Examples with RbmObservable cbit.vcell.model.RbmObservable used on opensource projects

Example 16 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class RulebasedMathMapping method addSpeciesPatterns.

private HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> addSpeciesPatterns(Domain domain, List<ReactionRule> rrList) throws MathException {
    // Particle Molecular Types
    // 
    Model model = getSimulationContext().getModel();
    List<RbmObservable> observableList = model.getRbmModelContainer().getObservableList();
    List<MolecularType> molecularTypeList = model.getRbmModelContainer().getMolecularTypeList();
    for (MolecularType molecularType : molecularTypeList) {
        ParticleMolecularType particleMolecularType = new ParticleMolecularType(molecularType.getName());
        for (MolecularComponent molecularComponent : molecularType.getComponentList()) {
            String pmcName = molecularComponent.getName();
            String pmcId = particleMolecularType.getName() + "_" + molecularComponent.getName();
            ParticleMolecularComponent particleMolecularComponent = new ParticleMolecularComponent(pmcId, pmcName);
            for (ComponentStateDefinition componentState : molecularComponent.getComponentStateDefinitions()) {
                ParticleComponentStateDefinition pcsd = particleMolecularComponent.getComponentStateDefinition(componentState.getName());
                if (pcsd == null) {
                    particleMolecularComponent.addComponentStateDefinition(new ParticleComponentStateDefinition(componentState.getName()));
                }
            }
            particleMolecularType.addMolecularComponent(particleMolecularComponent);
        }
        if (!molecularType.isAnchorAll()) {
            List<String> anchorList = new ArrayList<>();
            for (Structure struct : molecularType.getAnchors()) {
                anchorList.add(struct.getName());
            }
            particleMolecularType.setAnchorList(anchorList);
        }
        mathDesc.addParticleMolecularType(particleMolecularType);
    }
    // 
    // Assemble list of all Species Patterns (from observables, reaction rules, and seed species).
    // 
    // linked hash set maintains insertion order
    LinkedHashMap<SpeciesPattern, Structure> speciesPatternStructureMap = new LinkedHashMap<SpeciesPattern, Structure>();
    for (RbmObservable observable : observableList) {
        for (SpeciesPattern speciesPattern : observable.getSpeciesPatternList()) {
            speciesPatternStructureMap.put(speciesPattern, observable.getStructure());
        }
    }
    for (ReactionRule reactionRule : rrList) {
        for (ReactantPattern rp : reactionRule.getReactantPatterns()) {
            speciesPatternStructureMap.put(rp.getSpeciesPattern(), rp.getStructure());
        }
        for (ProductPattern pp : reactionRule.getProductPatterns()) {
            speciesPatternStructureMap.put(pp.getSpeciesPattern(), pp.getStructure());
        }
    }
    for (SpeciesContext sc : model.getSpeciesContexts()) {
        if (!sc.hasSpeciesPattern()) {
            continue;
        }
        speciesPatternStructureMap.put(sc.getSpeciesPattern(), sc.getStructure());
    }
    // 
    // add list of unique speciesPatterns
    // 
    HashMap<String, VolumeParticleSpeciesPattern> speciesPatternVCMLMap = new HashMap<String, VolumeParticleSpeciesPattern>();
    HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> speciesPatternMap = new HashMap<SpeciesPattern, VolumeParticleSpeciesPattern>();
    String speciesPatternName = "speciesPattern0";
    for (SpeciesPattern speciesPattern : speciesPatternStructureMap.keySet()) {
        VolumeParticleSpeciesPattern volumeParticleSpeciesPattern = new VolumeParticleSpeciesPattern(speciesPatternName, domain, speciesPatternStructureMap.get(speciesPattern).getName());
        for (MolecularTypePattern molecularTypePattern : speciesPattern.getMolecularTypePatterns()) {
            ParticleMolecularType particleMolecularType = mathDesc.getParticleMolecularType(molecularTypePattern.getMolecularType().getName());
            ParticleMolecularTypePattern particleMolecularTypePattern = new ParticleMolecularTypePattern(particleMolecularType);
            String participantMatchLabel = molecularTypePattern.getParticipantMatchLabel();
            if (molecularTypePattern.getParticipantMatchLabel() != null) {
                particleMolecularTypePattern.setMatchLabel(participantMatchLabel);
            }
            for (MolecularComponentPattern molecularComponentPattern : molecularTypePattern.getComponentPatternList()) {
                MolecularComponent molecularComponent = molecularComponentPattern.getMolecularComponent();
                ParticleMolecularComponent particleMolecularComponent = particleMolecularType.getMolecularComponent(molecularComponent.getName());
