Examples with NetworkConstraints org.vcell.model.rbm.NetworkConstraints used on opensource projects

Example 11 with NetworkConstraints

use of org.vcell.model.rbm.NetworkConstraints in project vcell by virtualcell.

the class IssuePanel method invokeHyperlink.

private void invokeHyperlink(Issue issue) {
    if (selectionManager != null) {
        // followHyperlink is no-op if selectionManger null, so no point in proceeding if it is
        IssueContext issueContext = issue.getIssueContext();
        IssueSource object = issue.getSource();
        if (object instanceof DecoratedIssueSource) {
            DecoratedIssueSource dis = (DecoratedIssueSource) object;
            dis.activateView(selectionManager);
        } else if (object instanceof Parameter) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.BIOMODEL_PARAMETERS_NODE, ActiveViewID.parameters_functions), new Object[] { object });
        } else if (object instanceof StructureMapping) {
            StructureMapping structureMapping = (StructureMapping) object;
            StructureMappingNameScope structureMappingNameScope = (StructureMappingNameScope) structureMapping.getNameScope();
            SimulationContext simulationContext = ((SimulationContextNameScope) (structureMappingNameScope.getParent())).getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.structure_mapping), new Object[] { object });
        } else if (object instanceof SpatialObject) {
            SpatialObject spatialObject = (SpatialObject) object;
            SimulationContext simulationContext = spatialObject.getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.spatial_objects), new Object[] { object });
        } else if (object instanceof SpatialProcess) {
            SpatialProcess spatialProcess = (SpatialProcess) object;
            SimulationContext simulationContext = spatialProcess.getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.spatial_processes), new Object[] { object });
        } else if (object instanceof GeometryContext.UnmappedGeometryClass) {
            UnmappedGeometryClass unmappedGeometryClass = (UnmappedGeometryClass) object;
            SimulationContext simulationContext = unmappedGeometryClass.getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.structure_mapping), new Object[] { object });
        } else if (object instanceof MicroscopeMeasurement) {
            SimulationContext simulationContext = ((MicroscopeMeasurement) object).getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.PROTOCOLS_NODE, ActiveViewID.microscope_measuremments), new Object[] { object });
        } else if (object instanceof BioEvent) {
            BioEvent be = (BioEvent) object;
            SimulationContext simulationContext = be.getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.PROTOCOLS_NODE, ActiveViewID.events), new Object[] { object });
        } else if (object instanceof OutputFunctionIssueSource) {
            SimulationOwner simulationOwner = ((OutputFunctionIssueSource) object).getOutputFunctionContext().getSimulationOwner();
            if (simulationOwner instanceof SimulationContext) {
                SimulationContext simulationContext = (SimulationContext) simulationOwner;
                followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.SIMULATIONS_NODE, ActiveViewID.output_functions), new Object[] { ((OutputFunctionIssueSource) object).getAnnotatedFunction() });
            } else if (simulationOwner instanceof MathModel) {
                followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MATH_OUTPUT_FUNCTIONS_NODE, ActiveViewID.math_output_functions), new Object[] { ((OutputFunctionIssueSource) object).getAnnotatedFunction() });
            }
        } else if (object instanceof Simulation) {
            Simulation simulation = (Simulation) object;
            SimulationOwner simulationOwner = simulation.getSimulationOwner();
            if (simulationOwner instanceof SimulationContext) {
                SimulationContext simulationContext = (SimulationContext) simulationOwner;
                followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.SIMULATIONS_NODE, ActiveViewID.simulations), new Object[] { simulation });
            } else if (simulationOwner instanceof MathModel) {
                followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MATH_SIMULATIONS_NODE, ActiveViewID.math_simulations), new Object[] { simulation });
            }
        } else if (object instanceof GeometryContext) {
            setActiveView(new ActiveView(((GeometryContext) object).getSimulationContext(), DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.geometry_definition));
        } else if (object instanceof Structure) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.STRUCTURES_NODE, ActiveViewID.structures), new Object[] { object });
        } else if (object instanceof MolecularType) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE, ActiveViewID.structures), new Object[] { object });
