Examples with KineticsParameter cbit.vcell.model.Kinetics.KineticsParameter used on opensource projects

Example 21 with KineticsParameter

use of cbit.vcell.model.Kinetics.KineticsParameter in project vcell by virtualcell.

the class KineticsTypeTemplatePanel method onSelectedObjectsChange.

@Override
protected void onSelectedObjectsChange(Object[] selectedObjects) {
    if (selectedObjects == null || selectedObjects.length != 1) {
        return;
    }
    if (selectedObjects[0] instanceof ReactionStep) {
        setReactionStep((ReactionStep) selectedObjects[0]);
    } else if (selectedObjects[0] instanceof ReactionSpec) {
        setReactionStep(((ReactionSpec) selectedObjects[0]).getReactionStep());
    } else if (selectedObjects[0] instanceof KineticsParameter) {
        KineticsParameter kineticsParameter = (KineticsParameter) selectedObjects[0];
        setReactionStep(kineticsParameter.getKinetics().getReactionStep());
        for (int i = 0; i < getParameterTableModel().getRowCount(); i++) {
            if (kineticsParameter == getParameterTableModel().getValueAt(i)) {
                getScrollPaneTable().setRowSelectionInterval(i, i);
                break;
            }
        }
    } else {
        setReactionStep(null);
    }
}

Example 22 with KineticsParameter

use of cbit.vcell.model.Kinetics.KineticsParameter in project vcell by virtualcell.

the class ParameterTableModel method setValueAt.

