objects
	 * Questions:
	 * - how to deal with the case that the reaction is existing in the model?
	 * 		+ add it in no matter what? 
	 * 				(this is the version we have now: 
	 * 					add the duplicated reactions in without name changing, 
	 * 				 	all duplicated reactions share the same participant objects)
	 *      + just modify the existing one?
	 */
private void createReactionStepFromPathway(BioModel bioModel, Process process, ReactionStep reactionStep, RelationshipObject relationshipObject, boolean addSubunits) throws Exception {
    // annotate the selected vcell object using linked pathway object
    // add non-existing speciesContexts from linked pathway conversion
    ReactionParticipant[] rpArray = parseReaction(reactionStep, bioModel, relationshipObject);
    // create a hashtable for interaction Participants
    Hashtable<String, BioPaxObject> participantTable = new Hashtable<String, BioPaxObject>();
    for (BioPaxObject bpObject : ((Conversion) relationshipObject.getBioPaxObject()).getLeft()) {
        if (((PhysicalEntity) bpObject).getName().size() == 0) {
            participantTable.put(getSafetyName(((PhysicalEntity) bpObject).getID()), bpObject);
        } else {
            participantTable.put(getSafetyName(((PhysicalEntity) bpObject).getName().get(0)), bpObject);
        }
    }
    for (BioPaxObject bpObject : ((Conversion) relationshipObject.getBioPaxObject()).getRight()) {
        if (((PhysicalEntity) bpObject).getName().size() == 0) {
            participantTable.put(getSafetyName(((PhysicalEntity) bpObject).getID()), bpObject);
        } else {
            participantTable.put(getSafetyName(((PhysicalEntity) bpObject).getName().get(0)), bpObject);
        }
    }
    for (ReactionParticipant rp : rpArray) {
        SpeciesContext speciesContext = rp.getSpeciesContext();
        if (bioModel.getModel().getSpeciesContext(speciesContext.getName()) == null) {
            // if the speciesContext is not existed, then add it to the bioModel and link it to the corresponding pathway object
            if (bioModel.getModel().getSpecies(speciesContext.getName()) == null) {
                bioModel.getModel().addSpecies(speciesContext.getSpecies());
            }
            bioModel.getModel().addSpeciesContext(speciesContext);
            RelationshipObject newSpeciesContext = new RelationshipObject(speciesContext, participantTable.get(speciesContext.getName()));
            bioModel.getRelationshipModel().addRelationshipObject(newSpeciesContext);
        } else {
            // if it is in the bioModel, then check whether it links to pathway object or not
            HashSet<RelationshipObject> linkedReObjects = bioModel.getRelationshipModel().getRelationshipObjects(bioModel.getModel().getSpeciesContext(speciesContext.getName()));
            if (linkedReObjects != null) {
                boolean isLinked = false;
                for (RelationshipObject reObject : linkedReObjects) {
                    if (reObject.getBioPaxObject() == participantTable.get(speciesContext.getName())) {
                        isLinked = true;
                        break;
                    }
                }
                if (!isLinked) {
                    RelationshipObject newSpeciesContext = new RelationshipObject(speciesContext, participantTable.get(speciesContext.getName()));
                    bioModel.getRelationshipModel().addRelationshipObject(newSpeciesContext);
                }
            } else {
                RelationshipObject newSpeciesContext = new RelationshipObject(speciesContext, participantTable.get(speciesContext.getName()));
                bioModel.getRelationshipModel().addRelationshipObject(newSpeciesContext);
            }
        }
    }
    (reactionStep).setReactionParticipants(rpArray);
    // add Control to the reaction
    if (process.getControl() != null) {
        for (InteractionParticipant pe : process.getControl().getParticipants()) {
            SpeciesContext newSpeciescontext = createSpeciesContextFromBioPaxObject(bioModel, pe.getPhysicalEntity(), addSubunits);
            (reactionStep).addReactionParticipant(new Catalyst(null, reactionStep, newSpeciescontext));
        }
    }
    addKinetics(reactionStep, process);
}