                ParticleMolecularComponentPattern particleMolecularComponentPattern = new ParticleMolecularComponentPattern(particleMolecularComponent);
                ComponentStatePattern componentState = molecularComponentPattern.getComponentStatePattern();
                if (componentState != null) {
                    if (componentState.isAny()) {
                        ParticleComponentStatePattern pcsp = new ParticleComponentStatePattern();
                        particleMolecularComponentPattern.setComponentStatePattern(pcsp);
                    } else {
                        String name = componentState.getComponentStateDefinition().getName();
                        ParticleComponentStateDefinition pcsd = particleMolecularComponent.getComponentStateDefinition(name);
                        // ParticleComponentStateDefinition pcsd = new ParticleComponentStateDefinition(componentState.getComponentStateDefinition().getName());
                        // particleMolecularComponent.addComponentStateDefinition(pcsd);
                        ParticleComponentStatePattern pcsp = new ParticleComponentStatePattern(pcsd);
                        particleMolecularComponentPattern.setComponentStatePattern(pcsp);
                    }
                } else {
                    ParticleComponentStatePattern pcsp = new ParticleComponentStatePattern();
                    particleMolecularComponentPattern.setComponentStatePattern(pcsp);
                }
                switch(molecularComponentPattern.getBondType()) {
                    case Specified:
                        {
                            particleMolecularComponentPattern.setBondType(ParticleBondType.Specified);
                            particleMolecularComponentPattern.setBondId(molecularComponentPattern.getBondId());
                            break;
                        }
                    case Exists:
                        {
                            particleMolecularComponentPattern.setBondType(ParticleBondType.Exists);
                            particleMolecularComponentPattern.setBondId(-1);
                            break;
                        }
                    case None:
                        {
                            particleMolecularComponentPattern.setBondType(ParticleBondType.None);
                            particleMolecularComponentPattern.setBondId(-1);
                            break;
                        }
                    case Possible:
                        {
                            particleMolecularComponentPattern.setBondType(ParticleBondType.Possible);
                            particleMolecularComponentPattern.setBondId(-1);
                            break;
                        }
                }
                particleMolecularTypePattern.addMolecularComponentPattern(particleMolecularComponentPattern);
            }
            volumeParticleSpeciesPattern.addMolecularTypePattern(particleMolecularTypePattern);
        }
        String speciesPatternVCML = volumeParticleSpeciesPattern.getVCML("tempName");
        VolumeParticleSpeciesPattern uniqueVolumeParticleSpeciesPattern = speciesPatternVCMLMap.get(speciesPatternVCML);
        if (uniqueVolumeParticleSpeciesPattern == null) {
            speciesPatternVCMLMap.put(speciesPatternVCML, volumeParticleSpeciesPattern);
            speciesPatternName = TokenMangler.getNextEnumeratedToken(speciesPatternName);
            speciesPatternMap.put(speciesPattern, volumeParticleSpeciesPattern);
        } else {
            speciesPatternMap.put(speciesPattern, uniqueVolumeParticleSpeciesPattern);
        }
    }
    return speciesPatternMap;
}

Example 17 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class RulebasedTransformer method transform.

private void transform(SimulationContext originalSimContext, SimulationContext transformedSimulationContext, ArrayList<ModelEntityMapping> entityMappings, MathMappingCallback mathMappingCallback) throws PropertyVetoException {
    Model newModel = transformedSimulationContext.getModel();
    Model originalModel = originalSimContext.getModel();
    ModelEntityMapping em = null;
    // list of rules created from the reactions; we apply the symmetry factor computed by bionetgen only to these
    Set<ReactionRule> fromReactions = new HashSet<>();
    for (SpeciesContext newSpeciesContext : newModel.getSpeciesContexts()) {
        final SpeciesContext originalSpeciesContext = originalModel.getSpeciesContext(newSpeciesContext.getName());
        // map new and old species contexts
        em = new ModelEntityMapping(originalSpeciesContext, newSpeciesContext);
        entityMappings.add(em);
        if (newSpeciesContext.hasSpeciesPattern()) {
            // it's perfect already and can't be improved
            continue;
        }
        try {