public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    Parameter parameter = getValueAt(rowIndex);
    // try {
    switch(columnIndex) {
        case COLUMN_NAME:
            {
                try {
                    if (aValue instanceof String) {
                        String newName = (String) aValue;
                        if (!parameter.getName().equals(newName)) {
                            if (parameter instanceof Kinetics.KineticsParameter) {
                                reactionStep.getKinetics().renameParameter(parameter.getName(), newName);
                            } else if (parameter instanceof Kinetics.KineticsProxyParameter) {
                                parameter.setName(newName);
                            }
                            fireTableRowsUpdated(rowIndex, rowIndex);
                        }
                    }
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter name:\n" + e.getMessage());
                } catch (java.beans.PropertyVetoException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter name:\n" + e.getMessage());
                }
                break;
            }
        case COLUMN_IS_GLOBAL:
            {
                if (aValue.equals(Boolean.FALSE)) {
                    // check box has been <unset> (<true> to <false>) : change param from global to local
                    if ((parameter instanceof KineticsProxyParameter) && ((((KineticsProxyParameter) parameter).getTarget() instanceof Model.ReservedSymbol) || (((KineticsProxyParameter) parameter).getTarget() instanceof SpeciesContext) || (((KineticsProxyParameter) parameter).getTarget() instanceof ModelQuantity))) {
                        PopupGenerator.showErrorDialog(ownerTable, "Parameter : \'" + parameter.getName() + "\' is a " + ((KineticsProxyParameter) parameter).getTarget().getClass() + " in the model; cannot convert it to a local kinetic parameter.");
                    } else {
                        try {
                            reactionStep.getKinetics().convertParameterType(parameter, false);
                        } catch (PropertyVetoException pve) {
                            pve.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, "Unable to convert parameter : \'" + parameter.getName() + "\' to local kinetics parameter : " + pve.getMessage());
                        } catch (ExpressionBindingException e) {
                            e.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, "Unable to convert parameter : \'" + parameter.getName() + "\' to local kinetics parameter : " + e.getMessage());
                        }
                    }
                } else {
                    // check box has been <set> (<false> to <true>) : change param from local to global
                    if ((parameter instanceof KineticsParameter) && (((KineticsParameter) parameter).getRole() != Kinetics.ROLE_UserDefined)) {
                        PopupGenerator.showErrorDialog(ownerTable, "Parameter : \'" + parameter.getName() + "\' is a pre-defined kinetics parameter (not user-defined); cannot convert it to a model level (global) parameter.");
                    } else {
                        ModelParameter mp = reactionStep.getKinetics().getReactionStep().getModel().getModelParameter(parameter.getName());
                        // model already had the model parameter 'param', but check if 'param' value is different from
                        // model parameter with same name. If it is, the local value will be overridden by global (model) param
                        // value, and user should be warned.
                        String choice = "Ok";
                        if (mp != null && !(mp.getExpression().compareEqual(parameter.getExpression()))) {
                            String msgStr = "Model already has a global parameter named : \'" + parameter.getName() + "\'; with value = \'" + mp.getExpression().infix() + "\'; This local parameter \'" + parameter.getName() + "\' with value = \'" + parameter.getExpression().infix() + "\' will be overridden by the global value. \nPress \'Ok' to override " + "local value with global value of \'" + parameter.getName() + "\'. \nPress \'Cancel\' to retain new local value.";
                            choice = PopupGenerator.showWarningDialog(ownerTable, msgStr, new String[] { "Ok", "Cancel" }, "Ok");
                        }
                        if (choice.equals("Ok")) {
                            try {
                                // Now 'parameter' is a local kinetic parameter. If it is not numeric, and if its expression
                                // contains other local kinetic parameters, warn user that 'parameter' cannot be promoted because
                                // of its expression containing other local parameters.
                                boolean bPromoteable = true;
                                if (!parameter.getExpression().isNumeric()) {
                                    String[] symbols = parameter.getExpression().getSymbols();
                                    for (int i = 0; i < symbols.length; i++) {
                                        if (reactionStep.getKinetics().getKineticsParameter(symbols[i]) != null) {
                                            PopupGenerator.showErrorDialog(ownerTable, "Parameter \'" + parameter.getName() + "\' contains other local kinetic parameters; Cannot convert it to global until the referenced parameters are global.");
                                            bPromoteable = false;
                                        }
                                    }
                                }
                                if (bPromoteable) {
                                    reactionStep.getKinetics().convertParameterType(parameter, true);
                                }
                            } catch (PropertyVetoException pve) {
                                pve.printStackTrace(System.out);
                                PopupGenerator.showErrorDialog(ownerTable, "Cannot convert parameter \'" + parameter.getName() + "\' to global parameter : " + pve.getMessage());
                            } catch (ExpressionBindingException e) {
                                e.printStackTrace(System.out);
                                PopupGenerator.showErrorDialog(ownerTable, "Cannot convert parameter \'" + parameter.getName() + "\' to global parameter : " + e.getMessage());
                            }
                        }
                    }
                }
                fireTableRowsUpdated(rowIndex, rowIndex);
                break;
            }
        case COLUMN_VALUE:
            {
                try {
                    if (aValue instanceof ScopedExpression) {
                        // }
                        throw new RuntimeException("unexpected value type ScopedExpression");
                    } else if (aValue instanceof String) {
                        String newExpressionString = (String) aValue;
                        if (parameter instanceof Kinetics.KineticsParameter) {
                            reactionStep.getKinetics().setParameterValue((Kinetics.KineticsParameter) parameter, new Expression(newExpressionString));
                        } else if (parameter instanceof Kinetics.KineticsProxyParameter) {
                            parameter.setExpression(new Expression(newExpressionString));
                        }
                    }
                    reactionStep.getKinetics().resolveUndefinedUnits();
                    fireTableRowsUpdated(rowIndex, rowIndex);
                } catch (java.beans.PropertyVetoException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error:\n" + e.getMessage());
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Expression error:\n" + e.getMessage());
                }
                break;
            }
        case COLUMN_UNITS:
            {
                try {
                    if (aValue instanceof String && parameter instanceof Kinetics.KineticsParameter && ((Kinetics.KineticsParameter) parameter).getRole() == Kinetics.ROLE_UserDefined) {
                        String newUnitString = (String) aValue;
                        Kinetics.KineticsParameter kineticsParm = (Kinetics.KineticsParameter) parameter;
                        ModelUnitSystem modelUnitSystem = reactionStep.getModel().getUnitSystem();
                        if (!kineticsParm.getUnitDefinition().getSymbol().equals(newUnitString)) {
                            kineticsParm.setUnitDefinition(modelUnitSystem.getInstance(newUnitString));
                            reactionStep.getKinetics().resolveUndefinedUnits();
                            fireTableRowsUpdated(rowIndex, rowIndex);
                        }
                    }
                } catch (VCUnitException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter unit:\n" + e.getMessage());
                }
                break;
            }
    }
// }catch (java.beans.PropertyVetoException e){
// e.printStackTrace(System.out);
// }
}

