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

Example 66 with ReactionStep

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

the class BiomodelVCMLModelInfoResource method createHtml.

public static StringBuffer createHtml(BioModel bm) {
    final SpeciesContext[] speciesContexts = bm.getModel().getSpeciesContexts();
    final ReactionStep[] reactionSteps = bm.getModel().getReactionSteps();
    // This contains a structure name mapped to Species and ReactionSteps
    TreeMap<String, ArrayList<Object>[]> structName_Species_Reactions_TS = new TreeMap<String, ArrayList<Object>[]>();
    // Store SpeciesContexts belonging to each Structure
    for (int i = 0; i < speciesContexts.length; i++) {
        final String name = speciesContexts[i].getStructure().getName();
        ArrayList<Object>[] items = structName_Species_Reactions_TS.get(name);
        if (items == null) {
            items = new ArrayList[] { new ArrayList<Structure>(), new ArrayList<SpeciesContext>(), new ArrayList<ReactionStep>() };
            items[ITEM_NAMES.structure.ordinal()].add(speciesContexts[i].getStructure());
            structName_Species_Reactions_TS.put(name, items);
        }
        items[ITEM_NAMES.species.ordinal()].add(speciesContexts[i]);
    }
    // Store ReactionStep belonging to each structure
    for (int i = 0; i < reactionSteps.length; i++) {
        final String name = reactionSteps[i].getStructure().getName();
        ArrayList<Object>[] items = structName_Species_Reactions_TS.get(name);
        if (items == null) {
            items = new ArrayList[] { new ArrayList<Structure>(), new ArrayList<SpeciesContext>(), new ArrayList<ReactionStep>() };
            items[ITEM_NAMES.structure.ordinal()].add(reactionSteps[i].getStructure());
            structName_Species_Reactions_TS.put(name, items);
        }
        items[ITEM_NAMES.reactions.ordinal()].add(reactionSteps[i]);
    }
    // Create html
    StringBuffer sb = new StringBuffer();
    sb.append("<strong>Compartments, Species, Reactions</strong><br/>");
    // iterate through all the structures and get the stored SpeciesContexts and ReactionSteps
    final Iterator<String> iterator = structName_Species_Reactions_TS.keySet().iterator();
    while (iterator.hasNext()) {
        // Get the structure name
        final String structName = iterator.next();
        // Get the stored items for the structure
        final ArrayList<Object>[] items = structName_Species_Reactions_TS.get(structName);
        sb.append("<ul><li> Compartment <strong>\"" + structName + "\"</strong>.  &nbsp; (type: " + ((Structure) items[ITEM_NAMES.structure.ordinal()].get(0)).getTypeName() + ")<ul>");
        // Add html for SpeciesContexts
        for (int i = 0; i < items[ITEM_NAMES.species.ordinal()].size(); i++) {
            sb.append("<li>Species <strong>\"" + StringEscapeUtils.escapeHtml(((SpeciesContext) items[ITEM_NAMES.species.ordinal()].get(i)).getName()) + "\"</strong></li>");
        }
        // Add html for ReactionSteps
        for (int i = 0; i < items[ITEM_NAMES.reactions.ordinal()].size(); i++) {
            final ReactionStep rxStep = (ReactionStep) items[ITEM_NAMES.reactions.ordinal()].get(i);
            ReactionDescription reactionDescription = createReactionDescription(rxStep, bm.getVersion().getVersionKey(), ((Structure) items[ITEM_NAMES.structure.ordinal()].get(0)).getKey());
            sb.append("<li>Reaction <strong>\"" + rxStep.getName() + "\"</strong> &nbsp; " + rxStep.getClass().getSimpleName() + " &nbsp; (" + StringEscapeUtils.escapeHtml(reactionDescription.toString()) + ")</li>");
        }
        sb.append("</ul></li></ul>");
    }
    return sb;
}

