Examples with RbmModelContainer cbit.vcell.model.Model.RbmModelContainer used on opensource projects

Example 6 with RbmModelContainer

use of cbit.vcell.model.Model.RbmModelContainer in project vcell by virtualcell.

the class XmlReader method getRbmObservableList.

// private void getRbmSeedSpeciesList(Element param, Model newModel) {
// RbmModelContainer mc = newModel.getRbmModelContainer();
// List<SeedSpecies> ssl = mc.getSeedSpeciesList();
// List<Element> children = param.getChildren(XMLTags.RbmSeedSpeciesTag, vcNamespace);
// for (Element element : children) {
// SeedSpecies s = getRbmSeedSpecies(element, newModel);
// if(s != null) { ssl.add(s); }
// }
// }
private void getRbmObservableList(Element param, Model newModel) throws ModelException, PropertyVetoException {
    RbmModelContainer mc = newModel.getRbmModelContainer();
    List<Element> children = new ArrayList<Element>();
    children = param.getChildren(XMLTags.RbmObservableTag, vcNamespace);
    for (Element element : children) {
        RbmObservable o = getRbmObservables(element, newModel);
        if (o != null) {
            mc.addObservable(o);
        }
    }
}

Example 7 with RbmModelContainer

use of cbit.vcell.model.Model.RbmModelContainer in project vcell by virtualcell.

the class XmlReader method getRbmMolecularTypeList.

private void getRbmMolecularTypeList(Element param, Model newModel) {
    RbmModelContainer mc = newModel.getRbmModelContainer();
    List<MolecularType> mtl = mc.getMolecularTypeList();
    List<Element> children = param.getChildren(XMLTags.RbmMolecularTypeTag, vcNamespace);
    for (Element element : children) {
        MolecularType t = getRbmMolecularType(element, newModel);
        if (t != null) {
            mtl.add(t);
        }
    }
}

Example 8 with RbmModelContainer

use of cbit.vcell.model.Model.RbmModelContainer in project vcell by virtualcell.

the class RuleParticipantSignatureDiagramShape method paintSelf.

// TODO: Override ElipseShape::isInside()
// our shape here is rounded rectangle while IsInside thinks it's an ellipse, which means
// that clicking near the corners of a long shape (with many molecules) fails to select the shape
// TODO: the RoundRectangle2D contour below needs to be recalculated with updated width, using the
// species pattern in the RuleParticipantSignature
@Override
public void paintSelf(Graphics2D g, int absPosX, int absPosY) {
    if (!bVisible) {
        return;
    }
    // we reserve space for at least 1 molecule
    int numMolecules = Math.max(1, ruleParticipantSignature.getSpeciesPattern().getMolecularTypePatterns().size());
    width = leftmargin + circleDiameter + displacement * (numMolecules - 1) + 1;
    getSpaceManager().setSize(width, height);
    int shapeHeight = getSpaceManager().getSize().height;
    int shapeWidth = getSpaceManager().getSize().width;
    Graphics2D g2D = g;
    Paint oldPaint = g2D.getPaint();
    g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
    Color exterior;
    // draw the contour around the whole rule participant
    // no need to really draw it if the shapes of the molecules fill it perfectly, because it won't be visible anyway
    // however, the "isInside" function will need exactly this RoundRectangle2D to compute whether the point is inside the shape
    RoundRectangle2D contour = new RoundRectangle2D.Double(absPosX, absPosY, shapeWidth, shapeHeight, shapeHeight, shapeHeight);
    g2D.setPaint(isSelected() ? AbstractComponentShape.componentMediumPalePink : AbstractComponentShape.componentPaleGreen);
    g2D.fill(contour);
    exterior = isSelected() ? Color.red.darker().darker() : Color.darkGray;
    g.setColor(exterior);
    g2D.draw(contour);
    Model model = ((ReactionCartoon) graphModel).getModel();
    RbmModelContainer rbmmc = model.getRbmModelContainer();
    List<MolecularType> mtList = rbmmc.getMolecularTypeList();
    List<MolecularType> ruleSignatureMolecularTypes = ruleParticipantSignature.getMolecularTypes();
    // draw the molecules (they are properly drawn because we use the sp as it is in the associated RuleParticipantSignature object)
    for (int i = 0; i < ruleSignatureMolecularTypes.size(); i++) {
        double offsetx = leftmargin + i * displacement - 1.4;
        int offsety = getSpaceManager().getSize().height - circleDiameter - 2;
        Ellipse2D icon = new Ellipse2D.Double(absPosX + offsetx, absPosY + offsety, circleDiameter, circleDiameter);
        // int offsetx = leftmargin + i*displacement;
        // int offsety = 0;
        // Rectangle2D icon = new Rectangle2D.Double(absPosX + offsetx, absPosY + offsety, displacement, shapeHeight-1);
        MolecularType mt = ruleSignatureMolecularTypes.get(i);
        int index = mtList.indexOf(mt);
        index = index % 7;
        defaultBG = Color.lightGray;
        Color interior = Color.white;
        if (graphModel instanceof ReactionCartoonFull) {
            // take color from molecular type color selection
            defaultBG = MolecularTypeLargeShape.colorTable[index];
        }
        backgroundColor = defaultBG;
        // darkerBackground = backgroundColor.darker().darker();
        exterior = !isSelected() ? backgroundColor.darker().darker() : backgroundColor.darker();
        Color[] colors = { interior, exterior };
        g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
        Point2D center = new Point2D.Double(absPosX + offsetx + circleDiameter / 2, absPosY + offsety + circleDiameter / 2);
        float radius = circleDiameter * 0.5f;
        Point2D focus = new Point2D.Double(absPosX + offsetx + circleDiameter / 2 - 2, absPosY + offsety + circleDiameter / 2 - 2);
        float[] dist = { 0.1f, 1.0f };
        RadialGradientPaint p = new RadialGradientPaint(center, radius, focus, dist, colors, CycleMethod.NO_CYCLE);
        // Paint p = defaultBG.darker().darker();
        g2D.setPaint(p);
        g2D.fill(icon);
        g.setColor(forgroundColor);
        g2D.draw(icon);
    }
    // TODO: see if RefreshLabel below works properly, if it does make a similar call to refresh the width!!!
    if (getLabel() != null && getLabel().length() > 0) {
        if (isSelected()) {
            // clear background and outline to make selected label stand out
            Rectangle outlineRectangle = getLabelOutline(absPosX, absPosY);
            drawRaisedOutline(outlineRectangle.x, outlineRectangle.y, outlineRectangle.width, outlineRectangle.height, g, Color.white, forgroundColor, Color.gray);
        }
        if (bDisplayLabel || isSelected()) {
            g.setColor(forgroundColor);
            g.drawString((isSelected() || smallLabel == null ? getLabel() : smallLabel), (isSelected() || smallLabel == null ? getLabelPos().x : smallLabelPos.x) + absPosX, getLabelPos().y - 2 + absPosY);
        }
    }
    if (linkText != null && linkText != "") {
        ShapePaintUtil.paintLinkMark(g2D, this, Color.BLACK);
    }
    g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF);
    g2D.setPaint(oldPaint);
}

Example 9 with RbmModelContainer

use of cbit.vcell.model.Model.RbmModelContainer 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 10 with RbmModelContainer

use of cbit.vcell.model.Model.RbmModelContainer 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 "";
    }
}