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

Example 31 with Structure

use of cbit.vcell.model.Structure 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 32 with Structure

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

the class StructureMappingCartoon method refreshAll.

@Override
public void refreshAll() {
    {
        if (getGeometryContext() == null || getGeometryContext().getGeometry() == null) {
            return;
        }
        GeometryClass[] geometryClasses = getGeometryContext().getGeometry().getGeometryClasses();
        if (geometryClasses == null) {
            return;
        }
        for (int i = 0; i < geometryClasses.length; i++) {
            Shape testShape = getShapeFromModelObject(geometryClasses[i]);
            if (testShape instanceof GeometryClassLegendShape) {
                geometryClasses[i].removePropertyChangeListener((GeometryClassLegendShape) testShape);
            }
        }
    }
    clearAllShapes();
    if (getSimulationContext() == null) {
        fireGraphChanged(new GraphEvent(this));
        return;
    }
    GeometryContextGeometryShape geometryShape = new GeometryContextGeometryShape(this, getGeometryContext().getGeometry());
    GeometryContextStructureShape structureContainerShape = new GeometryContextStructureShape(this, getGeometryContext().getModel());
    GeometryContextContainerShape containerShape = new GeometryContextContainerShape(this, getGeometryContext(), structureContainerShape, geometryShape);
    addShape(containerShape);
    addShape(geometryShape);
    addShape(structureContainerShape);
    getGeometryContext().removePropertyChangeListener(this);
    getGeometryContext().addPropertyChangeListener(this);
    // create all StructureShapes
    Structure[] structures = getGeometryContext().getModel().getStructures();
    for (int i = 0; i < structures.length; i++) {
        StructureMappingStructureShape smShape = new StructureMappingStructureShape((Structure) structures[i], getGeometryContext().getModel(), this);
        addShape(smShape);
        structureContainerShape.addChildShape(smShape);
        structures[i].removePropertyChangeListener(this);
        structures[i].addPropertyChangeListener(this);
    }
    // create all SubvolumeLegendShapes (for legend)
    GeometryClass[] geometryClasses = getGeometryContext().getGeometry().getGeometryClasses();
    for (int i = 0; i < geometryClasses.length; i++) {
        GeometryClassLegendShape geometryClassLegendShape = new GeometryClassLegendShape(geometryClasses[i], getGeometryContext().getGeometry(), this, 10);
        geometryClasses[i].addPropertyChangeListener(geometryClassLegendShape);
        addShape(geometryClassLegendShape);
        geometryShape.addChildShape(geometryClassLegendShape);
    }
    if ((subVolumeContainerShape == null) || (subVolumeContainerShape.getModelObject() != getGeometryContext().getGeometry())) {
        subVolumeContainerShape = new SubVolumeContainerShape(getGeometryContext().getGeometry(), this);
    }
    subVolumeContainerShape.removeAllChildren();
    subVolumeContainerShape.setBrightImage(getGeometryContext().getGeometry().getGeometrySpec().getThumbnailImage().getCurrentValue());
    addShape(subVolumeContainerShape);
    geometryShape.addChildShape(subVolumeContainerShape);
    StructureMapping[] structureMappings = getGeometryContext().getStructureMappings();
    for (int i = 0; i < structureMappings.length; i++) {
        StructureMapping structureMapping = structureMappings[i];
        structureMapping.removePropertyChangeListener(this);
        structureMapping.addPropertyChangeListener(this);
        if (structureMapping.getGeometryClass() != null) {
            StructureShape sShape = (StructureShape) getShapeFromModelObject(structureMapping.getStructure());
            GeometryClassLegendShape geometryClassLegendShape = (GeometryClassLegendShape) getShapeFromModelObject(structureMapping.getGeometryClass());
            StructureMappingShape smShape = new StructureMappingShape(structureMapping, sShape, geometryClassLegendShape, this);
            addShape(smShape);
            containerShape.addChildShape(smShape);
        }
    }
    // // assign children to shapes according to heirarchy in Model
    // int nullParentCount=0;
    // Collection<Shape> shapes = getShapes();
    // for(Shape shape : shapes) {
    // // for each featureShape, find corresponding featureShape
    // if (shape instanceof StructureShape){
    // StructureShape fs = (FeatureShape)shape;
    // if(!structureContainerShape.contains(fs)) {
    // structureContainerShape.addChildShape(fs);
    // }
    // nullParentCount++;
    // }
    // }
    fireGraphChanged(new GraphEvent(this));
}

Example 33 with Structure

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

the class AllStructureSuite method getStructures.

public List<Structure> getStructures() {
    if (bModelStructureOrder) {
        ArrayList<Structure> modelStructures = new ArrayList<Structure>();
        Diagram[] modelDiagrams = modelOwner.getModel().getDiagrams();
        for (Diagram diagram : modelDiagrams) {
            modelStructures.add(diagram.getStructure());
        }
        return modelStructures;
    }
    return Arrays.asList(StructureSorter.sortStructures(modelOwner.getModel()));
}

Example 34 with Structure

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

the class AbstractMathMapping method getDefaultGeometryClass.