Example 67 with ReactionStep

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

the class BNGOutputPanel method getCollapsedReactionSteps.

private ReactionStep[] getCollapsedReactionSteps(ReactionStep[] reactionSteps) {
    Vector<ReactionStep> collapsedRxnStepsVector = new Vector<ReactionStep>();
    Vector<ReactionStep> rxnStepsVector = new Vector<ReactionStep>();
    for (int i = 0; i < reactionSteps.length; i++) {
        rxnStepsVector.addElement(reactionSteps[i]);
    }
    for (int i = 0; i < rxnStepsVector.size(); i++) {
        ReactionStep fwdRStep = rxnStepsVector.elementAt(i);
        // Get the reactionParticipants and the corresponding reactants and products in an array
        ReactionParticipant[] rps = fwdRStep.getReactionParticipants();
        Vector<SpeciesContext> fwdReactantsVector = new Vector<SpeciesContext>();
        Vector<SpeciesContext> fwdProductsVector = new Vector<SpeciesContext>();
        for (int j = 0; j < rps.length; j++) {
            if (rps[j] instanceof Reactant) {
                fwdReactantsVector.addElement(rps[j].getSpeciesContext());
            } else if (rps[j] instanceof Product) {
                fwdProductsVector.addElement(rps[j].getSpeciesContext());
            }
        }
        SpeciesContext[] fwdReactants = (SpeciesContext[]) BeanUtils.getArray(fwdReactantsVector, SpeciesContext.class);
        SpeciesContext[] fwdProducts = (SpeciesContext[]) BeanUtils.getArray(fwdProductsVector, SpeciesContext.class);
        boolean bReverseReactionFound = false;
        // Loop through all the reactions to find the corresponding reverse reaction
        for (int ii = 0; ii < reactionSteps.length; ii++) {
            ReactionStep revRStep = reactionSteps[ii];
            // Get the reactionParticipants and the corresponding reactants and products in an array
            ReactionParticipant[] revRps = revRStep.getReactionParticipants();
            Vector<SpeciesContext> revReactantsVector = new Vector<SpeciesContext>();
            Vector<SpeciesContext> revProductsVector = new Vector<SpeciesContext>();
            for (int j = 0; j < revRps.length; j++) {
                if (revRps[j] instanceof Reactant) {
                    revReactantsVector.addElement(revRps[j].getSpeciesContext());
                } else if (revRps[j] instanceof Product) {
                    revProductsVector.addElement(revRps[j].getSpeciesContext());
                }
            }
            SpeciesContext[] revReactants = (SpeciesContext[]) BeanUtils.getArray(revReactantsVector, SpeciesContext.class);
            SpeciesContext[] revProducts = (SpeciesContext[]) BeanUtils.getArray(revProductsVector, SpeciesContext.class);
            // Check if reactants of reaction in outer 'for' loop match products in inner 'for' loop and vice versa.
            if (BeanUtils.arrayEquals(fwdReactants, revProducts) && BeanUtils.arrayEquals(fwdProducts, revReactants)) {
                // Set the reverse kinetic rate expression for the reaction in outer loop with the forward rate from reactionStep in inner loop
                // inner 'for' loop
                MassActionKinetics revMAKinetics = (MassActionKinetics) revRStep.getKinetics();
                // outer 'for' loop
                MassActionKinetics fwdMAKinetics = (MassActionKinetics) fwdRStep.getKinetics();
                try {
                    fwdMAKinetics.setParameterValue(fwdMAKinetics.getReverseRateParameter(), revMAKinetics.getForwardRateParameter().getExpression());
                    Kinetics.KineticsParameter param = revMAKinetics.getKineticsParameter(revMAKinetics.getForwardRateParameter().getExpression().infix());
                    fwdMAKinetics.setParameterValue(param, param.getExpression());
                } catch (Exception e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException(e.getMessage());
                }
                // Add this to the collapsedRxnStepsVector
                collapsedRxnStepsVector.addElement(fwdRStep);
                rxnStepsVector.removeElement(revRStep);
                bReverseReactionFound = true;
                break;
            }
        }
        // Add it as is to the 'collapsedRxnStepsVector'
        if (!bReverseReactionFound) {
            collapsedRxnStepsVector.addElement(fwdRStep);
        }
    }
    // Convert the vector into an array of reactionSteps and return
    ReactionStep[] collapsedRxnSteps = (ReactionStep[]) BeanUtils.getArray(collapsedRxnStepsVector, ReactionStep.class);
    return collapsedRxnSteps;
}