        } else if (object instanceof ReactionStep) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTIONS_NODE, ActiveViewID.reactions), new Object[] { object });
        } else if (object instanceof ReactionRule) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTIONS_NODE, ActiveViewID.reactions), new Object[] { object });
        } else if (object instanceof SpeciesContextSpec) {
            SpeciesContextSpec scs = (SpeciesContextSpec) object;
            ActiveView av = new ActiveView(scs.getSimulationContext(), DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.species_settings);
            followHyperlink(av, new Object[] { object });
        } else if (object instanceof ReactionCombo) {
            ReactionCombo rc = (ReactionCombo) object;
            followHyperlink(new ActiveView(rc.getReactionContext().getSimulationContext(), DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.reaction_setting), new Object[] { ((ReactionCombo) object).getReactionSpec() });
        } else if (object instanceof SpeciesContext) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.SPECIES_NODE, ActiveViewID.species), new Object[] { object });
        } else if (object instanceof RbmObservable) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.OBSERVABLES_NODE, ActiveViewID.observables), new Object[] { object });
        } else if (object instanceof MathDescription) {
            // followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MATH_SIMULATIONS_NODE, ActiveViewID.generated_math), new Object[] {object});
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.structure_mapping), new Object[] { object });
        } else if (object instanceof SpeciesPattern) {
            // if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
            // SpeciesContext thing = (SpeciesContext)issue.getIssueContext().getContextObject(ContextType.SpeciesContext);
            // followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.SPECIES_NODE, ActiveViewID.species), new Object[] {thing});
            // }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
            // ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
            // followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTIONS_NODE, ActiveViewID.reactions), new Object[] {thing});
            // }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
            // RbmObservable thing = (RbmObservable)issue.getIssueContext().getContextObject(ContextType.RbmObservable);
            // followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.OBSERVABLES_NODE, ActiveViewID.observables), new Object[] {thing});
            // } else {
            System.err.println("SpeciesPattern object missing a proper issue context.");
        // }
        } else if (object instanceof SimulationContext) {
            SimulationContext sc = (SimulationContext) object;
            IssueCategory ic = issue.getCategory();
            switch(ic) {
                case RbmNetworkConstraintsBad:
                    NetworkConstraints nc = sc.getNetworkConstraints();
                    if (issue.getMessage() == SimulationContext.IssueInsufficientMolecules) {
                        NetworkConstraintsEntity nce = new NetworkConstraintsEntity(NetworkConstraintsTableModel.sMaxMoleculesName, NetworkConstraintsTableModel.sValueType, nc.getMaxMoleculesPerSpecies() + "");
                        followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.network_setting), new Object[] { nce });
                    } else {
                        NetworkConstraintsEntity nce = new NetworkConstraintsEntity(NetworkConstraintsTableModel.sMaxIterationName, NetworkConstraintsTableModel.sValueType, nc.getMaxIteration() + "");
                        followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.network_setting), new Object[] { nce });
                    }
                    break;
                default:
                    followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.network_setting), new Object[] { object });
                    break;
            }
        } else if (object instanceof Geometry) {
            if (issueContext.hasContextType(ContextType.SimContext)) {
                SimulationContext simContext = (SimulationContext) issueContext.getContextObject(ContextType.SimContext);
                followHyperlink(new ActiveView(simContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.geometry_definition), new Object[] { object });
            } else if (issueContext.hasContextType(ContextType.MathModel)) {
                followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MATH_GEOMETRY_NODE, ActiveViewID.math_geometry), new Object[] { object });
            } else if (issueContext.hasContextType(ContextType.MathDescription)) {
                followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.geometry_definition), new Object[] { object });
            }
        } else {
            System.err.println("unknown object type in IssuePanel.invokeHyperlink(): " + object.getClass() + ", context type: " + issueContext.getContextType());
        }
    }
}