            MolecularType newmt = newModel.getRbmModelContainer().createMolecularType();
            newModel.getRbmModelContainer().addMolecularType(newmt, false);
            MolecularTypePattern newmtp_sc = new MolecularTypePattern(newmt);
            SpeciesPattern newsp_sc = new SpeciesPattern();
            newsp_sc.addMolecularTypePattern(newmtp_sc);
            newSpeciesContext.setSpeciesPattern(newsp_sc);
            RbmObservable newo = new RbmObservable(newModel, "O0_" + newmt.getName() + "_tot", newSpeciesContext.getStructure(), RbmObservable.ObservableType.Molecules);
            MolecularTypePattern newmtp_ob = new MolecularTypePattern(newmt);
            SpeciesPattern newsp_ob = new SpeciesPattern();
            newsp_ob.addMolecularTypePattern(newmtp_ob);
            newo.addSpeciesPattern(newsp_ob);
            newModel.getRbmModelContainer().addObservable(newo);
            // map new observable to old species context
            em = new ModelEntityMapping(originalSpeciesContext, newo);
            entityMappings.add(em);
        } catch (ModelException e) {
            e.printStackTrace();
            throw new RuntimeException("unable to transform species context: " + e.getMessage());
        } catch (PropertyVetoException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    ReactionSpec[] reactionSpecs = transformedSimulationContext.getReactionContext().getReactionSpecs();
    for (ReactionSpec reactionSpec : reactionSpecs) {
        if (reactionSpec.isExcluded()) {
            // we create rules only from those reactions which are not excluded
            continue;
        }
        ReactionStep rs = reactionSpec.getReactionStep();
        String name = rs.getName();
        String mangled = TokenMangler.fixTokenStrict(name);
        mangled = newModel.getReactionName(mangled);
        Kinetics k = rs.getKinetics();
        if (!(k instanceof MassActionKinetics)) {
            throw new RuntimeException("Only Mass Action Kinetics supported at this time, reaction \"" + rs.getName() + "\" uses kinetic law type \"" + rs.getKinetics().getName() + "\"");
        }
        boolean bReversible = rs.isReversible();
        ReactionRule rr = new ReactionRule(newModel, mangled, rs.getStructure(), bReversible);
        fromReactions.add(rr);
        MassActionKinetics massActionKinetics = (MassActionKinetics) k;
        List<Reactant> rList = rs.getReactants();
        List<Product> pList = rs.getProducts();
        // counting the stoichiometry - 2A+B means 3 reactants
        int numReactants = 0;
        for (Reactant r : rList) {
            numReactants += r.getStoichiometry();
            if (numReactants > 2) {
                String message = "NFSim doesn't support more than 2 reactants within a reaction: " + name;
                throw new RuntimeException(message);
            }
        }
        int numProducts = 0;
        for (Product p : pList) {
            numProducts += p.getStoichiometry();
            if (bReversible && numProducts > 2) {
                String message = "NFSim doesn't support more than 2 products within a reversible reaction: " + name;
                throw new RuntimeException(message);
            }
        }
        RateLawType rateLawType = RateLawType.MassAction;
        RbmKineticLaw kineticLaw = new RbmKineticLaw(rr, rateLawType);
        try {
            String forwardRateName = massActionKinetics.getForwardRateParameter().getName();
            Expression forwardRateExp = massActionKinetics.getForwardRateParameter().getExpression();
            String reverseRateName = massActionKinetics.getReverseRateParameter().getName();
            Expression reverseRateExp = massActionKinetics.getReverseRateParameter().getExpression();
            LocalParameter fR = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate);
            fR.setName(forwardRateName);
            LocalParameter rR = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate);
            rR.setName(reverseRateName);
            if (rs.hasReactant()) {
                kineticLaw.setParameterValue(fR, forwardRateExp, true);
            }
            if (rs.hasProduct()) {
                kineticLaw.setParameterValue(rR, reverseRateExp, true);
            }
            // 
            for (KineticsParameter reaction_p : massActionKinetics.getKineticsParameters()) {
                if (reaction_p.getRole() == Kinetics.ROLE_UserDefined) {
                    LocalParameter rule_p = kineticLaw.getLocalParameter(reaction_p.getName());
                    if (rule_p == null) {
                        // 
                        // after lazy parameter creation we didn't find a user-defined rule parameter with this same name.
                        // 
                        // there must be a global symbol with the same name, that the local reaction parameter has overridden.
