Examples with SimpleBounds cbit.vcell.constraints.SimpleBounds used on opensource projects

Example 1 with SimpleBounds

use of cbit.vcell.constraints.SimpleBounds in project vcell by virtualcell.

the class ConstraintsGraphModel method setConstraintContainerImpl.

public void setConstraintContainerImpl(ConstraintContainerImpl constraintContainerImpl) {
    ConstraintContainerImpl oldValue = fieldConstraintContainerImpl;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(this);
        GeneralConstraint[] oldConstraints = oldValue.getGeneralConstraints();
        for (int i = 0; i < oldConstraints.length; i++) {
            oldConstraints[i].removePropertyChangeListener(this);
        }
        SimpleBounds[] oldSimpleBounds = oldValue.getSimpleBounds();
        for (int i = 0; i < oldSimpleBounds.length; i++) {
            oldSimpleBounds[i].removePropertyChangeListener(this);
        }
    }
    fieldConstraintContainerImpl = constraintContainerImpl;
    if (fieldConstraintContainerImpl != null) {
        fieldConstraintContainerImpl.addPropertyChangeListener(this);
        GeneralConstraint[] newConstraints = fieldConstraintContainerImpl.getGeneralConstraints();
        for (int i = 0; i < newConstraints.length; i++) {
            newConstraints[i].addPropertyChangeListener(this);
        }
        SimpleBounds[] newSimpleBounds = fieldConstraintContainerImpl.getSimpleBounds();
        for (int i = 0; i < newSimpleBounds.length; i++) {
            newSimpleBounds[i].addPropertyChangeListener(this);
        }
    }
    firePropertyChange("constraintContainerImpl", oldValue, constraintContainerImpl);
    refreshAll();
}

Example 2 with SimpleBounds

use of cbit.vcell.constraints.SimpleBounds in project vcell by virtualcell.

the class ConstraintsGraphModel method refreshAll.

public void refreshAll() {
    Set<Shape> unwantedShapes = new HashSet<Shape>();
    unwantedShapes.addAll(getShapes());
    for (Shape shape : getShapes()) {
        if (shape instanceof ConstraintVarNode) {
            ((ConstraintVarNode) shape).setDegree(1);
        }
    }
    ContainerShape containerShape = (ContainerShape) getShapeFromModelObject(getConstraintContainerImpl());
    if (containerShape == null) {
        containerShape = new SimpleContainerShape(getConstraintContainerImpl(), this, "constraint network");
        containerShape.setLabel("constraint network");
        addShape(containerShape);
    }
    containerShape.refreshLabel();
    unwantedShapes.remove(containerShape);
    // 
    // add nodes for GeneralConstraints and edges to its Variables (add Variable when necessary)
    // 
    GeneralConstraint[] generalConstraints = getConstraintContainerImpl().getGeneralConstraints();
    for (int i = 0; i < generalConstraints.length; i++) {
        String[] symbols = generalConstraints[i].getExpression().getSymbols();
        if (symbols == null) {
            continue;
        }
        GeneralConstraintNode generalConstraintNode = (GeneralConstraintNode) getShapeFromModelObject(generalConstraints[i]);
        if (generalConstraintNode == null) {
            generalConstraintNode = new GeneralConstraintNode(generalConstraints[i], this, symbols.length);
            containerShape.addChildShape(generalConstraintNode);
            addShape(generalConstraintNode);
        }
        generalConstraintNode.refreshLabel();
        unwantedShapes.remove(generalConstraintNode);
        for (int j = 0; j < symbols.length; j++) {
            ConstraintVarNode constraintVarNode = (ConstraintVarNode) getShapeFromLabel(symbols[j]);
            if (constraintVarNode == null) {
                constraintVarNode = new ConstraintVarNode(symbols[j], this, 1);
                containerShape.addChildShape(constraintVarNode);
                addShape(constraintVarNode);
            } else {
                constraintVarNode.setDegree(constraintVarNode.getDegree() + 1);
            }
            constraintVarNode.refreshLabel();
            unwantedShapes.remove(constraintVarNode);
            ConstraintDependencyEdgeShape constraintDependencyEdgeShape = null;
            for (Shape shape : getShapes()) {
                if (shape instanceof ConstraintDependencyEdgeShape) {
                    if (((ConstraintDependencyEdgeShape) shape).getConstraintShape() == generalConstraintNode && ((ConstraintDependencyEdgeShape) shape).getVarShape() == constraintVarNode) {
                        constraintDependencyEdgeShape = (ConstraintDependencyEdgeShape) shape;
                    }
                }
            }
            if (constraintDependencyEdgeShape == null) {
                constraintDependencyEdgeShape = new ConstraintDependencyEdgeShape(generalConstraintNode, constraintVarNode, this);
                containerShape.addChildShape(constraintDependencyEdgeShape);
                addShape(constraintDependencyEdgeShape);
            }
            unwantedShapes.remove(constraintDependencyEdgeShape);
        }
    }
    // 
    // add nodes for SimpleBounds and edges to its Variables (add Variable when necessary)
    // 
    cbit.vcell.constraints.SimpleBounds[] simpleBounds = getConstraintContainerImpl().getSimpleBounds();
    for (int i = 0; i < simpleBounds.length; i++) {
        BoundsNode boundsNode = (BoundsNode) getShapeFromModelObject(simpleBounds[i]);
        if (boundsNode == null) {
            boundsNode = new BoundsNode(simpleBounds[i], this);
            containerShape.addChildShape(boundsNode);
            addShape(boundsNode);
        }
        boundsNode.refreshLabel();
        unwantedShapes.remove(boundsNode);
        ConstraintVarNode constraintVarNode = (ConstraintVarNode) getShapeFromLabel(simpleBounds[i].getIdentifier());
        if (constraintVarNode == null) {
            constraintVarNode = new ConstraintVarNode(simpleBounds[i].getIdentifier(), this, 1);
            containerShape.addChildShape(constraintVarNode);
            addShape(constraintVarNode);
        } else {
            constraintVarNode.setDegree(constraintVarNode.getDegree() + 1);
        }
        constraintVarNode.refreshLabel();
        unwantedShapes.remove(constraintVarNode);
        ConstraintDependencyEdgeShape constraintDependencyEdgeShape = null;
        for (Shape shape : getShapes()) {
            if (shape instanceof ConstraintDependencyEdgeShape) {
                if (((ConstraintDependencyEdgeShape) shape).getConstraintShape() == boundsNode && ((ConstraintDependencyEdgeShape) shape).getVarShape() == constraintVarNode) {
                    constraintDependencyEdgeShape = (ConstraintDependencyEdgeShape) shape;
                }
            }
        }
        if (constraintDependencyEdgeShape == null) {
            constraintDependencyEdgeShape = new ConstraintDependencyEdgeShape(boundsNode, constraintVarNode, this);
            containerShape.addChildShape(constraintDependencyEdgeShape);
            addShape(constraintDependencyEdgeShape);
        }
        constraintDependencyEdgeShape.refreshLabel();
        unwantedShapes.remove(constraintDependencyEdgeShape);
    }
    for (Shape unwantedShape : unwantedShapes) {
        removeShape(unwantedShape);
    }
    fireGraphChanged(new GraphEvent(this));
}

