Examples with SpatialProcess cbit.vcell.mapping.spatial.processes.SpatialProcess used on opensource projects

Example 26 with SpatialProcess

use of cbit.vcell.mapping.spatial.processes.SpatialProcess in project vcell by virtualcell.

the class SpatialProcessTableModel method propertyChange.

@Override
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    super.propertyChange(evt);
    if (evt.getPropertyName().equals("SpatialProcesss")) {
        SpatialProcess[] oldValue = (SpatialProcess[]) evt.getOldValue();
        if (oldValue != null) {
            for (SpatialProcess rr : oldValue) {
                rr.removePropertyChangeListener(this);
            }
        }
        SpatialProcess[] newValue = (SpatialProcess[]) evt.getNewValue();
        if (newValue != null) {
            for (SpatialProcess rr : newValue) {
                rr.addPropertyChangeListener(this);
            }
        }
    }
    refreshData();
}

Example 27 with SpatialProcess

use of cbit.vcell.mapping.spatial.processes.SpatialProcess 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 28 with SpatialProcess

use of cbit.vcell.mapping.spatial.processes.SpatialProcess 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;
}