                        // 
                        ParameterContext.LocalProxyParameter rule_proxy_parameter = null;
                        for (ProxyParameter proxyParameter : kineticLaw.getProxyParameters()) {
                            if (proxyParameter.getName().equals(reaction_p.getName())) {
                                rule_proxy_parameter = (LocalProxyParameter) proxyParameter;
                            }
                        }
                        if (rule_proxy_parameter != null) {
                            // we want to convert to local
                            boolean bConvertToGlobal = false;
                            kineticLaw.convertParameterType(rule_proxy_parameter, bConvertToGlobal);
                        } else {
                            // could find neither local parameter nor proxy parameter
                            throw new RuntimeException("user defined parameter " + reaction_p.getName() + " from reaction " + rs.getName() + " didn't map to a reactionRule parameter");
                        }
                    } else if (rule_p.getRole() == RbmKineticLawParameterType.UserDefined) {
                        kineticLaw.setParameterValue(rule_p, reaction_p.getExpression(), true);
                        rule_p.setUnitDefinition(reaction_p.getUnitDefinition());
                    } else {
                        throw new RuntimeException("user defined parameter " + reaction_p.getName() + " from reaction " + rs.getName() + " mapped to a reactionRule parameter with unexpected role " + rule_p.getRole().getDescription());
                    }
                }
            }
        } catch (ExpressionException e) {
            e.printStackTrace();
            throw new RuntimeException("Problem attempting to set RbmKineticLaw expression: " + e.getMessage());
        }
        rr.setKineticLaw(kineticLaw);
        KineticsParameter[] kpList = k.getKineticsParameters();
        ModelParameter[] mpList = rs.getModel().getModelParameters();
        ModelParameter mp = rs.getModel().getModelParameter(kpList[0].getName());
        ReactionParticipant[] rpList = rs.getReactionParticipants();
        for (ReactionParticipant p : rpList) {
            if (p instanceof Reactant) {
                int stoichiometry = p.getStoichiometry();
                for (int i = 0; i < stoichiometry; i++) {
                    SpeciesPattern speciesPattern = new SpeciesPattern(rs.getModel(), p.getSpeciesContext().getSpeciesPattern());
                    ReactantPattern reactantPattern = new ReactantPattern(speciesPattern, p.getStructure());
                    rr.addReactant(reactantPattern);
                }
            } else if (p instanceof Product) {
                int stoichiometry = p.getStoichiometry();
                for (int i = 0; i < stoichiometry; i++) {
                    SpeciesPattern speciesPattern = new SpeciesPattern(rs.getModel(), p.getSpeciesContext().getSpeciesPattern());
                    ProductPattern productPattern = new ProductPattern(speciesPattern, p.getStructure());
                    rr.addProduct(productPattern);
                }
            }
        }
        // commented code below is probably obsolete, we verify (above) in the reaction the number of participants,
        // no need to do it again in the corresponding rule
        // if(rr.getReactantPatterns().size() > 2) {
        // String message = "NFSim doesn't support more than 2 reactants within a reaction: " + name;
        // throw new RuntimeException(message);
        // }
        // if(rr.getProductPatterns().size() > 2) {
        // String message = "NFSim doesn't support more than 2 products within a reaction: " + name;
        // throw new RuntimeException(message);
        // }
        newModel.removeReactionStep(rs);
        newModel.getRbmModelContainer().addReactionRule(rr);
    }
    for (ReactionRuleSpec rrs : transformedSimulationContext.getReactionContext().getReactionRuleSpecs()) {
        if (rrs == null) {
            continue;
        }
        ReactionRule rr = rrs.getReactionRule();
        if (rrs.isExcluded()) {
            // delete those rules which are disabled (excluded) in the Specifications / Reaction table
            newModel.getRbmModelContainer().removeReactionRule(rr);
            continue;
        }
    }
    // now that we generated the rules we can delete the reaction steps they're coming from
    for (ReactionStep rs : newModel.getReactionSteps()) {
        newModel.removeReactionStep(rs);
    }
    try {
        // we invoke bngl just for the purpose of generating the xml file, which we'll then use to extract the symmetry factor
        generateNetwork(transformedSimulationContext, fromReactions, mathMappingCallback);
    } catch (ClassNotFoundException | IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    System.out.println("Finished RuleBased Transformer.");
}

Example 18 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class BNGExecutorServiceMultipass method preprocessInput.