Example 23 with KineticsParameter

use of cbit.vcell.model.Kinetics.KineticsParameter in project vcell by virtualcell.

the class SymbolTableEntryTableCellRenderer method getTableCellRendererComponent.

public java.awt.Component getTableCellRendererComponent(javax.swing.JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
    super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
    if (value == null) {
        setText("unmapped");
        return this;
    }
    SymbolTableEntry ste = (SymbolTableEntry) value;
    if (ste instanceof Model.ReservedSymbol) {
        setText(ste.getName());
    } else if (ste instanceof SpeciesContext) {
        setText("[" + ste.getName() + "]");
    } else if (ste instanceof KineticsParameter) {
        setText(ste.getNameScope().getName() + ":" + ste.getName());
    } else if (ste instanceof ModelParameter) {
        setText(ste.getName());
    } else if (ste instanceof ReservedVariable) {
        setText(ste.getName());
    } else {
        setText(ste.getNameScope().getAbsoluteScopePrefix() + ste.getName());
    }
    // setToolTipText("Kinetic parameter \""+ste.getName()+"\" in reaction "+);
    return this;
}

Example 24 with KineticsParameter

use of cbit.vcell.model.Kinetics.KineticsParameter in project vcell by virtualcell.

the class MathMapping_4_8 method refreshLocalNameCount.

protected void refreshLocalNameCount() {
    localNameCountHash.clear();
    ReactionStep[] reactionSteps = simContext.getModel().getReactionSteps();
    for (int j = 0; j < reactionSteps.length; j++) {
        KineticsParameter[] params = reactionSteps[j].getKinetics().getKineticsParameters();
        for (KineticsParameter kp : params) {
            String name = kp.getName();
            if (localNameCountHash.containsKey(name)) {
                localNameCountHash.put(name, localNameCountHash.get(name) + 1);
            } else {
                localNameCountHash.put(name, 1);
            }
        }
    }
    SpeciesContext[] scs = simContext.getModel().getSpeciesContexts();
    for (SpeciesContext sc : scs) {
        String name = sc.getName();
        if (localNameCountHash.containsKey(name)) {
            localNameCountHash.put(name, localNameCountHash.get(name) + 1);
        } else {
            localNameCountHash.put(name, 1);
        }
    }
    Species[] ss = simContext.getModel().getSpecies();
    for (Species s : ss) {
        String name = s.getCommonName();
        if (localNameCountHash.containsKey(name)) {
            localNameCountHash.put(name, localNameCountHash.get(name) + 1);
        } else {
            localNameCountHash.put(name, 1);
        }
    }
    ModelParameter[] mps = simContext.getModel().getModelParameters();
    for (ModelParameter mp : mps) {
        String name = mp.getName();
        if (localNameCountHash.containsKey(name)) {
            localNameCountHash.put(name, localNameCountHash.get(name) + 1);
        } else {
            localNameCountHash.put(name, 1);
        }
    }
}

Example 25 with KineticsParameter

use of cbit.vcell.model.Kinetics.KineticsParameter in project vcell by virtualcell.

the class StochMathMapping_4_8 method getProbabilityRate.

