Examples with BNGReaction cbit.vcell.bionetgen.BNGReaction used on opensource projects

Example 1 with BNGReaction

use of cbit.vcell.bionetgen.BNGReaction in project vcell by virtualcell.

the class ViewGeneratedReactionsPanel method updateShape.

public void updateShape(int selectedRow) {
    GeneratedReactionTableRow reactionTableRow = tableModel.getValueAt(selectedRow);
    String inputString = reactionTableRow.getExpression();
    System.out.println(selectedRow + ": " + inputString);
    // ReactionRule newReactionRule = (ReactionRule)RbmUtils.parseReactionRule(inputString, bioModel);
    Model tempModel = null;
    try {
        tempModel = new Model("MyTempModel");
        tempModel.addFeature("c0");
    } catch (ModelException | PropertyVetoException e1) {
        e1.printStackTrace();
    }
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        // This should not be possible
        throw new RuntimeException("Owner or SimulationContext are null.");
    }
    int arrowIndex = inputString.indexOf("<->");
    boolean bReversible = true;
    if (arrowIndex < 0) {
        arrowIndex = inputString.indexOf("->");
        bReversible = false;
    }
    String left = inputString.substring(0, arrowIndex).trim();
    String right = inputString.substring(arrowIndex + (bReversible ? 3 : 2)).trim();
    if (left.length() == 0 && right.length() == 0) {
        return;
    }
    // we recover the original rule that generated the flattened reaction we now try to transform back into a fake rule
    BNGReaction reactionObject = reactionTableRow.getReactionObject();
    String name = reactionObject.getRuleName();
    if (name.contains(GeneratedReactionTableModel.reverse)) {
        name = name.substring(GeneratedReactionTableModel.reverse.length());
    }
    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));
    }
    // get the name of the original structure from the original rule and make here another structure with the same name
    String strStructure = null;
    Structure ruleStructure;
    SimulationContext sc = owner.getSimulationContext();
    ReactionRule rr = sc.getModel().getRbmModelContainer().getReactionRule(name);
    if (rr != null && rr.getStructure() != null) {
        strStructure = rr.getStructure().getName();
    }
    if (strStructure != null) {
        if (tempModel.getStructure(strStructure) == null) {
            try {
                if (rr.getStructure().getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                    tempModel.addMembrane(strStructure);
                } else {
                    tempModel.addFeature(strStructure);
                }
            } catch (ModelException | PropertyVetoException e) {
                e.printStackTrace();
            }
        }
        ruleStructure = tempModel.getStructure(strStructure);
    } else {
        throw new RuntimeException("Failed to recover a Structure name from the Reaction Rule: " + name);
    }
    // making the fake rules just for display purpose, actually they are the flattened reactions resulted from bngl
    // the name is probably not unique, it's likely that many flattened reactions are derived from the same rule
    ReactionRule reactionRule = tempModel.getRbmModelContainer().createReactionRule(name, ruleStructure, bReversible);
    String regex = "[^!]\\+";
    String[] patterns = left.split(regex);
    for (String spString : patterns) {
        try {
            spString = spString.trim();
            // if compartments are present, we're cheating big time making some fake compartments just for compartment name display purposes
            SpeciesPattern speciesPattern = (SpeciesPattern) RbmUtils.parseSpeciesPattern(spString, tempModel);
            strStructure = RbmUtils.parseCompartment(spString, tempModel);
            speciesPattern.resolveBonds();
            Structure structure;
            if (strStructure != null) {
                if (tempModel.getStructure(strStructure) == null) {
                    if (sc.getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                        tempModel.addMembrane(strStructure);
                    } else {
                        tempModel.addFeature(strStructure);
                    }
                }
                structure = tempModel.getStructure(strStructure);
            } else {
                // if nothing explicit for a participant, we use by default the structure of the rule
                structure = ruleStructure;
            }
            reactionRule.addReactant(new ReactantPattern(speciesPattern, structure));
        } catch (Throwable ex) {
            ex.printStackTrace();
            // error (red circle)
            SpeciesPatternLargeShape spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanel, true, issueManager);
            reactantPatternShapeList.clear();
            productPatternShapeList.clear();
            reactantPatternShapeList.add(spls);
            shapePanel.repaint();
            return;
        }
    }
    patterns = right.split(regex);
    for (String spString : patterns) {
        try {
            spString = spString.trim();
            SpeciesPattern speciesPattern = (SpeciesPattern) RbmUtils.parseSpeciesPattern(spString, tempModel);
            strStructure = RbmUtils.parseCompartment(spString, tempModel);
            speciesPattern.resolveBonds();
            Structure structure;
            if (strStructure != null) {
                if (tempModel.getStructure(strStructure) == null) {
                    if (sc.getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                        tempModel.addMembrane(strStructure);
                    } else {
                        tempModel.addFeature(strStructure);
                    }
                }
                structure = tempModel.getStructure(strStructure);
            } else {
                structure = ruleStructure;
            }
            // BNGLParser parser = new BNGLParser(new StringReader(sp));
            // ASTSpeciesPattern astSpeciesPattern = parser.SpeciesPattern();
            // BnglObjectConstructionVisitor constructionVisitor = new BnglObjectConstructionVisitor(tempModel, null, false);
            // SpeciesPattern speciesPattern = (SpeciesPattern) astSpeciesPattern.jjtAccept(constructionVisitor, null);
            // for(MolecularTypePattern mtp : speciesPattern.getMolecularTypePatterns()) {
            // mtp.setParticipantMatchLabel("*");
            // }
            // System.out.println(speciesPattern.toString());
            reactionRule.addProduct(new ProductPattern(speciesPattern, structure));
        } catch (Throwable ex) {
            ex.printStackTrace();
            // error (red circle)
            SpeciesPatternLargeShape spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanel, true, issueManager);
            reactantPatternShapeList.clear();
            productPatternShapeList.clear();
            reactantPatternShapeList.add(spls);
            shapePanel.repaint();
            return;
        }
    }
    // ----------------------------------------------------------------------------------------------------
    List<ReactantPattern> rpList = reactionRule.getReactantPatterns();
    reactantPatternShapeList.clear();
    int xOffset = 20;
    int xOffsetRound = 20;
    if (rpList != null && rpList.size() > 0) {
        for (int i = 0; i < rpList.size(); i++) {
            SpeciesPattern sp = rpList.get(i).getSpeciesPattern();
            for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
                mtp.setParticipantMatchLabel("*");
            }
            SpeciesPatternLargeShape sps = new SpeciesPatternLargeShape(xOffset, 20, -1, sp, shapePanel, reactionRule, issueManager);
            // SpeciesPatternRoundShape sps = new SpeciesPatternRoundShape(xOffsetRound, 20, -1, sp, shapePanel, reactionRule);
            if (i < rpList.size() - 1) {
                sps.addEndText("+");
            } else {
                if (reactionRule.isReversible()) {
                    sps.addEndText("<->");
                } else {
                    sps.addEndText("->");
                }
            }
            xOffset = sps.getRightEnd() + 45;
            xOffsetRound = sps.getRightEnd() + 45;
            reactantPatternShapeList.add(sps);
        }
    }
    // space for the <-> sign
    xOffset += 15;
    List<ProductPattern> ppList = reactionRule.getProductPatterns();
    productPatternShapeList.clear();
    if (ppList != null && ppList.size() > 0) {
        for (int i = 0; i < ppList.size(); i++) {
            SpeciesPattern sp = ppList.get(i).getSpeciesPattern();
            for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
                mtp.setParticipantMatchLabel("*");
            }
            SpeciesPatternLargeShape sps = new SpeciesPatternLargeShape(xOffset, 20, -1, sp, shapePanel, reactionRule, issueManager);
            // SpeciesPatternRoundShape sps = new SpeciesPatternRoundShape(xOffset, 20, -1, sp, shapePanel, reactionRule);
            if (i < ppList.size() - 1) {
                sps.addEndText("+");
            }
            xOffset = sps.getRightEnd() + 45;
            productPatternShapeList.add(sps);
        }
    }
    Dimension preferredSize = new Dimension(xOffset + 90, 50);
    shapePanel.setPreferredSize(preferredSize);
    shapePanel.repaint();
}

