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

Example 11 with RbmObservable

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

the class ObservableTreeModel method valueForPathChanged.

@Override
public void valueForPathChanged(TreePath path, Object newValue) {
    Object obj = path.getLastPathComponent();
    if (obj == null || !(obj instanceof BioModelNode)) {
        return;
    }
    BioModelNode selectedNode = (BioModelNode) obj;
    BioModelNode parentNode = (BioModelNode) selectedNode.getParent();
    Object userObject = selectedNode.getUserObject();
    try {
        if (newValue instanceof String) {
            String inputString = (String) newValue;
            if (inputString == null || inputString.length() == 0) {
                return;
            }
            String mangled = TokenMangler.fixTokenStrict(inputString);
            if (!mangled.equals(inputString)) {
                String errMsg = ((Displayable) userObject).getDisplayType() + " '" + inputString + "' not legal identifier, try '" + mangled + "'";
                throw new RuntimeException(errMsg);
            }
            if (userObject instanceof RbmObservable) {
                // TODO: untested!!!
                ((RbmObservable) userObject).setName(inputString);
            }
        } else if (newValue instanceof MolecularComponentPattern) {
            MolecularComponentPattern newMcp = (MolecularComponentPattern) newValue;
            Object parentObject = parentNode == null ? null : parentNode.getUserObject();
            if (parentObject instanceof MolecularTypePattern) {
                MolecularTypePattern mtp = (MolecularTypePattern) parentObject;
                MolecularComponent mc = newMcp.getMolecularComponent();
                MolecularComponentPattern mcp = mtp.getMolecularComponentPattern(mc);
                mcp.setComponentStatePattern(newMcp.getComponentStatePattern());
                BondType bp = mcp.getBondType();
                BondType newbp = newMcp.getBondType();
                mcp.setBondType(newbp);
                // specified -> specified
                if (bp == BondType.Specified && newbp == BondType.Specified) {
                // bond didn't change
                } else if (bp == BondType.Specified && newbp != BondType.Specified) {
                    // specified -> non specified
                    // change the partner to possible
                    mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                    mcp.setBond(null);
                } else if (bp != BondType.Specified && newbp == BondType.Specified) {
                    // non specified -> specified
                    int newBondId = newMcp.getBondId();
                    mcp.setBondId(newBondId);
                    mcp.setBond(newMcp.getBond());
                    mcp.getBond().molecularComponentPattern.setBondId(newBondId);
                    for (SpeciesPattern sp : observable.getSpeciesPatternList()) {
                        sp.resolveBonds();
                    }
                } else {
                }
            }
        }
    } catch (Exception ex) {
        DialogUtils.showErrorDialog(ownerTree, ex.getMessage());
    }
}

Example 12 with RbmObservable

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

the class BioModel method getVCID.

public VCID getVCID(Identifiable identifiable) {
    String localName;
    String className;
    if (identifiable instanceof SpeciesContext) {
        localName = ((SpeciesContext) identifiable).getName();
        className = "SpeciesContext";
    } else if (identifiable instanceof Species) {
        localName = ((Species) identifiable).getCommonName();
        className = VCID.CLASS_SPECIES;
    } else if (identifiable instanceof Structure) {
        localName = ((Structure) identifiable).getName();
        className = "Structure";
    } else if (identifiable instanceof ReactionStep) {
        localName = ((ReactionStep) identifiable).getName();
        className = VCID.CLASS_REACTION_STEP;
    } else if (identifiable instanceof BioModel) {
        localName = ((BioModel) identifiable).getName();
        className = VCID.CLASS_BIOMODEL;
    // }else if (identifiable instanceof SimulationContext){
    // localName = ((SimulationContext)identifiable).getName();
    // className = "Application";
    } else if (identifiable instanceof BioPaxObject) {
        localName = ((BioPaxObject) identifiable).getID();
        className = "BioPaxObject";
    } else if (identifiable instanceof MolecularType) {
        localName = ((MolecularType) identifiable).getName();
        className = "MolecularType";
    } else if (identifiable instanceof ReactionRule) {
        localName = ((ReactionRule) identifiable).getName();
        className = "ReactionRule";
    } else if (identifiable instanceof RbmObservable) {
        localName = ((RbmObservable) identifiable).getName();
        className = "RbmObservable";
    } else {
        throw new RuntimeException("unsupported Identifiable class");
    }
    localName = TokenMangler.mangleVCId(localName);
    VCID vcid;
    try {
        vcid = VCID.fromString(className + "(" + localName + ")");
    } catch (VCID.InvalidVCIDException e) {
        e.printStackTrace();
        throw new RuntimeException(e.getMessage());
    }
    return vcid;
}