Example 68 with ReactionStep

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

the class ClientRequestManager method idToNameConversion.

public static void idToNameConversion(VCDocument vcDoc) {
    if (!(vcDoc instanceof BioModel)) {
        return;
    }
    BioModel vcBioModel = (BioModel) vcDoc;
    vcBioModel.getSimulationContext(0).setbIgnoreEvents(true);
    Map<String, String> entitiesToRename = new LinkedHashMap<>();
    for (SpeciesContext sc : vcBioModel.getModel().getSpeciesContexts()) {
        String id = sc.getName();
        String name = sc.getSbmlName();
        if (name == null || name.isEmpty()) {
            continue;
        }
        if (isRestrictedXYZT(name, vcBioModel)) {
            continue;
        }
        name = TokenMangler.fixTokenStrict(name, 60);
        while (true) {
            if (cbit.vcell.model.Model.isNameUnused(name, vcBioModel.getModel())) {
                break;
            }
            name = TokenMangler.getNextEnumeratedToken(name);
        }
        if (id.equals(name)) {
            continue;
        }
        try {
            System.out.println(name + " <-- " + id);
            sc.setName(name);
        } catch (PropertyVetoException e) {
            // we just keep the id rather than abort
            e.printStackTrace();
        }
        entitiesToRename.put(id, name);
    }
    for (ModelParameter mp : vcBioModel.getModel().getModelParameters()) {
        String id = mp.getName();
        String name = mp.getSbmlName();
        if (name == null || name.isEmpty()) {
            continue;
        }
        if (isRestrictedXYZT(name, vcBioModel)) {
            continue;
        }
        name = TokenMangler.fixTokenStrict(name, 60);
        while (true) {
            if (cbit.vcell.model.Model.isNameUnused(name, vcBioModel.getModel())) {
                break;
            }
            name = TokenMangler.getNextEnumeratedToken(name);
        }
        if (id.equals(name)) {
            continue;
        }
        try {
            System.out.println(name + " <-- " + id);
            mp.setName(name);
        } catch (PropertyVetoException e) {
            e.printStackTrace();
        }
        entitiesToRename.put(id, name);
    }
    for (Structure struct : vcBioModel.getModel().getStructures()) {
        String id = struct.getName();
        String name = struct.getSbmlName();
        if (name == null || name.isEmpty()) {
            continue;
        }
        if (isRestrictedXYZT(name, vcBioModel)) {
            continue;
        }
        name = TokenMangler.fixTokenStrict(name, 60);
        while (true) {
            if (cbit.vcell.model.Model.isNameUnused(name, vcBioModel.getModel())) {
                break;
            }
            name = TokenMangler.getNextEnumeratedToken(name);
        }
        if (id.equals(name)) {
            continue;
        }
        try {
            System.out.println(name + " <-- " + id);
            struct.setName(name, true);
        } catch (PropertyVetoException e) {
            e.printStackTrace();
        }
        entitiesToRename.put(id, name);
    }
    vcBioModel.getSimulationContext(0).substituteChangedNamesInExpressions(entitiesToRename);
    for (ReactionStep rs : vcBioModel.getModel().getReactionSteps()) {
        String id = rs.getName();
        String name = rs.getSbmlName();
        if (name == null || name.isEmpty()) {
            continue;
        }
        if (isRestrictedXYZT(name, vcBioModel)) {
            continue;
        }
        // name = TokenMangler.fixTokenStrict(name, 60);
        while (true) {
            if (cbit.vcell.model.Model.isNameUnused(name, vcBioModel.getModel())) {
                break;
            }
            name = TokenMangler.getNextEnumeratedToken(name);
        }
        if (id.equals(name)) {
            continue;
        }
        try {
            System.out.println(name + " <-- " + id);
            rs.setName(name);
        } catch (PropertyVetoException e) {
            e.printStackTrace();
        }
    }
    vcBioModel.getSimulationContext(0).setbIgnoreEvents(false);
}