// parse the compartmental bngl file and produce the "trick"
// where each molecule has an extra Site with the compartments as possible States
// a reserved name will be used for this Site
// 
private String preprocessInput(String cBngInputString) throws ParseException, PropertyVetoException, ExpressionBindingException {
    // take the cBNGL file (as string), parse it to recover the rules (we'll need them later)
    // and create the bngl string with the extra, fake site for the compartments
    BioModel bioModel = new BioModel(null);
    bioModel.setName("BngBioModel");
    model = new Model("model");
    bioModel.setModel(model);
    model.createFeature();
    simContext = bioModel.addNewSimulationContext("BioNetGen app", SimulationContext.Application.NETWORK_DETERMINISTIC);
    List<SimulationContext> appList = new ArrayList<SimulationContext>();
    appList.add(simContext);
    // set convention for initial conditions in generated application for seed species (concentration or count)
    BngUnitSystem bngUnitSystem = new BngUnitSystem(BngUnitOrigin.DEFAULT);
    InputStream is = new ByteArrayInputStream(cBngInputString.getBytes());
    BufferedReader br = new BufferedReader(new InputStreamReader(is));
    ASTModel astModel = RbmUtils.importBnglFile(br);
    if (astModel.hasCompartments()) {
        Structure struct = model.getStructure(0);
        if (struct != null) {
            try {
                model.removeStructure(struct);
            } catch (PropertyVetoException e) {
                e.printStackTrace();
            }
        }
    }
    BnglObjectConstructionVisitor constructionVisitor = null;
    constructionVisitor = new BnglObjectConstructionVisitor(model, appList, bngUnitSystem, true);
    astModel.jjtAccept(constructionVisitor, model.getRbmModelContainer());
    int numCompartments = model.getStructures().length;
    if (numCompartments == 0) {
        throw new RuntimeException("No structure present in the bngl file.");
    } else if (numCompartments == 1) {
        // for single compartment we don't need the 'trick'
        compartmentMode = CompartmentMode.hide;
    } else {
        compartmentMode = CompartmentMode.asSite;
    }
    // extract all polymer observables for special treatment at the end
    for (RbmObservable oo : model.getRbmModelContainer().getObservableList()) {
        if (oo.getSequence() == RbmObservable.Sequence.PolymerLengthEqual) {
            polymerEqualObservables.add(oo);
        } else if (oo.getSequence() == RbmObservable.Sequence.PolymerLengthGreater) {
            polymerGreaterObservables.add(oo);
        }
    }
    for (RbmObservable oo : polymerEqualObservables) {
        model.getRbmModelContainer().removeObservable(oo);
    }
    for (RbmObservable oo : polymerGreaterObservables) {
        model.getRbmModelContainer().removeObservable(oo);
    }
    // replace all reversible rules with 2 direct rules
    List<ReactionRule> newRRList = new ArrayList<>();
    for (ReactionRule rr : model.getRbmModelContainer().getReactionRuleList()) {
        if (rr.isReversible()) {
            ReactionRule rr1 = ReactionRule.deriveDirectRule(rr);
            newRRList.add(rr1);
            ReactionRule rr2 = ReactionRule.deriveInverseRule(rr);
            newRRList.add(rr2);
        } else {
            newRRList.add(rr);
        }
        model.getRbmModelContainer().removeReactionRule(rr);
    }
    // model.getRbmModelContainer().getReactionRuleList().clear();
    model.getRbmModelContainer().setReactionRules(newRRList);
    StringWriter bnglStringWriter = new StringWriter();
    PrintWriter writer = new PrintWriter(bnglStringWriter);
    writer.println(RbmNetworkGenerator.BEGIN_MODEL);
    writer.println();
    // RbmNetworkGenerator.writeCompartments(writer, model, null);
    RbmNetworkGenerator.writeParameters(writer, model.getRbmModelContainer(), false);
    RbmNetworkGenerator.writeMolecularTypes(writer, model, compartmentMode);
    RbmNetworkGenerator.writeSpeciesSortedAlphabetically(writer, model, simContext, compartmentMode);
    RbmNetworkGenerator.writeObservables(writer, model.getRbmModelContainer(), compartmentMode);
    // RbmNetworkGenerator.writeFunctions(writer, rbmModelContainer, ignoreFunctions);
    RbmNetworkGenerator.writeReactions(writer, model.getRbmModelContainer(), null, false, compartmentMode);
    writer.println(RbmNetworkGenerator.END_MODEL);
    writer.println();
    // we parse the real numbers from the bngl file provided by the caller, the nc in the simContext has the default ones
    NetworkConstraints realNC = extractNetworkConstraints(cBngInputString);
    simContext.getNetworkConstraints().setMaxMoleculesPerSpecies(realNC.getMaxMoleculesPerSpecies());
    simContext.getNetworkConstraints().setMaxIteration(realNC.getMaxIteration());
    RbmNetworkGenerator.generateNetworkEx(1, simContext.getNetworkConstraints().getMaxMoleculesPerSpecies(), writer, model.getRbmModelContainer(), simContext, NetworkGenerationRequirements.AllowTruncatedStandardTimeout);
    String sInputString = bnglStringWriter.toString();
    return sInputString;
}

Example 19 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class BioModelEditor method setRightBottomPanelOnSelection.