Example 13 with RbmObservable

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

the class AbstractComponentShape method isHidden.

protected static boolean isHidden(Displayable owner, MolecularComponentPattern mcp) {
    boolean hidden = false;
    if (owner == null || mcp == null) {
        return false;
    }
    if (owner instanceof RbmObservable) {
        hidden = true;
        if (mcp.isbVisible()) {
            hidden = false;
        }
        ComponentStatePattern csp = mcp.getComponentStatePattern();
        if (csp != null && mcp.isFullyDefined()) {
            if (!csp.isAny()) {
                hidden = false;
            }
        }
    }
    return hidden;
}

Example 14 with RbmObservable

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

the class NetworkTransformer method transform.

private void transform(SimulationContext simContext, SimulationContext transformedSimulationContext, ArrayList<ModelEntityMapping> entityMappings, MathMappingCallback mathMappingCallback, NetworkGenerationRequirements networkGenerationRequirements) {
    String msg = "Generating network: flattening...";
    mathMappingCallback.setMessage(msg);
    TaskCallbackMessage tcm = new TaskCallbackMessage(TaskCallbackStatus.Clean, "");
    simContext.appendToConsole(tcm);
    tcm = new TaskCallbackMessage(TaskCallbackStatus.TaskStart, msg);
    simContext.appendToConsole(tcm);
    long startTime = System.currentTimeMillis();
    System.out.println("Convert to bngl, execute BNG, retrieve the results.");
    try {
        BNGOutputSpec outputSpec = generateNetwork(simContext, mathMappingCallback, networkGenerationRequirements);
        if (mathMappingCallback.isInterrupted()) {
            msg = "Canceled by user.";
            tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
            simContext.appendToConsole(tcm);
            throw new UserCancelException(msg);
        }
        long endTime = System.currentTimeMillis();
        long elapsedTime = endTime - startTime;
        System.out.println("     " + elapsedTime + " milliseconds");
        Model model = transformedSimulationContext.getModel();
        ReactionContext reactionContext = transformedSimulationContext.getReactionContext();
        // ---- Parameters -----------------------------------------------------------------------------------------------
        startTime = System.currentTimeMillis();
        for (int i = 0; i < outputSpec.getBNGParams().length; i++) {
            BNGParameter p = outputSpec.getBNGParams()[i];
            // System.out.println(i+1 + ":\t\t"+ p.toString());
            if (model.getRbmModelContainer().getParameter(p.getName()) != null) {
                // if it's already there we don't try to add it again; this should be true for all of them!
                continue;
            }
            String s = p.getName();
            FakeSeedSpeciesInitialConditionsParameter fakeICParam = FakeSeedSpeciesInitialConditionsParameter.fromString(s);
            if (speciesEquivalenceMap.containsKey(fakeICParam)) {
                // we get rid of the fake parameters we use as keys
                continue;
            }
            FakeReactionRuleRateParameter fakeKineticParam = FakeReactionRuleRateParameter.fromString(s);
            if (fakeKineticParam != null) {
                System.out.println("found fakeKineticParam " + fakeKineticParam.fakeParameterName);
                // we get rid of the fake parameters we use as keys
                continue;
            }
            throw new RuntimeException("unexpected parameter " + p.getName() + " in internal BNG processing");
        // Expression exp = new Expression(p.getValue());
        // exp.bindExpression(model.getRbmModelContainer().getSymbolTable());
        // model.getRbmModelContainer().addParameter(p.getName(), exp, model.getUnitSystem().getInstance_TBD());
        }
        endTime = System.currentTimeMillis();
        elapsedTime = endTime - startTime;
        msg = "Adding " + outputSpec.getBNGParams().length + " parameters to model, " + elapsedTime + " ms";
        System.out.println(msg);
        // ---- Species ------------------------------------------------------------------------------------------------------------
        mathMappingCallback.setMessage("generating network: adding species...");
        mathMappingCallback.setProgressFraction(progressFractionQuota / 4.0f);
        startTime = System.currentTimeMillis();
        System.out.println("\nSpecies :");
