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

Example 11 with ReactionRule

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

the class BioPaxRelationshipTableModel method refreshData.

private void refreshData() {
    ArrayList<BioPaxRelationshipTableRow> entityRows = new ArrayList<BioPaxRelationshipTableRow>();
    if (bioModel != null) {
        HashSet<RelationshipObject> relationshipObjects = null;
        if (bioPaxObject != null) {
            relationshipObjects = bioModel.getRelationshipModel().getRelationshipObjects(bioPaxObject);
        }
        List<BioPaxRelationshipTableRow> allEntityRows = new ArrayList<BioPaxRelationshipTableRow>();
        if (bioPaxObject instanceof Conversion) {
            for (ReactionStep rs : bioModel.getModel().getReactionSteps()) {
                BioPaxRelationshipTableRow entityRow = new BioPaxRelationshipTableRow(rs);
                if (relationshipObjects != null) {
                    for (RelationshipObject ro : relationshipObjects) {
                        if (ro.getBioModelEntityObject() == rs) {
                            entityRow.setSelected(true);
                            break;
                        }
                    }
                }
                if (!bShowLinkOnly || entityRow.selected) {
                    allEntityRows.add(entityRow);
                }
            }
            for (ReactionRule rr : bioModel.getModel().getRbmModelContainer().getReactionRuleList()) {
                BioPaxRelationshipTableRow entityRow = new BioPaxRelationshipTableRow(rr);
                if (relationshipObjects != null) {
                    for (RelationshipObject ro : relationshipObjects) {
                        if (ro.getBioModelEntityObject() == rr) {
                            entityRow.setSelected(true);
                            break;
                        }
                    }
                }
                if (!bShowLinkOnly || entityRow.selected) {
                    allEntityRows.add(entityRow);
                }
            }
        } else if (bioPaxObject instanceof PhysicalEntity) {
            for (SpeciesContext rs : bioModel.getModel().getSpeciesContexts()) {
                BioPaxRelationshipTableRow entityRow = new BioPaxRelationshipTableRow(rs);
                if (relationshipObjects != null) {
                    for (RelationshipObject ro : relationshipObjects) {
                        if (ro.getBioModelEntityObject() == rs) {
                            entityRow.setSelected(true);
                            break;
                        }
                    }
                }
                if (!bShowLinkOnly || entityRow.selected) {
                    allEntityRows.add(entityRow);
                }
            }
        }
        if (searchText == null || searchText.length() == 0) {
            entityRows.addAll(allEntityRows);
        } else {
            for (BioPaxRelationshipTableRow rs : allEntityRows) {
                BioModelEntityObject object = rs.getBioModelEntityObject();
                String lowerCaseSearchText = searchText.toLowerCase();
                if (object.getName().toLowerCase().contains(lowerCaseSearchText) || object.getTypeLabel().toLowerCase().contains(lowerCaseSearchText)) {
                    entityRows.add(rs);
                }
            }
        }
    }
    setData(entityRows);
    GuiUtils.flexResizeTableColumns(ownerTable);
}

Example 12 with ReactionRule

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

the class SimulationContext method gatherIssues.