@Override
protected void setRightBottomPanelOnSelection(Object[] selections) {
    if (selections == null) {
        return;
    }
    JComponent bottomComponent = rightBottomEmptyPanel;
    int destComponentIndex = DocumentEditorTabID.object_properties.ordinal();
    boolean bShowInDatabaseProperties = false;
    boolean bShowPathway = false;
    if (selections.length == 1) {
        Object singleSelection = selections[0];
        if (singleSelection instanceof ReactionStep) {
            bottomComponent = getReactionPropertiesPanel();
        } else if (singleSelection instanceof ReactionRule) {
            bottomComponent = getReactionRulePropertiesPanel();
        } else if (singleSelection instanceof SpeciesContext) {
            bottomComponent = getSpeciesPropertiesPanel();
        } else if (singleSelection instanceof MolecularType) {
            bottomComponent = getMolecularTypePropertiesPanel();
        } else if (singleSelection instanceof RbmObservable) {
            bottomComponent = getObservablePropertiesPanel();
        } else if (singleSelection instanceof Structure) {
            bottomComponent = getStructurePropertiesPanel();
            getStructurePropertiesPanel().setModel(bioModel.getModel());
        } else if (singleSelection instanceof Parameter) {
            bottomComponent = getParameterPropertiesPanel();
        } else if (singleSelection instanceof SimulationContext) {
            bottomComponent = getApplicationPropertiesPanel();
        } else if (singleSelection instanceof ParameterEstimationTask) {
            bottomComponent = parameterEstimationTaskPropertiesPanel;
        } else if (singleSelection instanceof Product || singleSelection instanceof Reactant) {
            bottomComponent = getReactionParticipantPropertiesPanel();
        } else if (singleSelection instanceof BioModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = bioModelMetaDataPanel;
        } else if (singleSelection instanceof MathModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = mathModelMetaDataPanel;
        } else if (singleSelection instanceof GeometryInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = geometryMetaDataPanel;
        } else if (singleSelection instanceof SpeciesContextSpec) {
            bottomComponent = getSpeciesContextSpecPanel();
        } else if (singleSelection instanceof ReactionSpec) {
            bottomComponent = getKineticsTypeTemplatePanel();
        } else if (singleSelection instanceof ReactionRuleSpec) {
            // 
            bottomComponent = getReactionRuleSpecPropertiesPanel();
        } else if (singleSelection instanceof BioModelsNetModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = getBioModelsNetPropertiesPanel();
        } else if (singleSelection instanceof Simulation) {
            bottomComponent = getSimulationSummaryPanel();
        } else if (singleSelection instanceof DataSymbol) {
            bottomComponent = getDataSymbolsSpecPanel();
        } else if (singleSelection instanceof BioEvent) {
            bottomComponent = getEventPanel();
        } else if (singleSelection instanceof SpatialObject) {
            bottomComponent = getSpatialObjectPropertyPanel();
        } else if (singleSelection instanceof SpatialProcess) {
            bottomComponent = getSpatialProcessPropertyPanel();
        } else if (singleSelection instanceof BioPaxObject) {
            bottomComponent = bioPaxObjectPropertiesPanel;
        } else if (singleSelection instanceof BioModel || singleSelection instanceof VCMetaData) {
            bottomComponent = bioModelEditorAnnotationPanel;
        } else if (singleSelection instanceof PathwayData) {
            bShowPathway = true;
            bottomComponent = getBioModelEditorPathwayPanel();
        } else if (singleSelection instanceof Model) {
        } else if (singleSelection instanceof RuleParticipantSignature) {
            bottomComponent = getReactionRuleParticipantSignaturePropertiesPanel();
        } else if (singleSelection instanceof CSGObject) {
            bottomComponent = csgObjectPropertiesPanel;
            csgObjectPropertiesPanel.setSimulationContext(getSelectedSimulationContext());
        } else if (singleSelection instanceof DocumentEditorTreeFolderNode) {
            DocumentEditorTreeFolderClass folderClass = ((DocumentEditorTreeFolderNode) singleSelection).getFolderClass();
            if ((folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE) && !(singleSelection instanceof ReactionRule)) {
                bottomComponent = getReactionPropertiesPanel();
            } else if ((folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE) && (singleSelection instanceof ReactionRule)) {
                bottomComponent = getReactionRulePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.STRUCTURES_NODE) {
                bottomComponent = getStructurePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.SPECIES_NODE) {
                bottomComponent = getSpeciesPropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE) {
                bottomComponent = getMolecularTypePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.OBSERVABLES_NODE) {
                bottomComponent = getObservablePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.APPLICATIONS_NODE) {
                bottomComponent = getApplicationsPropertiesPanel();
                getApplicationsPropertiesPanel().setBioModel(bioModel);
            } else if (folderClass == DocumentEditorTreeFolderClass.PARAMETER_ESTIMATION_NODE) {