        // the reactions will need this map to recover the names of species knowing only the networkFileIndex
        HashMap<Integer, String> speciesMap = new HashMap<Integer, String>();
        LinkedHashMap<String, Species> sMap = new LinkedHashMap<String, Species>();
        LinkedHashMap<String, SpeciesContext> scMap = new LinkedHashMap<String, SpeciesContext>();
        LinkedHashMap<String, BNGSpecies> crossMap = new LinkedHashMap<String, BNGSpecies>();
        List<SpeciesContext> noMapForThese = new ArrayList<SpeciesContext>();
        // final int decimalTickCount = Math.max(outputSpec.getBNGSpecies().length/10, 1);
        for (int i = 0; i < outputSpec.getBNGSpecies().length; i++) {
            BNGSpecies s = outputSpec.getBNGSpecies()[i];
            // System.out.println(i+1 + ":\t\t"+ s.toString());
            String key = s.getConcentration().infix();
            FakeSeedSpeciesInitialConditionsParameter fakeParam = FakeSeedSpeciesInitialConditionsParameter.fromString(key);
            if (fakeParam != null) {
                Pair<SpeciesContext, Expression> value = speciesEquivalenceMap.get(fakeParam);
                // the species context of the original model
                SpeciesContext originalsc = value.one;
                Expression initial = value.two;
                // replace the fake initial condition with the real one
                s.setConcentration(initial);
                // we'll have to find the species context from the cloned model which correspond to the original species
                SpeciesContext sc = model.getSpeciesContext(originalsc.getName());
                // System.out.println(sc.getName() + ", " + sc.getSpecies().getCommonName() + "   ...is one of the original seed species.");
                // existing name
                speciesMap.put(s.getNetworkFileIndex(), sc.getName());
                sMap.put(sc.getName(), sc.getSpecies());
                scMap.put(sc.getName(), sc);
                crossMap.put(sc.getName(), s);
                noMapForThese.add(sc);
                continue;
            }
            // all these species are new!
            // generate unique name for the species
            int count = 0;
            String speciesName = null;
            String nameRoot = "s";
            String speciesPatternNameString = s.extractName();
            while (true) {
                speciesName = nameRoot + count;
                if (Model.isNameUnused(speciesName, model) && !sMap.containsKey(speciesName) && !scMap.containsKey(speciesName)) {
                    break;
                }
                count++;
            }
            // newly created name
            speciesMap.put(s.getNetworkFileIndex(), speciesName);
            SpeciesContext speciesContext;
            if (s.hasCompartment()) {
                String speciesPatternCompartmentString = s.extractCompartment();
                speciesContext = new SpeciesContext(new Species(speciesName, s.getName()), model.getStructure(speciesPatternCompartmentString), null);
            } else {
                speciesContext = new SpeciesContext(new Species(speciesName, s.getName()), model.getStructure(0), null);
            }
            speciesContext.setName(speciesName);
            try {
                if (speciesPatternNameString != null) {
                    SpeciesPattern sp = RbmUtils.parseSpeciesPattern(speciesPatternNameString, model);
                    speciesContext.setSpeciesPattern(sp);
                }
            } catch (ParseException e) {
                e.printStackTrace();
                throw new RuntimeException("Bad format for species pattern string: " + e.getMessage());
            }
            // speciesContext.setSpeciesPatternString(speciesPatternString);
            // model.addSpecies(speciesContext.getSpecies());
            // model.addSpeciesContext(speciesContext);
            sMap.put(speciesName, speciesContext.getSpecies());
            scMap.put(speciesName, speciesContext);
            crossMap.put(speciesName, s);
            // }
            if (mathMappingCallback.isInterrupted()) {
                msg = "Canceled by user.";
                tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
                simContext.appendToConsole(tcm);
                throw new UserCancelException(msg);
            }
        // if(i%50 == 0) {
        // System.out.println(i+"");
        // }
        // if(i%decimalTickCount == 0) {
        // int multiplier = i/decimalTickCount;