Example 3 with SimpleBounds

use of cbit.vcell.constraints.SimpleBounds in project vcell by virtualcell.

the class ConstraintSolverTableModel method setConstraintSolver.

/**
 * Sets the constraintContainerImpl property (cbit.vcell.constraints.ConstraintContainerImpl) value.
 * @param constraintContainerImpl The new value for the property.
 * @see #getConstraintContainerImpl
 */
public void setConstraintSolver(ConstraintSolver constraintSolver) {
    ConstraintSolver oldValue = fieldConstraintSolver;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(this);
        if (oldValue.getConstraintContainerImpl() != null) {
            oldValue.getConstraintContainerImpl().removePropertyChangeListener(this);
            SimpleBounds[] oldSimpleBounds = oldValue.getConstraintContainerImpl().getSimpleBounds();
            for (int i = 0; i < oldSimpleBounds.length; i++) {
                oldSimpleBounds[i].removePropertyChangeListener(this);
            }
        }
    }
    fieldConstraintSolver = constraintSolver;
    firePropertyChange("constraintSolver", oldValue, constraintSolver);
    if (constraintSolver != null) {
        constraintSolver.addPropertyChangeListener(this);
        if (constraintSolver.getConstraintContainerImpl() != null) {
            constraintSolver.getConstraintContainerImpl().addPropertyChangeListener(this);
            SimpleBounds[] newSimpleBounds = constraintSolver.getConstraintContainerImpl().getSimpleBounds();
            for (int i = 0; i < newSimpleBounds.length; i++) {
                newSimpleBounds[i].removePropertyChangeListener(this);
            }
        }
    }
}

Example 4 with SimpleBounds

use of cbit.vcell.constraints.SimpleBounds in project vcell by virtualcell.

the class SimpleBoundsTableModel method setConstraintContainerImpl.