public void gatherIssues(IssueContext issueContext, List<Issue> issueVector, boolean bIgnoreMathDescription) {
    // issueContext = issueContext.newChildContext(ContextType.SimContext, this);
    if (applicationType.equals(Application.RULE_BASED_STOCHASTIC)) {
        for (ReactionRuleSpec rrs : getReactionContext().getReactionRuleSpecs()) {
            if (rrs.isExcluded()) {
                continue;
            }
            ReactionRule rr = rrs.getReactionRule();
            if (rr.getReactantPatterns().size() > 2) {
                String message = "NFSim doesn't support more than 2 reactants within a reaction rule.";
                issueVector.add(new Issue(rr, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
            }
            if (rr.isReversible() && rr.getProductPatterns().size() > 2) {
                String message = "NFSim doesn't support more than 2 products within a reversible reaction rule.";
                issueVector.add(new Issue(rr, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
            }
        }
        for (ReactionSpec rrs : getReactionContext().getReactionSpecs()) {
            if (rrs.isExcluded()) {
                continue;
            }
            ReactionStep rs = rrs.getReactionStep();
            if (rs.getNumReactants() > 2) {
                String message = "NFSim doesn't support more than 2 reactants within a reaction step.";
                issueVector.add(new Issue(rs, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
            }
            if (rs.isReversible() && rs.getNumProducts() > 2) {
                String message = "NFSim doesn't support more than 2 products within a reversible reaction step.";
                issueVector.add(new Issue(rs, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
            }
        }
        // we give warning when we have plain reactions with participants with patterns;
        // making rules from these may result in inconsistent interpretation for the constant rates
        boolean isParticipantWithPattern = false;
        for (ReactionSpec rrs : getReactionContext().getReactionSpecs()) {
            if (rrs.isExcluded()) {
                continue;
            }
            ReactionStep rs = rrs.getReactionStep();
            for (Reactant r : rs.getReactants()) {
                if (r.getSpeciesContext().hasSpeciesPattern()) {
                    isParticipantWithPattern = true;
                    break;
                }
            }
            if (isParticipantWithPattern) {
                break;
            }
            for (Product p : rs.getProducts()) {
                if (p.getSpeciesContext().hasSpeciesPattern()) {
                    isParticipantWithPattern = true;
                    break;
                }
            }
            if (isParticipantWithPattern) {
                break;
            }
        }
        if (isParticipantWithPattern) {
            String message = SimulationContext.rateWarning2;
            String tooltip = SimulationContext.rateWarning;
            issueVector.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, tooltip, Issue.Severity.WARNING));
        }
        for (Structure struct : getModel().getStructures()) {
            String name = struct.getName();
            if (!name.equals(TokenMangler.fixTokenStrict(name))) {
                String msg = "'" + name + "' not legal identifier for rule-based stochastic applications, try '" + TokenMangler.fixTokenStrict(name) + "'.";
                issueVector.add(new Issue(struct, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.ERROR));
            }
        }
    }
    if (fieldBioEvents != null) {
        for (BioEvent bioEvent : fieldBioEvents) {
            bioEvent.gatherIssues(issueContext, issueVector);
        }
    }
    if (spatialObjects != null) {
        for (SpatialObject spatialObject : spatialObjects) {
            spatialObject.gatherIssues(issueContext, issueVector);
        }
    }
    if (spatialProcesses != null) {
        for (SpatialProcess spatialProcess : spatialProcesses) {
            spatialProcess.gatherIssues(issueContext, issueVector);
        }
    }
    if (applicationType.equals(Application.NETWORK_DETERMINISTIC) && getModel().getRbmModelContainer().getMolecularTypeList().size() > 0) {
        // we're going to use network transformer to flatten (or we already did)
        if (isInsufficientIterations()) {
            issueVector.add(new Issue(this, issueContext, IssueCategory.RbmNetworkConstraintsBad, IssueInsufficientIterations, Issue.Severity.WARNING));
        }
        if (isInsufficientMaxMolecules()) {
            issueVector.add(new Issue(this, issueContext, IssueCategory.RbmNetworkConstraintsBad, IssueInsufficientMolecules, Issue.Severity.WARNING));
        }
    }
    getReactionContext().gatherIssues(issueContext, issueVector);
    getGeometryContext().gatherIssues(issueContext, issueVector);
    if (fieldAnalysisTasks != null) {
        for (AnalysisTask analysisTask : fieldAnalysisTasks) {
            analysisTask.gatherIssues(issueContext, issueVector);
        }
    }
    getOutputFunctionContext().gatherIssues(issueContext, issueVector);
    getMicroscopeMeasurement().gatherIssues(issueContext, issueVector);
    if (getMathDescription() != null && !bIgnoreMathDescription) {
        getMathDescription().gatherIssues(issueContext, issueVector);
    }
    if (networkConstraints == null) {
    // issueVector.add(new Issue(this, issueContext, IssueCategory.RbmNetworkConstraintsBad, "Network Constraints is null", Issue.Severity.ERROR));
    } else {
        networkConstraints.gatherIssues(issueContext, issueVector);
    }
}

Example 13 with ReactionRule

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

the class SpeciesPatternRoundShape method paintCompartment.