        // float progress = progressFractionQuota/4.0f + progressFractionQuotaSpecies*multiplier;
        // mathMappingCallback.setProgressFraction(progress);
        // }
        }
        for (SpeciesContext sc1 : model.getSpeciesContexts()) {
            boolean found = false;
            for (Map.Entry<String, SpeciesContext> entry : scMap.entrySet()) {
                SpeciesContext sc2 = entry.getValue();
                if (sc1.getName().equals(sc2.getName())) {
                    found = true;
                    // System.out.println("found species context " + sc1.getName() + " of species " + sc1.getSpecies().getCommonName() + " // " + sc2.getSpecies().getCommonName());
                    break;
                }
            }
            if (found == false) {
                // we add to the map the species context and the species which exist in the model but which are not in the map yet
                // the only ones in this situation should be plain species which were not given to bngl for flattening (they are flat already)
                // System.out.println("species context " + sc1.getName() + " not found in the map. Adding it.");
                scMap.put(sc1.getName(), sc1);
                sMap.put(sc1.getName(), sc1.getSpecies());
                noMapForThese.add(sc1);
            }
        }
        for (Species s1 : model.getSpecies()) {
            boolean found = false;
            for (Map.Entry<String, Species> entry : sMap.entrySet()) {
                Species s2 = entry.getValue();
                if (s1.getCommonName().equals(s2.getCommonName())) {
                    found = true;
                    // System.out.println("found species " + s1.getCommonName());
                    break;
                }
            }
            if (found == false) {
                System.err.println("species " + s1.getCommonName() + " not found in the map!");
            }
        }
        SpeciesContext[] sca = new SpeciesContext[scMap.size()];
        scMap.values().toArray(sca);
        Species[] sa = new HashSet<Species>(sMap.values()).toArray(new Species[0]);
        model.setSpecies(sa);
        model.setSpeciesContexts(sca);
        boolean isSpatial = transformedSimulationContext.getGeometry().getDimension() > 0;
        for (SpeciesContext sc : sca) {
            if (noMapForThese.contains(sc)) {
                continue;
            }
            SpeciesContextSpec scs = reactionContext.getSpeciesContextSpec(sc);
            Parameter param = scs.getParameter(SpeciesContextSpec.ROLE_InitialConcentration);
            BNGSpecies s = crossMap.get(sc.getName());
            param.setExpression(s.getConcentration());
            SpeciesContext origSpeciesContext = simContext.getModel().getSpeciesContext(s.getName());
            if (origSpeciesContext != null) {
                ModelEntityMapping em = new ModelEntityMapping(origSpeciesContext, sc);
                entityMappings.add(em);
            } else {
                ModelEntityMapping em = new ModelEntityMapping(new GeneratedSpeciesSymbolTableEntry(sc), sc);
                if (isSpatial) {
                    scs.initializeForSpatial();
                }
                entityMappings.add(em);
            }
        }
        // for(SpeciesContext sc : sca) {		// clean all the species patterns from the flattened species, we have no sp now
        // sc.setSpeciesPattern(null);
        // }
        endTime = System.currentTimeMillis();
        elapsedTime = endTime - startTime;
        msg = "Adding " + outputSpec.getBNGSpecies().length + " species to model, " + elapsedTime + " ms";
        System.out.println(msg);
        // ---- Reactions -----------------------------------------------------------------------------------------------------
        mathMappingCallback.setMessage("generating network: adding reactions...");
        mathMappingCallback.setProgressFraction(progressFractionQuota / 4.0f * 3.0f);
        startTime = System.currentTimeMillis();
        System.out.println("\nReactions :");
        Map<String, HashSet<String>> ruleKeyMap = new HashMap<String, HashSet<String>>();
        Map<String, BNGReaction> directBNGReactionsMap = new HashMap<String, BNGReaction>();
        Map<String, BNGReaction> reverseBNGReactionsMap = new HashMap<String, BNGReaction>();
        for (int i = 0; i < outputSpec.getBNGReactions().length; i++) {
            BNGReaction r = outputSpec.getBNGReactions()[i];
            if (!r.isRuleReversed()) {
                // direct
                directBNGReactionsMap.put(r.getKey(), r);