/**
 * Sets the constraintContainerImpl property (cbit.vcell.constraints.ConstraintContainerImpl) value.
 * @param constraintContainerImpl The new value for the property.
 * @see #getConstraintContainerImpl
 */
public void setConstraintContainerImpl(ConstraintContainerImpl constraintContainerImpl) {
    ConstraintContainerImpl oldValue = fieldConstraintContainerImpl;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(this);
        SimpleBounds[] oldBounds = oldValue.getSimpleBounds();
        for (int i = 0; i < oldBounds.length; i++) {
            oldBounds[i].removePropertyChangeListener(this);
        }
    }
    fieldConstraintContainerImpl = constraintContainerImpl;
    firePropertyChange("constraintContainerImpl", oldValue, constraintContainerImpl);
    if (constraintContainerImpl != null) {
        constraintContainerImpl.addPropertyChangeListener(this);
        SimpleBounds[] newBounds = constraintContainerImpl.getSimpleBounds();
        for (int i = 0; i < newBounds.length; i++) {
            newBounds[i].addPropertyChangeListener(this);
        }
    }
}

Example 5 with SimpleBounds

use of cbit.vcell.constraints.SimpleBounds in project vcell by virtualcell.

the class ApplicationConstraintsGenerator method steadyStateFromApplication.