public void paintCompartment(Graphics g) {
    Color structureColor = Color.black;
    Structure structure = null;
    if (owner instanceof ReactionRule && !speciesShapes.isEmpty()) {
        ReactionRule rr = (ReactionRule) owner;
        ReactantPattern rp = rr.getReactantPattern(sp);
        ProductPattern pp = rr.getProductPattern(sp);
        if (rp != null) {
            structure = rp.getStructure();
        } else if (pp != null) {
            structure = pp.getStructure();
        } else {
            structure = ((ReactionRule) owner).getStructure();
        }
    } else if (owner instanceof SpeciesContext && ((SpeciesContext) owner).hasSpeciesPattern()) {
        structure = ((SpeciesContext) owner).getStructure();
        structureColor = Color.gray;
    } else if (owner instanceof RbmObservable && !speciesShapes.isEmpty()) {
        structure = ((RbmObservable) owner).getStructure();
    } else {
        // other things don't have structure
        return;
    }
    if (structure == null) {
        return;
    }
    // don't have a real structure, so we show them structureless (for now)
    if (structure.getName() == null) {
        return;
    }
    Graphics2D g2 = (Graphics2D) g;
    Color colorOld = g2.getColor();
    Paint paintOld = g2.getPaint();
    Font fontOld = g2.getFont();
    Font font;
    // width of compartment shape, adjusted continuously based on zoom factor
    int w;
    String name = structure.getName();
    int z = shapePanel.getZoomFactor();
    if (z > -3) {
        font = fontOld.deriveFont(Font.BOLD);
        g.setFont(font);
        w = 46 + 3 * z;
        name = buildCompartmentName(g, name, "..", w);
    } else if (z < LargeShapeCanvas.SmallestZoomFactorWithText) {
        font = fontOld.deriveFont(fontOld.getSize2D() * 0.8f);
        g.setFont(font);
        w = 20;
        name = buildCompartmentName(g, name, ".", w);
    } else {
        font = fontOld;
        g.setFont(font);
        w = 44 + 3 * z;
        name = buildCompartmentName(g, name, "..", w);
    }
    // a bit darker for border
    Color darker = Color.gray;
    Rectangle2D border = new Rectangle2D.Double(xPos - 9, yPos - 4, w, 58);
    g2.setColor(darker);
    g2.draw(border);
    Color lighter = new Color(224, 224, 224);
    Rectangle2D filling = new Rectangle2D.Double(xPos - 9, yPos - 3, w, 57);
    g2.setPaint(lighter);
    g2.fill(filling);
    g.setColor(structureColor);
    g2.drawString(name, xPos - 4, yPos + 48);
    g2.setFont(fontOld);
    g2.setPaint(paintOld);
    g2.setColor(colorOld);
}

Example 14 with ReactionRule

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

the class IssueTableModel method getSourceObjectPathDescription.