                bottomComponent = parameterEstimationTaskPropertiesPanel;
            }
        }
    }
    if (bShowPathway) {
        for (destComponentIndex = 0; destComponentIndex < rightBottomTabbedPane.getTabCount(); destComponentIndex++) {
            if (rightBottomTabbedPane.getComponentAt(destComponentIndex) == bottomComponent) {
                break;
            }
        }
        String tabTitle = "Pathway Preview";
        if (rightBottomTabbedPane.getTabCount() == destComponentIndex) {
            rightBottomTabbedPane.addTab(tabTitle, new TabCloseIcon(), bottomComponent);
        }
    } else if (bShowInDatabaseProperties) {
        for (destComponentIndex = 0; destComponentIndex < rightBottomTabbedPane.getTabCount(); destComponentIndex++) {
            Component c = rightBottomTabbedPane.getComponentAt(destComponentIndex);
            if (c == bioModelMetaDataPanel || c == mathModelMetaDataPanel || c == geometryMetaDataPanel || c == getBioModelsNetPropertiesPanel()) {
                break;
            }
        }
        if (rightBottomTabbedPane.getTabCount() == destComponentIndex) {
            rightBottomTabbedPane.addTab(DATABASE_PROPERTIES_TAB_TITLE, new TabCloseIcon(), bottomComponent);
        }
    }
    if (rightBottomTabbedPane.getComponentAt(destComponentIndex) != bottomComponent) {
        bottomComponent.setBorder(GuiConstants.TAB_PANEL_BORDER);
        rightBottomTabbedPane.setComponentAt(destComponentIndex, bottomComponent);
        rightSplitPane.repaint();
    }
    if (rightBottomTabbedPane.getSelectedComponent() != bottomComponent) {
        rightBottomTabbedPane.setSelectedComponent(bottomComponent);
    }
}

Example 20 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class BioModelEditor method popupMenuActionPerformed.

@Override
protected void popupMenuActionPerformed(DocumentEditorPopupMenuAction action, String actionCommand) {
    Model model = bioModel.getModel();
    final SimulationContext selectedSimulationContext = getSelectedSimulationContext();
    switch(action) {
        case add_new:
            try {
                Object obj = documentEditorTree.getLastSelectedPathComponent();
                if (obj == null || !(obj instanceof BioModelNode)) {
                    return;
                }
                BioModelNode selectedNode = (BioModelNode) obj;
                Object userObject = selectedNode.getUserObject();
                if (userObject instanceof DocumentEditorTreeFolderNode) {
                    DocumentEditorTreeFolderClass folderClass = ((DocumentEditorTreeFolderNode) userObject).getFolderClass();
                    Object newObject = null;
                    switch(folderClass) {
                        case REACTIONS_NODE:
                            // TODO: should add a Add New Rule menu item
                            newObject = model.createSimpleReaction(model.getStructure(0));
                            break;
                        case STRUCTURES_NODE:
                            newObject = model.createFeature();
                            break;
                        case SPECIES_NODE:
                            newObject = model.createSpeciesContext(model.getStructure(0));
                            break;
                        case MOLECULAR_TYPES_NODE:
                            MolecularType mt = model.getRbmModelContainer().createMolecularType();
                            model.getRbmModelContainer().addMolecularType(mt, true);
                            newObject = mt;
                            break;
                        case OBSERVABLES_NODE:
                            if (bioModel.getModel().getRbmModelContainer().getMolecularTypeList().isEmpty()) {
                                PopupGenerator.showInfoDialog(this, VCellErrorMessages.MustBeRuleBased);
                                return;
                            }
                            RbmObservable o = model.getRbmModelContainer().createObservable(RbmObservable.ObservableType.Molecules);
                            model.getRbmModelContainer().addObservable(o);
                            SpeciesPattern sp = new SpeciesPattern();
                            o.addSpeciesPattern(sp);
                            newObject = o;
                            break;
                        case SIMULATIONS_NODE:
                            if (selectedSimulationContext != null) {
                                AsynchClientTask task1 = new AsynchClientTask("new simulation", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                                    @Override
                                    public void run(Hashtable<String, Object> hashTable) throws Exception {
                                        MathMappingCallback callback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
                                        selectedSimulationContext.refreshMathDescription(callback, NetworkGenerationRequirements.AllowTruncatedStandardTimeout);
                                    }
                                };
                                AsynchClientTask task2 = new AsynchClientTask("new simulation", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                                    @Override
                                    public void run(Hashtable<String, Object> hashTable) throws Exception {
                                        MathMappingCallback callback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
