Examples with NetworkConstraintsEntity org.vcell.model.rbm.common.NetworkConstraintsEntity used on opensource projects

Example 1 with NetworkConstraintsEntity

use of org.vcell.model.rbm.common.NetworkConstraintsEntity in project vcell by virtualcell.

the class NetworkConstraintsTableModel method computeData.

protected ArrayList<NetworkConstraintsEntity> computeData() {
    ArrayList<NetworkConstraintsEntity> nceList = new ArrayList<NetworkConstraintsEntity>();
    Model model = simContext.getModel();
    RbmModelContainer rbmModelContainer = model.getRbmModelContainer();
    if (rbmModelContainer == null) {
        return nceList;
    }
    String s1, s2, s3, s4;
    NetworkConstraintsEntity nce;
    NetworkConstraints networkConstraints = simContext.getNetworkConstraints();
    if (networkConstraints != null) {
        s1 = networkConstraints.getMaxIteration() + "";
        s2 = networkConstraints.getMaxMoleculesPerSpecies() + "";
        s3 = networkConstraints.getSpeciesLimit() + "";
        s4 = networkConstraints.getReactionsLimit() + "";
    } else {
        s1 = "?";
        s2 = "?";
        s3 = "?";
        s4 = "?";
    }
    nce = new NetworkConstraintsEntity(sMaxIterationName, s1, NetworkTransformer.defaultMaxIteration + "");
    nceList.add(nce);
    nce = new NetworkConstraintsEntity(sMaxMoleculesName, s2, NetworkTransformer.defaultMaxMoleculesPerSpecies + "");
    nceList.add(nce);
    nce = new NetworkConstraintsEntity(sSpeciesLimitName, s3, NetworkTransformer.defaultSpeciesLimit + "");
    nceList.add(nce);
    nce = new NetworkConstraintsEntity(sReactionsLimitName, s4, NetworkTransformer.defaultReactionsLimit + "");
    nceList.add(nce);
    Map<MolecularType, Integer> stoichiometryMap = networkConstraints.getMaxStoichiometry(simContext);
    Iterator<Entry<MolecularType, Integer>> it = stoichiometryMap.entrySet().iterator();
    while (it.hasNext()) {
        // first clean any entry that doesn't exist anymore (should never happen!)
        MolecularType mt = it.next().getKey();
        if (rbmModelContainer.getMolecularType(mt.getName()) == null) {
            it.remove();
        }
    }
    for (MolecularType mt : rbmModelContainer.getMolecularTypeList()) {
        // add any new molecule that's not already there, with the default max stoichiometry
        if (!stoichiometryMap.containsKey(mt)) {
            stoichiometryMap.put(mt, NetworkConstraints.defaultMaxStoichiometry);
        }
    }
    for (Map.Entry<MolecularType, Integer> entry : stoichiometryMap.entrySet()) {
        MolecularType mt = entry.getKey();
        Integer value = entry.getValue();
        nce = new NetworkConstraintsEntity("Max molecules " + mt.getDisplayName() + " / Species", value + "", NetworkConstraints.defaultMaxStoichiometry + "");
        nceList.add(nce);
    }
    return nceList;
}

Example 2 with NetworkConstraintsEntity

use of org.vcell.model.rbm.common.NetworkConstraintsEntity in project vcell by virtualcell.

the class NetworkConstraintsTableModel method getValueAt.

@Override
public Object getValueAt(int row, int column) {
    if (simContext == null) {
        return null;
    }
    NetworkConstraintsEntity nce = getValueAt(row);
    String colName = nce.getName();
    String colValue = nce.getValue();
    String colDefault = nce.getDefaultValue();
    NetworkConstraints networkConstraints = simContext.getNetworkConstraints();
    if (row == 0) {
        colValue = networkConstraints.getMaxIteration() + "";
    } else if (row == 1) {
        colValue = networkConstraints.getMaxMoleculesPerSpecies() + "";
    } else if (row == 2) {
        colValue = networkConstraints.getSpeciesLimit() + "";
    } else if (row == 3) {
        colValue = networkConstraints.getReactionsLimit() + "";
    }
    if (nce != null) {
        switch(column) {
            case iColName:
                return colName;
            case iColValue:
                return colValue;
            case iColDefault:
                return colDefault;
        }
    }
    return null;
}

Example 3 with NetworkConstraintsEntity

use of org.vcell.model.rbm.common.NetworkConstraintsEntity 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 AssignmentRule) {
            AssignmentRule ar = (AssignmentRule) object;
            SimulationContext sc = ar.getSimulationContext();
            followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.PROTOCOLS_NODE, ActiveViewID.assignmentRules), new Object[] { ar });
        } else if (object instanceof RateRule) {
            RateRule rr = (RateRule) object;
            SimulationContext sc = rr.getSimulationContext();
            followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.PROTOCOLS_NODE, ActiveViewID.rateRules), new Object[] { rr });
        } 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, nc.getMaxMoleculesPerSpecies() + "", NetworkTransformer.defaultMaxMoleculesPerSpecies + "");
                        followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.network_setting), new Object[] { nce });
                    } else {
                        NetworkConstraintsEntity nce = new NetworkConstraintsEntity(NetworkConstraintsTableModel.sMaxIterationName, nc.getMaxIteration() + "", NetworkTransformer.defaultMaxIteration + "");
                        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());
        }
    }
}