            } else {
                reverseBNGReactionsMap.put(r.getKey(), r);
            }
            // 
            // for each rule name, store set of keySets (number of unique keysets are number of generated reactions from this ruleName).
            // 
            HashSet<String> keySet = ruleKeyMap.get(r.getRuleName());
            if (keySet == null) {
                keySet = new HashSet<String>();
                ruleKeyMap.put(r.getRuleName(), keySet);
            }
            keySet.add(r.getKey());
        }
        Map<String, ReactionStep> reactionStepMap = new HashMap<String, ReactionStep>();
        for (int i = 0; i < outputSpec.getBNGReactions().length; i++) {
            BNGReaction bngReaction = outputSpec.getBNGReactions()[i];
            // System.out.println(i+1 + ":\t\t"+ r.writeReaction());
            String baseName = bngReaction.getRuleName();
            String reactionName = null;
            HashSet<String> keySetsForThisRule = ruleKeyMap.get(bngReaction.getRuleName());
            if (keySetsForThisRule.size() == 1 && model.getReactionStep(bngReaction.getRuleName()) == null && !reactionStepMap.containsKey(bngReaction.getRuleName())) {
                // we can reuse the reaction rule labels
                reactionName = bngReaction.getRuleName();
            } else {
                reactionName = bngReaction.getRuleName() + "_0";
                while (true) {
                    if (model.getReactionStep(reactionName) == null && !reactionStepMap.containsKey(reactionName)) {
                        // we can reuse the reaction rule labels
                        break;
                    }
                    reactionName = TokenMangler.getNextEnumeratedToken(reactionName);
                }
            }
            // 
            if (directBNGReactionsMap.containsValue(bngReaction)) {
                BNGReaction forwardBNGReaction = bngReaction;
                BNGReaction reverseBNGReaction = reverseBNGReactionsMap.get(bngReaction.getKey());
                String name = forwardBNGReaction.getRuleName();
                if (name.endsWith(ReactionRule.DirectHalf)) {
                    name = name.substring(0, name.indexOf(ReactionRule.DirectHalf));
                }
                if (name.endsWith(ReactionRule.InverseHalf)) {
                    name = name.substring(0, name.indexOf(ReactionRule.InverseHalf));
                }
                ReactionRule rr = model.getRbmModelContainer().getReactionRule(name);
                Structure structure = rr.getStructure();
                boolean bReversible = reverseBNGReaction != null;
                SimpleReaction sr = new SimpleReaction(model, structure, reactionName, bReversible);
                for (int j = 0; j < forwardBNGReaction.getReactants().length; j++) {
                    BNGSpecies s = forwardBNGReaction.getReactants()[j];
                    String scName = speciesMap.get(s.getNetworkFileIndex());
                    SpeciesContext sc = model.getSpeciesContext(scName);
                    Reactant reactant = sr.getReactant(scName);
                    if (reactant == null) {
                        int stoichiometry = 1;
                        sr.addReactant(sc, stoichiometry);
                    } else {
                        int stoichiometry = reactant.getStoichiometry();
                        stoichiometry += 1;
                        reactant.setStoichiometry(stoichiometry);
                    }
                }
                for (int j = 0; j < forwardBNGReaction.getProducts().length; j++) {
                    BNGSpecies s = forwardBNGReaction.getProducts()[j];
                    String scName = speciesMap.get(s.getNetworkFileIndex());
                    SpeciesContext sc = model.getSpeciesContext(scName);
                    Product product = sr.getProduct(scName);
                    if (product == null) {
                        int stoichiometry = 1;
                        sr.addProduct(sc, stoichiometry);
                    } else {
                        int stoichiometry = product.getStoichiometry();
                        stoichiometry += 1;
                        product.setStoichiometry(stoichiometry);
                    }
                }
                MassActionKinetics targetKinetics = new MassActionKinetics(sr);
                sr.setKinetics(targetKinetics);
                KineticsParameter kforward = targetKinetics.getForwardRateParameter();
