Examples with NameScope cbit.vcell.parser.NameScope used on opensource projects

Example 6 with NameScope

use of cbit.vcell.parser.NameScope in project vcell by virtualcell.

the class ParameterContext method renameLocalParameter.

/**
 * Insert the method's description here.
 * Creation date: (5/24/01 4:05:36 PM)
 */
public void renameLocalParameter(String oldName, String newName) throws ExpressionException, java.beans.PropertyVetoException {
    if (oldName == null || newName == null) {
        throw new RuntimeException("renameParameter from '" + oldName + "' to '" + newName + "', nulls are not allowed");
    }
    NameScope nameScope = getNameScope();
    String prefix = AbstractNameScope.getPrefix(newName);
    String strippedName = AbstractNameScope.getStrippedIdentifier(newName);
    if (prefix != null) {
        NameScope prefixNameScope = nameScope.getNameScopeFromPrefix(prefix);
        if (prefixNameScope != nameScope) {
            // from different namescope, then strip any prefix.
            throw new ExpressionException("reaction parameter cannot be renamed to '" + newName + "', name is scoped to '" + prefixNameScope.getName() + "'");
        }
    }
    newName = strippedName;
    if (oldName.equals(newName)) {
        throw new RuntimeException("renameParameter from '" + oldName + "' to '" + newName + "', same name not allowed");
    }
    LocalParameter existingParameter = getLocalParameterFromName(newName);
    if (existingParameter != null) {
        throw new RuntimeException("Parameter '" + newName + "' already exists.");
    }
    LocalParameter parameter = getLocalParameterFromName(oldName);
    if (parameter != null) {
        // 
        // must change name in ElectricalStimulusParameter directly
        // then change all references to this name in the other parameter's expressions.
        // 
        LocalParameter[] newParameters = (LocalParameter[]) getLocalParameters().clone();
        // 
        // replaces parameter with name 'oldName' with new parameter with name 'newName' and original expression.
        // 
        parameter.fieldParameterName = newName;
        // 
        for (int i = 0; i < newParameters.length; i++) {
            if (newParameters[i].getExpression() != null) {
                Expression newExp = newParameters[i].getExpression().renameBoundSymbols(getNameScope());
                newParameters[i].setExpression(newExp);
            }
        }
        setLocalParameters(newParameters);
        // 
        try {
            cleanupParameters();
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new RuntimeException(e.getMessage());
        }
        parameter.firePropertyChange("name", oldName, newName);
    }
}

Example 7 with NameScope

use of cbit.vcell.parser.NameScope in project vcell by virtualcell.

the class ExpressionCanvas method setNameScope.

/**
 * Sets the nameScope property (cbit.vcell.parser.NameScope) value.
 * @param nameScope The new value for the property.
 * @see #getNameScope
 */
public void setNameScope(NameScope nameScope) {
    cbit.vcell.parser.NameScope oldValue = fieldNameScope;
    fieldNameScope = nameScope;
    firePropertyChange("nameScope", oldValue, nameScope);
}

Example 8 with NameScope

use of cbit.vcell.parser.NameScope in project vcell by virtualcell.

the class SBPAXHMMRevLawBuilder method addKinetics.

public void addKinetics(KineticContext context) {
    try {
        ReactionStep reaction = context.getReaction();
        HMM_REVKinetics kinetics = new HMM_REVKinetics((SimpleReaction) reaction);
        NameScope modelScope = reaction.getModel().getNameScope();
        ModelParameter kMichaelisFwd = context.getParameter(SBOList.MICHAELIS_CONST_FORW);
        if (kMichaelisFwd != null) {
            KineticsParameter kmfParameter = kinetics.getKmFwdParameter();
            kmfParameter.setExpression(new Expression(kMichaelisFwd, modelScope));
            kmfParameter.setUnitDefinition(kMichaelisFwd.getUnitDefinition());
        }
        ModelParameter kcatf = context.getParameter(SBOList.CATALYTIC_RATE_CONST_FORW);
        if (kcatf != null && context.getCatalysts().size() == 1) {
            KineticsParameter vmaxfParameter = kinetics.getVmaxFwdParameter();
            Catalyst catalyst = context.getCatalysts().iterator().next();
            vmaxfParameter.setExpression(Expression.mult(new Expression(kcatf, modelScope), new Expression(catalyst.getSpeciesContext(), modelScope)));
        // vmaxParameter.setUnitDefinition(vMax.getUnitDefinition());
        } else {
            ModelParameter vMaxf = context.getParameter(SBOList.MAXIMAL_VELOCITY_FORW);
            if (vMaxf != null) {
                KineticsParameter vmaxfParameter = kinetics.getVmaxFwdParameter();
                vmaxfParameter.setExpression(new Expression(vMaxf, modelScope));
                vmaxfParameter.setUnitDefinition(vMaxf.getUnitDefinition());
            }
        }
        ModelParameter kMichaelisRev = context.getParameter(SBOList.MICHAELIS_CONST_REV);
        if (kMichaelisRev != null) {
            KineticsParameter kmrParameter = kinetics.getKmRevParameter();
            kmrParameter.setExpression(new Expression(kMichaelisRev, modelScope));
            kmrParameter.setUnitDefinition(kMichaelisRev.getUnitDefinition());
        }
        ModelParameter kcatr = context.getParameter(SBOList.CATALYTIC_RATE_CONST_FORW);
        if (kcatr != null && context.getCatalysts().size() == 1) {
            KineticsParameter vmaxrParameter = kinetics.getVmaxRevParameter();
            Catalyst catalyst = context.getCatalysts().iterator().next();
            vmaxrParameter.setExpression(Expression.mult(new Expression(kcatr, modelScope), new Expression(catalyst.getSpeciesContext(), modelScope)));
        // vmaxParameter.setUnitDefinition(vMax.getUnitDefinition());
        } else {
            ModelParameter vMaxr = context.getParameter(SBOList.MAXIMAL_VELOCITY_REV);
            if (vMaxr != null) {
                KineticsParameter vmaxrParameter = kinetics.getVmaxRevParameter();
                vmaxrParameter.setExpression(new Expression(vMaxr, modelScope));
                vmaxrParameter.setUnitDefinition(vMaxr.getUnitDefinition());
            }
        }
    } catch (ExpressionException e) {
        e.printStackTrace();
    }
}