/**
 * Get probability expression for the specific elementary reaction.
 * Input: ReactionStep, the reaction. isForwardDirection, if the elementary reaction is forward from the reactionstep.
 * Output: Expression. the probability expression.
 * Creation date: (9/14/2006 3:22:58 PM)
 */
Expression getProbabilityRate(ReactionStep rs, boolean isForwardDirection) throws MappingException {
    ReactionStep reactionStep = rs;
    Expression probExp = null;
    // get kinetics of the reaction step
    Kinetics kinetics = reactionStep.getKinetics();
    // to compose the rate constant expression e.g. Kf, Kr
    Expression rateConstantExpr = null;
    // to compose the stochastic variable(species) expression, e.g. s*(s-1)*(s-2)* speciesFactor.
    Expression rxnProbabilityExpr = null;
    // to compose the factor that the probability expression multiplies with, which convert the rate expression under stochastic context
    Expression factorExpr = null;
    // the structure where reaction happens
    StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(rs.getStructure());
    Model model = getSimulationContext().getModel();
    try {
        if (// forward reaction
        isForwardDirection) {
            // for HMMs, it's a bit complicated. Vmax/(Km+s)-->Vmax*Size_s/(Km*Size_s+Ns)
            if (kinetics.getKineticsDescription().equals(KineticsDescription.MassAction)) {
                KineticsParameter kfp = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KForward);
                rateConstantExpr = new Expression(kfp, getNameScope());
            // rateConstantExpr.bindExpression(this);
            }
            // get convert factor for rate constant( membrane:rateConstant*membrane_Size (factor is membrane_size), feature : rateConstant*(feature_size/KMole)(factor is feature_size/KMOLE)) )
            if (sm.getStructure() instanceof Membrane) {
                factorExpr = new Expression(sm.getStructure().getStructureSize(), getNameScope());
            } else {
                factorExpr = new Expression(sm.getStructure().getStructureSize(), getNameScope());
                Expression kmoleExpr = new Expression(1.0 / 602.0);
                factorExpr = Expression.mult(factorExpr, kmoleExpr);
            }
            // complete the probability expression by the reactants' stoichiometries if it is Mass Action rate law
            if (kinetics.getKineticsDescription().equals(KineticsDescription.MassAction)) {
                ReactionParticipant[] reacPart = reactionStep.getReactionParticipants();
                for (int i = 0; i < reacPart.length; i++) {
                    int stoichiometry = 0;
                    if (reacPart[i] instanceof Reactant) {
                        stoichiometry = ((Reactant) reacPart[i]).getStoichiometry();
                        // ******the following part is to form the s*(s-1)(s-2)..(s-stoi+1).portion of the probability rate.
                        StructureMapping reactSM = getSimulationContext().getGeometryContext().getStructureMapping(reacPart[i].getStructure());
                        // factor expression for species
                        Expression speciesFactor = null;
                        // convert speceis' unit from moles/liter to molecules.
                        if (reactSM.getStructure() instanceof Membrane) {
                            speciesFactor = Expression.invert(new Expression(reactSM.getStructure().getStructureSize(), getNameScope()));
                        } else {
                            Expression exp1 = new Expression(1.0 / 602.0);
                            Expression exp2 = new Expression(reactSM.getStructure().getStructureSize(), getNameScope());
                            speciesFactor = Expression.div(Expression.invert(exp1), exp2);
                        }
                        // s*(s-1)(s-2)..(s-stoi+1)
                        SpeciesCountParameter spCountParam = getSpeciesCountParameter(reacPart[i].getSpeciesContext());
                        Expression spCount_exp = new Expression(spCountParam, getNameScope());
                        // species from uM to No. of Particles, form s*(s-1)*(s-2)
                        Expression tempExpr = new Expression(spCount_exp);
                        for (int j = 1; j < stoichiometry; j++) {
                            tempExpr = Expression.mult(tempExpr, Expression.add(spCount_exp, new Expression(-j)));
                        }
                        // update total factor with speceies factor
                        if (stoichiometry == 1) {
                            factorExpr = Expression.mult(factorExpr, speciesFactor);
                        } else if (stoichiometry > 1) {
                            // rxnProbExpr * (structSize^stoichiometry)
                            Expression powerExpr = Expression.power(speciesFactor, new Expression(stoichiometry));
                            factorExpr = Expression.mult(factorExpr, powerExpr);
                        }
                        if (rxnProbabilityExpr == null) {
                            rxnProbabilityExpr = new Expression(tempExpr);
                        } else {
                            // for more than one reactant
                            rxnProbabilityExpr = Expression.mult(rxnProbabilityExpr, tempExpr);
                        }
                    }
                }
            }
        } else // reverse reaction
        {
            if (kinetics.getKineticsDescription().equals(KineticsDescription.MassAction)) {
                KineticsParameter krp = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KReverse);