Example 69 with ReactionStep

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

the class ClientRequestManager method createBioModelFromApplication.

public void createBioModelFromApplication(final BioModelWindowManager requester, final String name, final SimulationContext simContext) {
    if (simContext == null) {
        PopupGenerator.showErrorDialog(requester, "Selected Application is null, cannot generate corresponding bio model");
        return;
    }
    if (simContext.isRuleBased()) {
        createRuleBasedBioModelFromApplication(requester, name, simContext);
        return;
    }
    AsynchClientTask task1 = new AsynchClientTask("Creating BioModel from BioModel Application", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            MathMappingCallback dummyCallback = new MathMappingCallback() {

                public void setProgressFraction(float percentDone) {
                }

                public void setMessage(String message) {
                }

                public boolean isInterrupted() {
                    return false;
                }
            };
            MathMapping transformedMathMapping = simContext.createNewMathMapping(dummyCallback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
            BioModel newBioModel = new BioModel(null);
            SimulationContext transformedSimContext = transformedMathMapping.getTransformation().transformedSimContext;
            Model newModel = transformedSimContext.getModel();
            newBioModel.setModel(newModel);
            RbmModelContainer rbmmc = newModel.getRbmModelContainer();
            for (RbmObservable o : rbmmc.getObservableList()) {
                rbmmc.removeObservable(o);
            }
            for (ReactionRule r : rbmmc.getReactionRuleList()) {
                rbmmc.removeReactionRule(r);
            }
            for (ReactionStep rs : newModel.getReactionSteps()) {
                String oldName = rs.getName();
                if (oldName.startsWith("_reverse_")) {
                    String newName = newModel.getReactionName("rev", oldName.substring("_reverse_".length()));
                    rs.setName(newName);
                }
            }
            hashTable.put("newBioModel", newBioModel);
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("Creating BioModel from BioModel Application", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            BioModel newBioModel = (BioModel) hashTable.get("newBioModel");
            DocumentWindowManager windowManager = createDocumentWindowManager(newBioModel);
            // if(simContext.getBioModel().getVersion() != null){
            // ((BioModelWindowManager)windowManager). setCopyFromBioModelAppVersionableTypeVersion(
            // new VersionableTypeVersion(VersionableType.BioModelMetaData, simContext.getBioModel().getVersion()));
            // }
            getMdiManager().createNewDocumentWindow(windowManager);
        }
    };
    ClientTaskDispatcher.dispatch(requester.getComponent(), new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 }, false);
}

Example 70 with ReactionStep

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

the class ReactionPropertiesPanel method setReactionStep.

/**
 * Sets the kinetics property (cbit.vcell.model.Kinetics) value.
 * @param kinetics The new value for the property.
 * @see #getKinetics
 */
private void setReactionStep(ReactionStep newValue) {
    if (reactionStep == newValue) {
        return;
    }
    ReactionStep oldValue = reactionStep;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(eventHandler);
    }
    // commit the changes before switch to another reaction step
    changeName();
    changeSbmlName();
    reactionStep = newValue;
    if (newValue != null) {
        newValue.addPropertyChangeListener(eventHandler);
    }
    getParameterTableModel().setReactionStep(reactionStep);
    updateInterface();
}