                KineticsParameter kreverse = targetKinetics.getReverseRateParameter();
                String kforwardNewName = rr.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate).getName();
                if (!kforward.getName().equals(kforwardNewName)) {
                    targetKinetics.renameParameter(kforward.getName(), kforwardNewName);
                    kforward = targetKinetics.getForwardRateParameter();
                }
                final String kreverseNewName = rr.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate).getName();
                if (!kreverse.getName().equals(kreverseNewName)) {
                    targetKinetics.renameParameter(kreverse.getName(), kreverseNewName);
                    kreverse = targetKinetics.getReverseRateParameter();
                }
                applyKineticsExpressions(forwardBNGReaction, kforward, targetKinetics);
                if (reverseBNGReaction != null) {
                    applyKineticsExpressions(reverseBNGReaction, kreverse, targetKinetics);
                }
                // String fieldParameterName = kforward.getName();
                // fieldParameterName += "_" + r.getRuleName();
                // kforward.setName(fieldParameterName);
                reactionStepMap.put(reactionName, sr);
            } else if (reverseBNGReactionsMap.containsValue(bngReaction) && !directBNGReactionsMap.containsKey(bngReaction.getKey())) {
                // reverse only (must be irreversible)
                BNGReaction reverseBNGReaction = reverseBNGReactionsMap.get(bngReaction.getKey());
                ReactionRule rr = model.getRbmModelContainer().getReactionRule(reverseBNGReaction.extractRuleName());
                Structure structure = rr.getStructure();
                boolean bReversible = false;
                SimpleReaction sr = new SimpleReaction(model, structure, reactionName, bReversible);
                for (int j = 0; j < reverseBNGReaction.getReactants().length; j++) {
                    BNGSpecies s = reverseBNGReaction.getReactants()[j];
                    String scName = speciesMap.get(s.getNetworkFileIndex());
                    SpeciesContext sc = model.getSpeciesContext(scName);
                    Reactant reactant = sr.getReactant(scName);
                    if (reactant == null) {
                        int stoichiometry = 1;
                        sr.addReactant(sc, stoichiometry);
                    } else {
                        int stoichiometry = reactant.getStoichiometry();
                        stoichiometry += 1;
                        reactant.setStoichiometry(stoichiometry);
                    }
                }
                for (int j = 0; j < reverseBNGReaction.getProducts().length; j++) {
                    BNGSpecies s = reverseBNGReaction.getProducts()[j];
                    String scName = speciesMap.get(s.getNetworkFileIndex());
                    SpeciesContext sc = model.getSpeciesContext(scName);
                    Product product = sr.getProduct(scName);
                    if (product == null) {
                        int stoichiometry = 1;
                        sr.addProduct(sc, stoichiometry);
                    } else {
                        int stoichiometry = product.getStoichiometry();
                        stoichiometry += 1;
                        product.setStoichiometry(stoichiometry);
                    }
                }
                MassActionKinetics k = new MassActionKinetics(sr);
                sr.setKinetics(k);
                KineticsParameter kforward = k.getForwardRateParameter();
                KineticsParameter kreverse = k.getReverseRateParameter();
                String kforwardNewName = rr.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate).getName();
                if (!kforward.getName().equals(kforwardNewName)) {
                    k.renameParameter(kforward.getName(), kforwardNewName);
                    kforward = k.getForwardRateParameter();
                }
                final String kreverseNewName = rr.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate).getName();
                if (!kreverse.getName().equals(kreverseNewName)) {
                    k.renameParameter(kreverse.getName(), kreverseNewName);
                    kreverse = k.getReverseRateParameter();
                }
                applyKineticsExpressions(reverseBNGReaction, kforward, k);
                // String fieldParameterName = kforward.getName();
                // fieldParameterName += "_" + r.getRuleName();