                                        Object newsim = selectedSimulationContext.addNewSimulation(SimulationOwner.DEFAULT_SIM_NAME_PREFIX, callback, NetworkGenerationRequirements.AllowTruncatedStandardTimeout);
                                        selectionManager.setSelectedObjects(new Object[] { newsim });
                                    }
                                };
                                ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
                            }
                            break;
                        default:
                            break;
                    }
                    if (newObject != null) {
                        selectionManager.setSelectedObjects(new Object[] { newObject });
                    }
                }
            } catch (Exception ex) {
                DialogUtils.showErrorDialog(this, ex.getMessage());
            }
            break;
        case add_new_app_deterministic:
            newApplication(Application.NETWORK_DETERMINISTIC);
            break;
        case add_new_app_stochastic:
            newApplication(Application.NETWORK_STOCHASTIC);
            break;
        case add_new_app_rulebased:
            {
                // if(model.getStructures().length > 1) {
                // DialogUtils.showErrorDialog(this, VCellErrorMessages.NFSimAppNotAllowedForMultipleStructures);
                // return;
                // }
                newApplication(Application.RULE_BASED_STOCHASTIC);
                break;
            }
        case copy_app:
            ApplicationActionCommand acc = ApplicationActionCommand.lookup(actionCommand);
            switch(acc.actionType()) {
                case COPY_AS_IS:
                    copyApplication();
                    break;
                case COPY_CHANGE:
                    boolean bothSpatial = acc.isSourceSpatial() && acc.isDestSpatial();
                    // if(acc.getAppType().equals(SimulationContext.Application.RULE_BASED_STOCHASTIC) && model.getStructures().length > 1) {
                    // DialogUtils.showErrorDialog(this, VCellErrorMessages.NFSimAppNotAllowedForMultipleStructures);
                    // return;
                    // }
                    copyApplication(bothSpatial, acc.getAppType());
                    break;
                case CREATE:
                    // not used in this menu
                    throw new UnsupportedOperationException();
            }
            break;
        case app_new_biomodel:
            if (actionCommand.equals(GuiConstants.MENU_TEXT_APP_NEWBIOMODEL)) {
                createNewBiomodelFromApp();
            }
            break;
        case delete:
            try {
                if (selectedSimulationContext != null) {
                    String confirm = PopupGenerator.showOKCancelWarningDialog(this, "Deleting application", "You are going to delete the Application '" + selectedSimulationContext.getName() + "'. Continue?");
                    if (confirm.equals(UserMessage.OPTION_CANCEL)) {
                        return;
                    }
                    deleteSimulationcontexts(new SimulationContext[] { selectedSimulationContext });
                }
            } catch (Exception ex) {
                DialogUtils.showErrorDialog(this, ex.getMessage());
            }
            break;
        case deleteChoose:
            try {
                SimulationContext[] allSimContexts = Arrays.copyOf(getBioModelWindowManager().getVCDocument().getSimulationContexts(), getBioModelWindowManager().getVCDocument().getSimulationContexts().length);
                Arrays.sort(allSimContexts, new Comparator<SimulationContext>() {

                    @Override
                    public int compare(SimulationContext o1, SimulationContext o2) {
                        return o1.getName().compareToIgnoreCase(o2.getName());
                    }
                });
                String[][] rowDataOrig = new String[allSimContexts.length][2];
                for (int i = 0; i < allSimContexts.length; i++) {
                    rowDataOrig[i][0] = allSimContexts[i].getName();
                    rowDataOrig[i][1] = allSimContexts[i].getSimulations().length + "";
                }
                final String DELETE = "Delete";
                final String CANCEL = "Cancel";
                TableListResult result = DialogUtils.showComponentOptionsTableList(this, "Select Applications (and associated Simulations) to delete.", new String[] { "Application", "# of Sims" }, rowDataOrig, ListSelectionModel.MULTIPLE_INTERVAL_SELECTION, null, new String[] { DELETE, CANCEL }, CANCEL, null);
                if (result != null && result.selectedOption != null && result.selectedOption.equals(DELETE) && result.selectedTableRows != null && result.selectedTableRows.length > 0) {
                    ArrayList<SimulationContext> deleteTheseSimcontexts = new ArrayList<SimulationContext>();
                    for (int i = 0; i < result.selectedTableRows.length; i++) {
                        deleteTheseSimcontexts.add(allSimContexts[result.selectedTableRows[i]]);
                    }
                    deleteSimulationcontexts(deleteTheseSimcontexts.toArray(new SimulationContext[0]));
                }
            } catch (Exception ex) {
                DialogUtils.showErrorDialog(this, ex.getMessage());
            }
            break;
        default:
            break;
    }
}