/**
 * Insert the method's description here.
 * Creation date: (6/26/01 8:25:55 AM)
 * @return cbit.vcell.constraints.ConstraintContainerImpl
 */
public static ConstraintContainerImpl steadyStateFromApplication(SimulationContext simContext, double tolerance) {
    try {
        ConstraintContainerImpl ccImpl = new ConstraintContainerImpl();
        // ====================
        // add physical limits
        // ====================
        // 
        // no negative concentrations
        // 
        cbit.vcell.model.Model model = simContext.getModel();
        cbit.vcell.model.SpeciesContext[] speciesContexts = model.getSpeciesContexts();
        for (int i = 0; i < speciesContexts.length; i++) {
            ccImpl.addSimpleBound(new SimpleBounds(speciesContexts[i].getName(), new RealInterval(0, Double.POSITIVE_INFINITY), AbstractConstraint.PHYSICAL_LIMIT, "non-negative concentration"));
        }
        for (int i = 0; i < speciesContexts.length; i++) {
            SpeciesContextSpecParameter initParam = (simContext.getReactionContext().getSpeciesContextSpec(speciesContexts[i])).getInitialConditionParameter();
            if (initParam != null) {
                double initialValue = initParam.getExpression().evaluateConstant();
                double lowInitialValue = Math.min(initialValue / tolerance, initialValue * tolerance);
                double highInitialValue = Math.max(initialValue / tolerance, initialValue * tolerance);
                ccImpl.addSimpleBound(new SimpleBounds(speciesContexts[i].getName(), new RealInterval(lowInitialValue, highInitialValue), AbstractConstraint.MODELING_ASSUMPTION, "close to specified \"initialCondition\""));
            }
        }
        // =========================
        // add modeling assumptions
        // =========================
        // 
        // mass action forward and reverse rates should be non-negative
        // 
        cbit.vcell.model.ReactionStep[] reactionSteps = model.getReactionSteps();
        for (int i = 0; i < reactionSteps.length; i++) {
            Kinetics kinetics = reactionSteps[i].getKinetics();
            if (kinetics instanceof MassActionKinetics) {
                Expression forwardRateConstraintExp = new Expression(((MassActionKinetics) kinetics).getForwardRateParameter().getExpression().infix() + ">=0");
                forwardRateConstraintExp = getSteadyStateExpression(forwardRateConstraintExp);
                if (!forwardRateConstraintExp.compareEqual(new Expression(1.0))) {
                    ccImpl.addGeneralConstraint(new GeneralConstraint(forwardRateConstraintExp, AbstractConstraint.MODELING_ASSUMPTION, "non-negative forward rate"));
                }
                Expression reverseRateConstraintExp = new Expression(((MassActionKinetics) kinetics).getReverseRateParameter().getExpression().infix() + ">=0");
                reverseRateConstraintExp = getSteadyStateExpression(reverseRateConstraintExp);
                if (!reverseRateConstraintExp.compareEqual(new Expression(1.0))) {
                    ccImpl.addGeneralConstraint(new GeneralConstraint(reverseRateConstraintExp, AbstractConstraint.MODELING_ASSUMPTION, "non-negative reverse rate"));
                }
            }
            KineticsParameter authoritativeParameter = kinetics.getAuthoritativeParameter();
            Expression kineticRateConstraintExp = new Expression(authoritativeParameter.getName() + "==" + authoritativeParameter.getExpression().infix());
            kineticRateConstraintExp = getSteadyStateExpression(kineticRateConstraintExp);
            if (!kineticRateConstraintExp.compareEqual(new Expression(1.0))) {
                ccImpl.addGeneralConstraint(new GeneralConstraint(kineticRateConstraintExp, AbstractConstraint.MODELING_ASSUMPTION, "definition"));
            }
        }
        // 
        try {
            simContext.setMathDescription(simContext.createNewMathMapping().getMathDescription());
        } catch (Throwable e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("cannot create mathDescription");
        }
        MathDescription mathDesc = simContext.getMathDescription();
        if (mathDesc.getGeometry().getDimension() > 0) {
            throw new RuntimeException("spatial simulations not yet supported");
        }
        CompartmentSubDomain subDomain = (CompartmentSubDomain) mathDesc.getSubDomains().nextElement();
        java.util.Enumeration<Equation> enumEquations = subDomain.getEquations();
        while (enumEquations.hasMoreElements()) {
            Equation equation = (Equation) enumEquations.nextElement();
            Expression rateConstraintExp = new Expression(equation.getRateExpression().infix() + "==0");
            rateConstraintExp = getSteadyStateExpression(rateConstraintExp);
            if (!rateConstraintExp.compareEqual(new Expression(1.0))) {
                // not a trivial constraint (always true)
                ccImpl.addGeneralConstraint(new GeneralConstraint(rateConstraintExp, AbstractConstraint.PHYSICAL_LIMIT, "definition of steady state"));
            }
        }
        // 
        for (int i = 0; i < reactionSteps.length; i++) {
            Kinetics kinetics = reactionSteps[i].getKinetics();
            Kinetics.KineticsParameter[] parameters = kinetics.getKineticsParameters();
            for (int j = 0; j < parameters.length; j++) {
                Expression exp = parameters[j].getExpression();
                if (exp.getSymbols() == null || exp.getSymbols().length == 0) {
                    // 
                    try {
                        double constantValue = exp.evaluateConstant();
                        double lowValue = Math.min(constantValue / tolerance, constantValue * tolerance);
                        double highValue = Math.max(constantValue / tolerance, constantValue * tolerance);
                        RealInterval interval = new RealInterval(lowValue, highValue);
                        ccImpl.addSimpleBound(new SimpleBounds(parameters[j].getName(), interval, AbstractConstraint.MODELING_ASSUMPTION, "parameter close to model default"));
                    } catch (cbit.vcell.parser.ExpressionException e) {
                        System.out.println("error evaluating parameter " + parameters[j].getName() + " in reaction step " + reactionSteps[i].getName());
                    }
                } else {
                    Expression parameterDefinitionExp = new Expression(parameters[j].getName() + "==" + parameters[j].getExpression().infix());
                    ccImpl.addGeneralConstraint(new GeneralConstraint(getSteadyStateExpression(parameterDefinitionExp), AbstractConstraint.MODELING_ASSUMPTION, "parameter definition"));
                }
            }
        }
        ccImpl.addSimpleBound(new SimpleBounds(model.getFARADAY_CONSTANT().getName(), new RealInterval(model.getFARADAY_CONSTANT().getExpression().evaluateConstant()), AbstractConstraint.PHYSICAL_LIMIT, "Faraday's constant"));
        ccImpl.addSimpleBound(new SimpleBounds(model.getTEMPERATURE().getName(), new RealInterval(300), AbstractConstraint.PHYSICAL_LIMIT, "Absolute Temperature Kelvin"));
        ccImpl.addSimpleBound(new SimpleBounds(model.getGAS_CONSTANT().getName(), new RealInterval(model.getGAS_CONSTANT().getExpression().evaluateConstant()), AbstractConstraint.PHYSICAL_LIMIT, "ideal gas constant"));
        ccImpl.addSimpleBound(new SimpleBounds(model.getKMILLIVOLTS().getName(), new RealInterval(model.getKMILLIVOLTS().getExpression().evaluateConstant()), AbstractConstraint.PHYSICAL_LIMIT, "ideal gas constant"));
        // 
        // add K_fluxs
        // 
        java.util.Enumeration<Variable> enumVars = mathDesc.getVariables();
        while (enumVars.hasMoreElements()) {
            Variable var = (Variable) enumVars.nextElement();
            if (var.getName().startsWith("Kflux_") && var instanceof Function) {
                Expression kfluxExp = new Expression(((Function) var).getExpression());
                kfluxExp.bindExpression(mathDesc);
                kfluxExp = MathUtilities.substituteFunctions(kfluxExp, mathDesc);
                kfluxExp = kfluxExp.flatten();
                ccImpl.addSimpleBound(new SimpleBounds(var.getName(), new RealInterval(kfluxExp.evaluateConstant()), AbstractConstraint.MODELING_ASSUMPTION, "flux conversion factor"));
            }
        }
        return ccImpl;
    } catch (cbit.vcell.parser.ExpressionException e) {
        e.printStackTrace(System.out);
        return null;
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        return null;
    }
}