Example 12 with NetworkConstraints

use of org.vcell.model.rbm.NetworkConstraints in project vcell by virtualcell.

the class BNGExecutorServiceMultipass method executeBNG.

@Override
public BNGOutput executeBNG() throws BNGException, ParseException, PropertyVetoException, ExpressionBindingException {
    this.startTime = System.currentTimeMillis();
    // elapsed time in doWork
    long eltDoWork = 0;
    // elapsed time executing bngl
    long eltExecBng = 0;
    // elapsed time executing isomorphism
    eltIsomorph = 0;
    // elapsed time on final Observable run
    long eltObserv = 0;
    String cBngInputString = cBngInput.getInputString();
    String anchorsString = extractAnchors(cBngInputString);
    anchorsMap = parseAnchors(anchorsString);
    // the "trick" - the modified molecules, species, etc
    // everything has an extra Site with the compartments as possible States
    // and yet another site that we use to certify the compartment validity
    String sBngInputString = preprocessInput(cBngInputString);
    BNGInput sBngInput = new BNGInput(sBngInputString);
    // output after each iteration
    BNGOutput sBngOutput = null;
    String sBngOutputString = null;
    // the seedSpecies which were given as input for the current iteration
    String oldSeedSpeciesString;
    // the BNGReactions as they are at the end of the current iteration, after corrections of the species
    String correctedReactionsString = null;
    // before the first iteration we show the original seed species
    oldSeedSpeciesString = extractOriginalSeedSpecies(sBngInputString);
    // consoleNotification("======= Original Seed Species ===========================\n" + oldSeedSpeciesString);
    // initial number of seed species
    int speciesCount = org.apache.commons.lang3.StringUtils.countMatches(oldSeedSpeciesString, "\n");
    displayIterationMessage(0, speciesCount);
    List<BNGSpecies> initialSpeciesList = BNGOutputFileParser.createBngSpeciesOutputSpec(oldSeedSpeciesString);
    for (BNGSpecies s : initialSpeciesList) {
        // populate the isomorphism signature map with the initial seed species
        isomorphismSignaturesMap.put(s.getName(), s.getName());
        shortSignaturesSet.add(BNGSpecies.getShortSignature(s, sigDetailLevel));
    }
    NetworkConstraints nc = simContext.getNetworkConstraints();
    // iterations counter
    int i;
    for (i = 0; i < nc.getMaxIteration(); i++) {
        correctedReactionsString = null;
        this.onepassBngService = new BNGExecutorServiceNative(sBngInput, timeoutDurationMS);
        // we are the only callback for the native service, acting as middleman
        this.onepassBngService.registerBngUpdaterCallback(this);
        long st1 = System.currentTimeMillis();
        sBngOutput = this.onepassBngService.executeBNG();
        long et1 = System.currentTimeMillis();
        eltExecBng += (et1 - st1);
        this.onepassBngService = null;
        // .net file
        sBngOutputString = sBngOutput.getNetFileContent();
        // String delta = "";
        String rawSeedSpeciesString = "";
        // this bloc is dealing with the strings, used for console display only
        rawSeedSpeciesString = extractSeedSpecies(sBngOutputString);
        dump("dumpIteration" + (i + 1) + ".txt", rawSeedSpeciesString);
        // delta = rawSeedSpeciesString.substring(oldSeedSpeciesString.length());
        String rs = extractReactions(sBngOutputString);
        // String s = "  --- Iteration " + (i+1) + " ---------------------------";
        // s += "\n" + delta;
        // s += "---------------------------------------\n" + rs;
        // consoleNotification(s);
        long st2 = System.currentTimeMillis();