                // kforward.setName(fieldParameterName);
                reactionStepMap.put(reactionName, sr);
            }
        }
        for (ReactionStep rs : model.getReactionSteps()) {
            reactionStepMap.put(rs.getName(), rs);
        }
        ReactionStep[] reactionSteps = new ReactionStep[reactionStepMap.size()];
        reactionStepMap.values().toArray(reactionSteps);
        model.setReactionSteps(reactionSteps);
        if (mathMappingCallback.isInterrupted()) {
            msg = "Canceled by user.";
            tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
            simContext.appendToConsole(tcm);
            throw new UserCancelException(msg);
        }
        endTime = System.currentTimeMillis();
        elapsedTime = endTime - startTime;
        msg = "Adding " + outputSpec.getBNGReactions().length + " reactions to model, " + elapsedTime + " ms";
        System.out.println(msg);
        // clean all the reaction rules
        model.getRbmModelContainer().getReactionRuleList().clear();
        // ---- Observables -------------------------------------------------------------------------------------------------
        mathMappingCallback.setMessage("generating network: adding observables...");
        mathMappingCallback.setProgressFraction(progressFractionQuota / 8.0f * 7.0f);
        startTime = System.currentTimeMillis();
        System.out.println("\nObservables :");
        RbmModelContainer rbmmc = model.getRbmModelContainer();
        for (int i = 0; i < outputSpec.getObservableGroups().length; i++) {
            ObservableGroup o = outputSpec.getObservableGroups()[i];
            if (rbmmc.getParameter(o.getObservableGroupName()) != null) {
                System.out.println("   ...already exists.");
                // if it's already there we don't try to add it again; this should be true for all of them!
                continue;
            }
            ArrayList<Expression> terms = new ArrayList<Expression>();
            for (int j = 0; j < o.getListofSpecies().length; j++) {
                Expression term = Expression.mult(new Expression(o.getSpeciesMultiplicity()[j]), new Expression(speciesMap.get(o.getListofSpecies()[j].getNetworkFileIndex())));
                terms.add(term);
            }
            Expression exp = Expression.add(terms.toArray(new Expression[terms.size()])).flatten();
            exp.bindExpression(rbmmc.getSymbolTable());
            RbmObservable originalObservable = rbmmc.getObservable(o.getObservableGroupName());
            VCUnitDefinition observableUnitDefinition = originalObservable.getUnitDefinition();
            rbmmc.removeObservable(originalObservable);
            Parameter newParameter = rbmmc.addParameter(o.getObservableGroupName(), exp, observableUnitDefinition);
            RbmObservable origObservable = simContext.getModel().getRbmModelContainer().getObservable(o.getObservableGroupName());
            ModelEntityMapping em = new ModelEntityMapping(origObservable, newParameter);
            entityMappings.add(em);
        }
        if (mathMappingCallback.isInterrupted()) {
            msg = "Canceled by user.";
            tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
            simContext.appendToConsole(tcm);
            throw new UserCancelException(msg);
        }
        endTime = System.currentTimeMillis();
        elapsedTime = endTime - startTime;
        msg = "Adding " + outputSpec.getObservableGroups().length + " observables to model, " + elapsedTime + " ms";
        System.out.println(msg);
    } catch (PropertyVetoException ex) {
        ex.printStackTrace(System.out);
        throw new RuntimeException(ex.getMessage());
    } catch (ExpressionBindingException ex) {
        ex.printStackTrace(System.out);
        throw new RuntimeException(ex.getMessage());
    } catch (ModelException ex) {
        ex.printStackTrace(System.out);
        throw new RuntimeException(ex.getMessage());
    } catch (ExpressionException ex) {
        ex.printStackTrace(System.out);
        throw new RuntimeException(ex.getMessage());
    } catch (ClassNotFoundException ex) {
        throw new RuntimeException(ex.getMessage());
    } catch (IOException ex) {
        throw new RuntimeException(ex.getMessage());
    }
    System.out.println("Done transforming");
    msg = "Generating math...";
    System.out.println(msg);
    mathMappingCallback.setMessage(msg);
    mathMappingCallback.setProgressFraction(progressFractionQuota);
}