private String getSourceObjectPathDescription(VCDocument vcDocument, Issue issue) {
    VCAssert.assertValid(issue);
    Object source = issue.getSource();
    {
        IssueOrigin io = BeanUtils.downcast(IssueOrigin.class, source);
        if (io != null) {
            return io.getDescription();
        }
    }
    if (vcDocument instanceof BioModel) {
        BioModel bioModel = (BioModel) vcDocument;
        String description = "";
        if (source instanceof SymbolTableEntry) {
            if (source instanceof SpeciesContext) {
                description = "Model / Species";
            } else if (source instanceof RbmObservable) {
                description = "Model / Observables";
            } else {
                description = ((SymbolTableEntry) source).getNameScope().getPathDescription();
            }
        } else if (source instanceof MolecularType) {
            description = "Model / Molecules";
        } else if (source instanceof ReactionStep) {
            ReactionStep reactionStep = (ReactionStep) source;
            description = ((ReactionNameScope) reactionStep.getNameScope()).getPathDescription();
        } else if (source instanceof ReactionRule) {
            ReactionRule reactionRule = (ReactionRule) source;
            description = ((ReactionRuleNameScope) reactionRule.getNameScope()).getPathDescription();
        } else if (source instanceof SpeciesPattern) {
            // if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
            // description = "Model / Species";
            // }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
            // ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
            // description = ((ReactionRuleNameScope)thing.getNameScope()).getPathDescription();
            // }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
            // description = "Model / Observables";
            // } else {
            System.err.println("Bad issue context for " + ((SpeciesPattern) source).toString());
            description = ((SpeciesPattern) source).toString();
        // }
        } else if (source instanceof Structure) {
            Structure structure = (Structure) source;
            description = "Model / " + structure.getTypeName() + "(" + structure.getName() + ")";
        } else if (source instanceof StructureMapping) {
            StructureMapping structureMapping = (StructureMapping) source;
            description = ((StructureMappingNameScope) structureMapping.getNameScope()).getPathDescription();
        } else if (source instanceof OutputFunctionIssueSource) {
            SimulationContext simulationContext = (SimulationContext) ((OutputFunctionIssueSource) source).getOutputFunctionContext().getSimulationOwner();
            description = "App(" + simulationContext.getName() + ") / " + "Simulations" + " / " + "Output Functions";
        } else if (source instanceof Simulation) {
            Simulation simulation = (Simulation) source;
            try {
                SimulationContext simulationContext = bioModel.getSimulationContext(simulation);
                description = "App(" + simulationContext.getName() + ") / Simulations";
            } catch (ObjectNotFoundException e) {
                e.printStackTrace();
                description = "App(" + "unknown" + ") / Simulations";
            }
        } else if (source instanceof UnmappedGeometryClass) {
            UnmappedGeometryClass unmappedGC = (UnmappedGeometryClass) source;
            description = "App(" + unmappedGC.getSimulationContext().getName() + ") / Subdomain(" + unmappedGC.getGeometryClass().getName() + ")";
        } else if (source instanceof GeometryContext) {
            description = "App(" + ((GeometryContext) source).getSimulationContext().getName() + ")";
        } else if (source instanceof ModelOptimizationSpec) {
            description = "App(" + ((ModelOptimizationSpec) source).getSimulationContext().getName() + ") / Parameter Estimation";
        } else if (source instanceof MicroscopeMeasurement) {
            description = "App(" + ((MicroscopeMeasurement) source).getSimulationContext().getName() + ") / Microscope Measurements";
        } else if (source instanceof SpatialObject) {
            description = "App(" + ((SpatialObject) source).getSimulationContext().getName() + ") / Spatial Objects";
        } else if (source instanceof SpatialProcess) {
            description = "App(" + ((SpatialProcess) source).getSimulationContext().getName() + ") / Spatial Processes";
        } else if (source instanceof SpeciesContextSpec) {
            SpeciesContextSpec scs = (SpeciesContextSpec) source;
            description = "App(" + scs.getSimulationContext().getName() + ") / Specifications / Species";
        } else if (source instanceof ReactionCombo) {
            ReactionCombo rc = (ReactionCombo) source;
            description = "App(" + rc.getReactionContext().getSimulationContext().getName() + ") / Specifications / Reactions";
        } else if (source instanceof RbmModelContainer) {
            IssueCategory ic = issue.getCategory();
            switch(ic) {
                case RbmMolecularTypesTableBad:
                    description = "Model / " + MolecularType.typeName + "s";
                    break;
                case RbmReactionRulesTableBad:
                    description = "Model / Reactions";
                    break;
                case RbmObservablesTableBad:
                    description = "Model / Observables";
                    break;
                case RbmNetworkConstraintsBad:
                    description = "Network Constrains";
                    break;
                default:
                    description = "Model";
                    break;
            }
        } else if (source instanceof SimulationContext) {
            SimulationContext sc = (SimulationContext) source;
            IssueCategory ic = issue.getCategory();
            switch(ic) {
                case RbmNetworkConstraintsBad:
                    description = "Specifications / Network";
                    break;
                default:
                    description = "Application";
                    break;
            }
        } else if (source instanceof Model) {
            description = "Model";
        } else if (source instanceof BioEvent) {
            return "Protocols / Events";
        } else if (source instanceof MathDescription) {
            return "Math Description";
        } else {
            System.err.println("unknown source type in IssueTableModel.getSourceObjectPathDescription(): " + source.getClass());
        }
        return description;
    } else if (vcDocument instanceof MathModel) {
        if (source instanceof Geometry) {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_GEOMETRY;
        } else if (source instanceof OutputFunctionIssueSource) {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_OUTPUTFUNCTIONS;
        } else if (source instanceof Simulation) {
            return "Simulation(" + ((Simulation) source).getName() + ")";
        } else {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_VCML;
        }
    } else {
        System.err.println("unknown document type in IssueTableModel.getSourceObjectPathDescription()");
        return "";
    }
}

Example 15 with ReactionRule

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

the class IssueTableModel method getSourceObjectDescription.