Example 2 with BNGReaction

use of cbit.vcell.bionetgen.BNGReaction in project vcell by virtualcell.

the class GeneratedReactionTableModel method getValueAt.

public Object getValueAt(int iRow, int iCol) {
    GeneratedReactionTableRow reactionTableRow = getValueAt(iRow);
    BNGReaction reactionObject = reactionTableRow.getReactionObject();
    String name = reactionObject.getRuleName();
    switch(iCol) {
        case iColRule:
            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));
                name += " (rev)";
            }
            return name;
        case iColStructure:
            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));
            }
            SimulationContext sc = owner.getSimulationContext();
            ReactionRule rr = sc.getModel().getRbmModelContainer().getReactionRule(name);
            if (rr != null && rr.getStructure() != null) {
                return rr.getStructure().getName();
            } else {
                return "?";
            }
        case iColDepiction:
        case iColDefinition:
            return reactionTableRow.getExpression();
        default:
            return null;
    }
}

Example 3 with BNGReaction

use of cbit.vcell.bionetgen.BNGReaction 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 4 with BNGReaction

use of cbit.vcell.bionetgen.BNGReaction in project vcell by virtualcell.

the class BNGExecutorServiceMultipass method extractCorrectedReactionsAsString.

private static String extractCorrectedReactionsAsString(CorrectedSR corrected) {
    String correctedReactionsString = "";
    for (int i = 0; i < corrected.reactionsList.size(); i++) {
        BNGReaction r = corrected.reactionsList.get(i);
        correctedReactionsString += (i + 1) + " " + r.toBnglString() + "\n";
    }
    return correctedReactionsString;
}

Example 5 with BNGReaction

use of cbit.vcell.bionetgen.BNGReaction in project vcell by virtualcell.

the class GeneratedReactionTableModel method refreshData.

private void refreshData() {
    allGeneratedReactionsList = new ArrayList<GeneratedReactionTableRow>();
    for (int i = 0; i < reactions.length; i++) {
        BNGReaction reaction = reactions[i];
        GeneratedReactionTableRow newRow = createTableRow(reaction, i + 1, reaction.toStringShort());
        allGeneratedReactionsList.add(newRow);
    }
    // apply text search function for particular columns
    ArrayList<GeneratedReactionTableRow> reactionObjectList = new ArrayList<GeneratedReactionTableRow>();
    if (searchText == null || searchText.length() == 0) {
        reactionObjectList.addAll(allGeneratedReactionsList);
    } else {
        String lowerCaseSearchText = searchText.toLowerCase();
        for (GeneratedReactionTableRow rs : allGeneratedReactionsList) {
            boolean added = false;
            if (rs.getExpression().toLowerCase().contains(lowerCaseSearchText)) {
                reactionObjectList.add(rs);
                added = true;
            }
            if (!added && rs.getReactionRule().getDisplayName().toLowerCase().contains(lowerCaseSearchText)) {
                reactionObjectList.add(rs);
                added = true;
            }
            if (!added && rs.getReactionRule().getStructure().getName().toLowerCase().contains(lowerCaseSearchText)) {
                reactionObjectList.add(rs);
                added = true;
            }
        }
    }
    setData(reactionObjectList);
    GuiUtils.flexResizeTableColumns(ownerTable);
}