        CorrectedSR correctedSR = doWork(oldSeedSpeciesString, sBngOutputString);
        long et2 = System.currentTimeMillis();
        eltDoWork += (et2 - st2);
        String correctedSeedSpeciesString = extractCorrectedSeedSpeciesAsString(correctedSR);
        correctedReactionsString = extractCorrectedReactionsAsString(correctedSR);
        oldSeedSpeciesString += correctedSeedSpeciesString;
        speciesCount += correctedSR.speciesList.size();
        int reactionsCount = correctedSR.reactionsList.size();
        displayIterationMessage(i + 1, speciesCount);
        if (speciesCount >= NetworkTransformer.speciesLimit) {
            // don't continue iterations if we reach species limit
            break;
        }
        if (reactionsCount >= NetworkTransformer.reactionsLimit) {
            break;
        }
        if (correctedSR.speciesList.isEmpty()) {
            // if the current iteration didn't provide any VALID NEW species (after correction) then we are done
            break;
        }
        sBngInputString = prepareNewBnglString(sBngInputString, oldSeedSpeciesString);
        // the new input for next iteration
        sBngInput = new BNGInput(sBngInputString);
    }
    // run one more iteration with all the seed species calculated above and with one single fake
    // rule (so that no new seed species will be created), to properly compute the observables
    long st3 = System.currentTimeMillis();
    // the ObservableGroups
    String obsInputString = prepareObservableRun(sBngInputString);
    BNGInput obsBngInput = new BNGInput(obsInputString);
    this.onepassBngService = new BNGExecutorServiceNative(obsBngInput, timeoutDurationMS);
    this.onepassBngService.registerBngUpdaterCallback(this);
    BNGOutput obsBngOutput = this.onepassBngService.executeBNG();
    String correctedObservablesString = extractCorrectedObservablesAsString(obsBngOutput);
    correctedObservablesString = extractPolymerObservablesAsString(correctedObservablesString, oldSeedSpeciesString);
    long et3 = System.currentTimeMillis();
    eltObserv += (et3 - st3);
    // oldSeedSpeciesString contains the final list of seed species
    sBngOutput.insertEntitiesInNetFile(oldSeedSpeciesString, "species");
    sBngOutput.insertEntitiesInNetFile(correctedReactionsString, "reactions");
    sBngOutput.insertEntitiesInNetFile(correctedObservablesString, "groups");
    // analyze the sBnglOutput, strip the fake "compartment" site and produce the proper cBnglOutput
    if (model.getStructures().length > 1) {
        // converts the net file inside sBngOutput
        sBngOutput.extractCompartmentsFromNetFile();
    }
    BNGOutput cBngOutput = sBngOutput;
    // String cBngOutputString = cBngOutput.getNetFileContent();
    // System.out.println(cBngOutputString);
    long endTime = System.currentTimeMillis();
    long elapsedTime = endTime - startTime;
    System.out.println("Done " + i + " Iterations in " + (int) (elapsedTime / 1000.0) + " s.");
    // System.out.println("out of which " + (int)(eltDoWork/1000.0) + " s was spent in 'doWork'.");
    System.out.println("- in BioNetGen: " + (int) (eltExecBng / 1000.0));
    // doWork except isomorphism
    System.out.println("- in DoWork   : " + (int) ((eltDoWork - eltIsomorph) / 1000.0));
    System.out.println("- in Isomorph : " + (int) (eltIsomorph / 1000.0));
    System.out.println("- in Observ   : " + (int) (eltObserv / 1000.0));
    // algorithms outside doWork
    System.out.println("- in rest     : " + (int) ((elapsedTime - eltExecBng - eltDoWork - eltObserv) / 1000.0));
    // we basically return the "corrected" bng output from the last iteration run
    return cBngOutput;
}