private String getSourceObjectDescription(VCDocument vcDocument, Issue issue) {
    if (vcDocument instanceof BioModel) {
        Object object = issue.getSource();
        {
            DecoratedIssueSource dis = BeanUtils.downcast(DecoratedIssueSource.class, object);
            if (dis != null) {
                return dis.getSourcePath();
            }
        }
        String description = "";
        if (object instanceof SymbolTableEntry) {
            description = ((SymbolTableEntry) object).getName();
        } else if (object instanceof ReactionStep) {
            description = ((ReactionStep) object).getName();
        } else if (object instanceof ReactionRule) {
            description = ((ReactionRule) object).getName();
        } else if (object instanceof SpeciesPattern) {
            // Object parent = issue.getIssueContext().getContextObject();
            // if (parent instanceof SpeciesContext){
            // description = ((SpeciesContext)parent).getName();
            // }
            // if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
            // SpeciesContext thing = (SpeciesContext)issue.getIssueContext().getContextObject(ContextType.SpeciesContext);
            // description = thing.getName();
            // }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
            // ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
            // description = thing.getName();
            // }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
            // RbmObservable thing = (RbmObservable)issue.getIssueContext().getContextObject(ContextType.RbmObservable);
            // description = thing.getName();
            // } else {
            System.err.println("Bad issue context for " + ((SpeciesPattern) object).toString());
            description = ((SpeciesPattern) object).toString();
        // }
        } else if (object instanceof MolecularType) {
            description = ((MolecularType) object).getName();
        } else if (object instanceof MolecularComponent) {
            description = ((MolecularComponent) object).getName();
        } else if (object instanceof ComponentStateDefinition) {
            description = ((ComponentStateDefinition) object).getName();
        } else if (object instanceof Structure) {
            description = ((Structure) object).getName();
        } else if (object instanceof SubDomain) {
            description = ((SubDomain) object).getName();
        } else if (object instanceof Geometry) {
            description = ((Geometry) object).getName();
        } else if (object instanceof StructureMapping) {
            description = ((StructureMapping) object).getStructure().getName();
        } else if (object instanceof OutputFunctionIssueSource) {
            description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
        } else if (object instanceof UnmappedGeometryClass) {
            description = ((UnmappedGeometryClass) object).getGeometryClass().getName();
        } else if (object instanceof MicroscopeMeasurement) {
            description = ((MicroscopeMeasurement) object).getName();
        } else if (object instanceof SpatialObject) {
            description = ((SpatialObject) object).getName();
        } else if (object instanceof SpatialProcess) {
            description = ((SpatialProcess) object).getName();
        } else if (object instanceof GeometryContext) {
            description = "Geometry";
        } else if (object instanceof ModelOptimizationSpec) {
            description = ((ModelOptimizationSpec) object).getParameterEstimationTask().getName();
        } else if (object instanceof Simulation) {
            description = ((Simulation) object).getName();
        } else if (object instanceof SpeciesContextSpec) {
            SpeciesContextSpec scs = (SpeciesContextSpec) object;
            description = scs.getSpeciesContext().getName();
        } else if (object instanceof ReactionCombo) {
            ReactionSpec rs = ((ReactionCombo) object).getReactionSpec();
            description = rs.getReactionStep().getName();
        } else if (object instanceof RbmModelContainer) {
            // RbmModelContainer mc = (RbmModelContainer)object;
            description = "Rules validator";
        } else if (object instanceof SimulationContext) {
            SimulationContext sc = (SimulationContext) object;
            description = sc.getName();
        } else if (object instanceof Model) {
            Model m = (Model) object;
            description = m.getName();
        } else if (object instanceof BioEvent) {
            return ((BioEvent) object).getName() + "";
        } else if (object instanceof MathDescription) {
            return ((MathDescription) object).getName() + "";
        } else {
            System.err.println("unknown object type in IssueTableModel.getSourceObjectDescription(): " + object.getClass());
        }
        return description;
    } else if (vcDocument instanceof MathModel) {
        Object object = issue.getSource();
        String description = "";
        if (object instanceof Variable) {
            description = ((Variable) object).getName();
        } else if (object instanceof SubDomain) {
            description = ((SubDomain) object).getName();
        } else if (object instanceof Geometry) {
            description = "Geometry";
        } else if (object instanceof OutputFunctionIssueSource) {
            description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
        } else if (object instanceof MathDescription) {
            return "math";
        } else if (object instanceof Simulation) {
            return "Simulation " + ((Simulation) object).getName() + "";
        }
        return description;
    } else {
        System.err.println("unknown document type in IssueTableModel.getSourceObjectDescription()");
        return "";
    }
}