Example 15 with RbmObservable

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

the class RulebasedMathMapping method refreshVariables.

/**
 * This method was created in VisualAge.
 * @Override
 */
@Override
protected void refreshVariables() throws MappingException {
    Domain defaultDomain = new Domain(this.getSimulationContext().getGeometry().getGeometryClasses()[0]);
    // 
    // non-constant independent variables require either a membrane or volume variable
    // 
    Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
        SpeciesContextSpec scs = getSimulationContext().getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        // stochastic variable is always a function of size.
        SpeciesCountParameter spCountParm = null;
        try {
            String countName = scs.getSpeciesContext().getName() + BIO_PARAM_SUFFIX_SPECIES_COUNT;
            Expression countExp = new Expression(0.0);
            spCountParm = addSpeciesCountParameter(countName, countExp, PARAMETER_ROLE_SPECIES_COUNT, scs.getInitialCountParameter().getUnitDefinition(), scs.getSpeciesContext());
        } catch (PropertyVetoException pve) {
            pve.printStackTrace();
            throw new MappingException(pve.getMessage());
        }
        // add concentration of species as MathMappingParameter - this will map to species concentration function
        try {
            String concName = scs.getSpeciesContext().getName() + BIO_PARAM_SUFFIX_SPECIES_CONCENTRATION;
            Expression concExp = getExpressionAmtToConc(new Expression(spCountParm, getNameScope()), scs.getSpeciesContext().getStructure());
            concExp.bindExpression(this);
            addSpeciesConcentrationParameter(concName, concExp, PARAMETER_ROLE_SPECIES_CONCENRATION, scs.getSpeciesContext().getUnitDefinition(), scs.getSpeciesContext());
        } catch (Exception e) {
            e.printStackTrace();
            throw new MappingException(e.getMessage());
        }
        // we always add variables, all species are independent variables, no matter they are constant or not.
        String countMathSymbol = getMathSymbol(spCountParm, getSimulationContext().getGeometryContext().getStructureMapping(scs.getSpeciesContext().getStructure()).getGeometryClass());
        scm.setVariable(new VolumeParticleVariable(countMathSymbol, defaultDomain));
        mathSymbolMapping.put(scm.getSpeciesContext(), scm.getVariable().getName());
    }
    for (RbmObservable observable : simContext.getModel().getRbmModelContainer().getObservableList()) {
        // stochastic variable is always a function of size.
        ObservableCountParameter observableCountParm = null;
        try {
            String countName = observable.getName() + BIO_PARAM_SUFFIX_SPECIES_COUNT;
            Expression countExp = new Expression(0.0);
            observableCountParm = addObservableCountParameter(countName, countExp, PARAMETER_ROLE_OBSERVABLE_COUNT, simContext.getModel().getUnitSystem().getStochasticSubstanceUnit(), observable);
        } catch (PropertyVetoException pve) {
            pve.printStackTrace();
            throw new MappingException(pve.getMessage());
        }
        // add concentration of species as MathMappingParameter - this will map to species concentration function
        try {
            String concName = observable.getName() + BIO_PARAM_SUFFIX_SPECIES_CONCENTRATION;
            Expression concExp = getExpressionAmtToConc(new Expression(observableCountParm, getNameScope()), observable.getStructure());
            concExp.bindExpression(this);
            addObservableConcentrationParameter(concName, concExp, PARAMETER_ROLE_OBSERVABLE_CONCENTRATION, observable.getUnitDefinition(), observable);
        } catch (Exception e) {
            e.printStackTrace();
            throw new MappingException(e.getMessage());
        }
    // //we always add variables, all species are independent variables, no matter they are constant or not.
    // String countMathSymbol = getMathSymbol(observableCountParm, getSimulationContext().getGeometryContext().getStructureMapping(scs.getSpeciesContext().getStructure()).getGeometryClass());
    // scm.setVariable(new VolumeParticleVariable(countMathSymbol,defaultDomain));
    // mathSymbolMapping.put(observable,scm.getVariable().getName());
    }
}