Example 13 with NetworkConstraints

use of org.vcell.model.rbm.NetworkConstraints in project vcell by virtualcell.

the class BNGExecutorServiceMultipass method extractNetworkConstraints.

private static NetworkConstraints extractNetworkConstraints(String cBngInputString) {
    NetworkConstraints nc = new NetworkConstraints();
    String s1 = cBngInputString.substring(cBngInputString.indexOf("max_iter=>") + "max_iter=>".length());
    s1 = s1.substring(0, s1.indexOf(","));
    int maxi = Integer.parseInt(s1);
    nc.setMaxIteration(maxi);
    String s2 = cBngInputString.substring(cBngInputString.indexOf("max_agg=>") + "max_agg=>".length());
    s2 = s2.substring(0, s2.indexOf(","));
    int maxa = Integer.parseInt(s2);
    nc.setMaxMoleculesPerSpecies(maxa);
    return nc;
}

Example 14 with NetworkConstraints

use of org.vcell.model.rbm.NetworkConstraints in project vcell by virtualcell.

the class SimContextTable method getAppComponentsForDatabase.

/**
 * getXMLStringForDatabase : this returns the XML string for the container element <AppComponents> for application-related protocols
 * and other extra specifications. For now, BioEvents falls under this category, so the BioEvents element (list of bioevents)
 * is obtained from the simContext (via the XMLProducer) and added as content to <AppComponents> element. The <AppComponents>
 * element is converted to XML string which is the return value of this method. This string is stored in the database in the
 * SimContextTable. Instead of creating new fields for each possible application component, it is convenient to store them
 * all under a blanket XML element <AppComponents>.
 * @param simContext
 * @return
 */
public static String getAppComponentsForDatabase(SimulationContext simContext) {
    Element appComponentsElement = new Element(XMLTags.ApplicationComponents);
    // for now, create the element only if application is stochastic. Can change it later.
    if (simContext.isStoch()) {
        // add 'randomizeInitCondition' flag only if simContext is non-spatial
        if (simContext.getGeometry().getDimension() == 0) {
            Element appRelatedFlagsElement = new Element(XMLTags.ApplicationSpecificFlagsTag);
            if (simContext.isRandomizeInitCondition()) {
                appRelatedFlagsElement.setAttribute(XMLTags.RandomizeInitConditionTag, "true");
            } else {
                appRelatedFlagsElement.setAttribute(XMLTags.RandomizeInitConditionTag, "false");
            }
            appComponentsElement.addContent(appRelatedFlagsElement);
        }
    }
    if (simContext.isInsufficientIterations()) {
        appComponentsElement.setAttribute(XMLTags.InsufficientIterationsTag, "true");
    } else {
        appComponentsElement.setAttribute(XMLTags.InsufficientIterationsTag, "false");
    }
    if (simContext.isInsufficientMaxMolecules()) {
        appComponentsElement.setAttribute(XMLTags.InsufficientMaxMoleculesTag, "true");
    } else {
        appComponentsElement.setAttribute(XMLTags.InsufficientMaxMoleculesTag, "false");
    }
    Xmlproducer xmlProducer = new Xmlproducer(false);
    NetworkConstraints constraints = simContext.getNetworkConstraints();
    if (constraints != null) {
        appComponentsElement.addContent(xmlProducer.getXML(constraints));
    }
    // first fill in bioevents from simContext
    BioEvent[] bioEvents = simContext.getBioEvents();
    if (bioEvents != null && bioEvents.length > 0) {
        try {
            Element bioEventsElement = xmlProducer.getXML(bioEvents);
            appComponentsElement.addContent(bioEventsElement);
        } catch (XmlParseException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error generating XML for bioevents : " + e.getMessage());
        }
    }
    SimulationContextParameter[] appParams = simContext.getSimulationContextParameters();
    if (appParams != null && appParams.length > 0) {
        try {
            Element appParamsElement = xmlProducer.getXML(appParams);
            appComponentsElement.addContent(appParamsElement);
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error generating XML for application parameters : " + e.getMessage());
        }
    }
    SpatialObject[] spatialObjects = simContext.getSpatialObjects();
    if (spatialObjects != null && spatialObjects.length > 0) {
        try {
            Element spatialObjectsElement = xmlProducer.getXML(spatialObjects);
            appComponentsElement.addContent(spatialObjectsElement);
        } catch (XmlParseException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error generating XML for spatialObjects : " + e.getMessage());
        }
    }
    SpatialProcess[] spatialProcesses = simContext.getSpatialProcesses();
    if (spatialProcesses != null && spatialProcesses.length > 0) {
        try {
            Element spatialProcessesElement = xmlProducer.getXML(spatialProcesses);
            appComponentsElement.addContent(spatialProcessesElement);
        } catch (XmlParseException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error generating XML for spatialProcesses : " + e.getMessage());
        }
    }
    // microscope measurements
    Element element = xmlProducer.getXML(simContext.getMicroscopeMeasurement());
    appComponentsElement.addContent(element);
    // rate rules
    RateRule[] rateRules = simContext.getRateRules();
    if (rateRules != null && rateRules.length > 0) {
        try {
            Element rateRulesElement = xmlProducer.getXML(rateRules);
            appComponentsElement.addContent(rateRulesElement);
        } catch (XmlParseException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error generating XML for bioevents : " + e.getMessage());
        }
    }
    // ReactionRuleSpecs
    ReactionRuleSpec[] reactionRuleSpecs = simContext.getReactionContext().getReactionRuleSpecs();
    if (reactionRuleSpecs != null && reactionRuleSpecs.length > 0) {
        Element reactionRuleSpecsElement = xmlProducer.getXML(reactionRuleSpecs);
        appComponentsElement.addContent(reactionRuleSpecsElement);
    }
    String appComponentsXMLStr = null;
    if (appComponentsElement.getContent() != null) {
        appComponentsXMLStr = XmlUtil.xmlToString(appComponentsElement);
    }
    return appComponentsXMLStr;
}