                rateConstantExpr = new Expression(krp, getNameScope());
            // rateConstantExpr.bindExpression(this);
            }
            // get convert factor for rate constant( membrane:rateConstant*membrane_Size (factor is membrane_size), feature : rateConstant*(feature_size/KMole)(factor is feature_size/KMOLE)) )
            if (sm.getStructure() instanceof Membrane) {
                factorExpr = new Expression(sm.getStructure().getStructureSize(), getNameScope());
            } else {
                factorExpr = new Expression(sm.getStructure().getStructureSize(), getNameScope());
                Expression exp = new Expression(1.0 / 602.0);
                factorExpr = Expression.mult(factorExpr, exp);
            }
            // complete the remaining part of the probability expression by the products' stoichiometries.
            if (kinetics.getKineticsDescription().equals(KineticsDescription.MassAction)) {
                ReactionParticipant[] reacPart = reactionStep.getReactionParticipants();
                for (int i = 0; i < reacPart.length; i++) {
                    int stoichiometry = 0;
                    if (reacPart[i] instanceof Product) {
                        stoichiometry = ((Product) reacPart[i]).getStoichiometry();
                        // ******the following part is to form the s*(s-1)*(s-2)...(s-stoi+1).portion of the probability rate.
                        StructureMapping reactSM = getSimulationContext().getGeometryContext().getStructureMapping(reacPart[i].getStructure());
                        // factor expression for species
                        Expression speciesFactor = null;
                        // convert speceis' unit from moles/liter to molecules.
                        if (reactSM.getStructure() instanceof Membrane) {
                            speciesFactor = Expression.invert(new Expression(reactSM.getStructure().getStructureSize(), getNameScope()));
                        } else {
                            Expression exp1 = new Expression(1.0 / 602.0);
                            Expression exp2 = new Expression(reactSM.getStructure().getStructureSize(), getNameScope());
                            speciesFactor = Expression.div(Expression.invert(exp1), exp2);
                        }
                        // s*(s-1)*(s-2)...(s-stoi+1)
                        SpeciesCountParameter spCountParam = getSpeciesCountParameter(reacPart[i].getSpeciesContext());
                        Expression spCount_exp = new Expression(spCountParam, getNameScope());
                        // species from uM to No. of Particles, form s*(s-1)*(s-2)
                        Expression tempExpr = new Expression(spCount_exp);
                        for (int j = 1; j < stoichiometry; j++) {
                            tempExpr = Expression.mult(tempExpr, Expression.add(spCount_exp, new Expression(-j)));
                        }
                        // update total factor with speceies factor
                        if (stoichiometry == 1) {
                            factorExpr = Expression.mult(factorExpr, speciesFactor);
                        } else if (stoichiometry > 1) {
                            // rxnProbExpr * (structSize^stoichiometry)
                            Expression powerExpr = Expression.power(speciesFactor, new Expression(stoichiometry));
                            factorExpr = Expression.mult(factorExpr, powerExpr);
                        }
                        if (rxnProbabilityExpr == null) {
                            rxnProbabilityExpr = new Expression(tempExpr);
                        } else {
                            rxnProbabilityExpr = Expression.mult(rxnProbabilityExpr, tempExpr);
                        }
                    }
                }
            }
        }
        // Now construct the probability expression.
        if (rateConstantExpr == null) {
            throw new MappingException("Can not find reaction rate constant in reaction: " + reactionStep.getName());
        } else if (rxnProbabilityExpr == null) {
            probExp = new Expression(rateConstantExpr);
        } else if ((rateConstantExpr != null) && (rxnProbabilityExpr != null)) {
            probExp = Expression.mult(rateConstantExpr, rxnProbabilityExpr);
        }
        // simplify the factor
        RationalExp factorRatExp = RationalExpUtils.getRationalExp(factorExpr);
        factorExpr = new Expression(factorRatExp.infixString());
        factorExpr.bindExpression(this);
        // get probability rate with converting factor
        probExp = Expression.mult(probExp, factorExpr);
        probExp = probExp.flatten();
    // //
    // // round trip to rational expression for simplifying terms like KMOLE/KMOLE ...
    // // we don't want to loose the symbol binding ... so we make a temporary symbolTable from the original binding.
    // //
    // final Expression finalExp = new Expression(probExp);
    // SymbolTable symbolTable = new SymbolTable(){
    // public void getEntries(Map<String, SymbolTableEntry> entryMap) {
    // throw new RuntimeException("should not be called");
    // }
    // public SymbolTableEntry getEntry(String identifierString) throws ExpressionBindingException {
    // return finalExp.getSymbolBinding(identifierString);
    // }
    // };
    // cbit.vcell.matrix.RationalExp ratExp = cbit.vcell.parser.RationalExpUtils.getRationalExp(probExp);
    // probExp = new Expression(ratExp.infixString());
    // probExp.bindExpression(symbolTable);
    } catch (ExpressionException e) {
        e.printStackTrace();
    }
    return probExp;
}