protected GeometryClass getDefaultGeometryClass(Expression expr) throws ExpressionException, MappingException {
    GeometryClass geometryClass = null;
    if (simContext.getGeometry().getDimension() == 0) {
        return null;
    }
    String[] symbols = expr.getSymbols();
    // if expr has no symbols, model param cannot be localized to a domain (its a const).
    if (symbols == null) {
        return null;
    } else {
        Expression modelParamExpr = substituteGlobalParameters(expr);
        symbols = modelParamExpr.getSymbols();
        for (int k = 0; symbols != null && k < symbols.length; k++) {
            Structure symbolStructure = null;
            SymbolTableEntry ste = modelParamExpr.getSymbolBinding(symbols[k]);
            if (ste instanceof SpeciesContext) {
                symbolStructure = ((SpeciesContext) ste).getStructure();
            } else if (ste instanceof StructureSize) {
                symbolStructure = ((StructureSize) ste).getStructure();
            } else if (ste instanceof MembraneVoltage) {
                symbolStructure = ((MembraneVoltage) ste).getMembrane();
            }
            if (symbolStructure != null) {
                StructureMapping sm = simContext.getGeometryContext().getStructureMapping(symbolStructure);
                GeometryClass symbolGeomClass = sm.getGeometryClass();
                if (geometryClass == null) {
                    geometryClass = symbolGeomClass;
                } else {
                    if (geometryClass != symbolGeomClass) {
                        if (geometryClass instanceof SurfaceClass) {
                            if (symbolGeomClass instanceof SurfaceClass) {
                                throw new MappingException("The expression '" + expr.infix() + "' references variables in surface domain '" + geometryClass.getName() + "' & surface domain '" + symbolGeomClass.getName() + "' that cannot be evaluated.");
                            } else if (symbolGeomClass instanceof SubVolume) {
                                // geomClass : surfaceClass; symbolGeomClass : subVol
                                if (!((SurfaceClass) geometryClass).isAdjacentTo((SubVolume) symbolGeomClass)) {
                                    throw new MappingException("The expression '" + expr.infix() + "' references variables in surface domain '" + geometryClass.getName() + "' & volume domain '" + symbolGeomClass.getName() + "' that cannot be evaluated.");
                                }
                            } else {
                                throw new MappingException("unexpected geometry class : " + symbolGeomClass.getClass());
                            }
                        } else if (geometryClass instanceof SubVolume) {
                            // geometryClass is a SubVolume
                            if (symbolGeomClass instanceof SubVolume) {
                                // check if adjacent; if so, choose separating membrane.
                                SurfaceClass surfaceClass = simContext.getGeometry().getGeometrySurfaceDescription().getSurfaceClass((SubVolume) symbolGeomClass, (SubVolume) geometryClass);
                                if (surfaceClass != null) {
                                    geometryClass = surfaceClass;
                                } else {
                                    throw new MappingException("The expression '" + expr.infix() + "' references variables in volume domain '" + geometryClass.getName() + "' & volume domain '" + symbolGeomClass.getName() + "' that cannot be evaluated.");
                                }
                            } else {
                                // geomClass : subVol; symbolGeomClass = surfaceClass
                                SurfaceClass surfaceSymbolGeomClass = (SurfaceClass) symbolGeomClass;
                                if (!surfaceSymbolGeomClass.isAdjacentTo((SubVolume) geometryClass)) {
                                    throw new MappingException("The expression '" + expr.infix() + "' references variables in surface domain '" + surfaceSymbolGeomClass.getName() + "' & volume domain '" + geometryClass.getName() + "' that cannot be evaluated.");
                                } else {
                                    geometryClass = symbolGeomClass;
                                }
                            }
                        } else {
                            throw new MappingException("unexpected geometry class : " + geometryClass.getClass());
                        }
                    }
                }
            }
        }
    }
    return geometryClass;
}

Example 35 with Structure

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

the class DiffEquMathMapping method computeBoundaryConditionSource.

// determine membrane inside and outside subvolume
public static Pair<SubVolume, SubVolume> computeBoundaryConditionSource(Model model, SimulationContext simContext, SurfaceClass surfaceClass) {
    SubVolume outerSubVolume = null;
    SubVolume innerSubVolume = null;
    Structure[] mappedStructures = simContext.getGeometryContext().getStructuresFromGeometryClass(surfaceClass);
    // inside and outside correspond to structure hierarchy when present
    for (Structure s : mappedStructures) {
        if (s instanceof Membrane) {
            Membrane m = (Membrane) s;
            Feature infeature = model.getStructureTopology().getInsideFeature(m);
            if (infeature != null) {
                FeatureMapping insm = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(infeature);
                if (insm.getGeometryClass() instanceof SubVolume) {
                    innerSubVolume = (SubVolume) insm.getGeometryClass();
                }
            }
            Feature outfeature = model.getStructureTopology().getOutsideFeature(m);
            if (outfeature != null) {
                FeatureMapping outsm = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(outfeature);
                if (outsm.getGeometryClass() instanceof SubVolume) {
                    outerSubVolume = (SubVolume) outsm.getGeometryClass();
                }
            }
        }
    }
    // make the choice deterministic
    if (innerSubVolume == null || outerSubVolume == null || innerSubVolume == outerSubVolume) {
        Set<SubVolume> sv = surfaceClass.getAdjacentSubvolumes();
        Iterator<SubVolume> iterator = sv.iterator();
        innerSubVolume = iterator.next();
        outerSubVolume = iterator.next();
        if (innerSubVolume.getName().compareTo(outerSubVolume.getName()) > 0) {
            SubVolume temp = innerSubVolume;
            innerSubVolume = outerSubVolume;
            outerSubVolume = temp;
        }
    }
    Pair<SubVolume, SubVolume> ret = new Pair<>(innerSubVolume, outerSubVolume);
    return ret;
}