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

Example 61 with Expression

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

the class CellQuanVCTranslator method processVariables.

protected void processVariables() {
    @SuppressWarnings("unchecked") List<Element> compElementList = sRoot.getChildren(CELLMLTags.COMPONENT, sNamespace);
    Iterator<Element> compElementIterator = compElementList.iterator();
    Element comp, var, varRef, temp;
    String compName, varName, publicIn, privateIn, mangledName;
    while (compElementIterator.hasNext()) {
        comp = compElementIterator.next();
        compName = comp.getAttributeValue(CELLMLTags.name, sAttNamespace);
        @SuppressWarnings("unchecked") List<Element> varElementList = comp.getChildren(CELLMLTags.VARIABLE, sNamespace);
        Iterator<Element> varElementIterator = varElementList.iterator();
        // clear const and volVars vectors for each component
        while (varElementIterator.hasNext()) {
            var = varElementIterator.next();
            publicIn = var.getAttributeValue(CELLMLTags.public_interface, sAttNamespace);
            privateIn = var.getAttributeValue(CELLMLTags.private_interface, sAttNamespace);
            if ((publicIn != null && publicIn.equals(CELLMLTags.inInterface)) || (privateIn != null && privateIn.equals(CELLMLTags.inInterface)))
                continue;
            varName = var.getAttributeValue(CELLMLTags.name, sAttNamespace);
            mangledName = nm.getMangledName(compName, varName);
            String uniqueVarName = getUniqueParamName(mangledName);
            System.out.println("Vars: " + compName + "." + varName + " " + mangledName + " " + uniqueVarName);
            // declare any differential free variables as VolumeVariable's
            temp = getMathElementIdentifier(comp, varName, MathMLTags.DIFFERENTIAL);
            try {
                if (temp != null) {
                    // formula ignored at this point
                    Domain domain = null;
                    VolVariable volVar = new VolVariable(mangledName, domain);
                    varsHash.addVariable(volVar);
                    continue;
                }
                // any LHS variables of an eq operator are functions
                temp = getMathElementIdentifier(comp, varName, MathMLTags.IDENTIFIER);
                if (temp != null) {
                    Function fn = addFunction(temp, comp, mangledName);
                    varsHash.addVariable(fn);
                    continue;
                }
                // Handle delta variables as a special case function
                varRef = getMatchingVarRef(comp, varName);
                if (varRef != null) {
                    // 2 functions with same name?
                    Function rateFn = addRateFunction(varRef, compName, uniqueVarName);
                    varsHash.addVariable(rateFn);
                    continue;
                }
                // check if it is the time variable, if not add as a constant. No handling for a specific value for the time var.
                if (!isTimeVar(varName)) {
                    Constant constant = new Constant(uniqueVarName, new Expression(getInitial(comp, varName)));
                    varsHash.addVariable(constant);
                }
            } catch (Exception e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Error adding variable to variablesHash : " + e.getMessage());
            }
        }
    // end iteration for VARIABLES
    }
    // add the variables from varsHash to mathDescription
    try {
        mathDescription.setAllVariables(varsHash.getAlphabeticallyOrderedVariables());
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("Error adding variables to mathDescription : " + e.getMessage());
    }
}

Example 62 with Expression

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

the class CellQuanVCTranslator method addFunction.

private Function addFunction(Element temp, Element comp, String mangledName) {
    String expStr = null;
    Expression exp = null;
    Element parent = (Element) temp.getParent();
    Element sibling = parent.getChild(MathMLTags.APPLY, mathns);
    if (sibling == null) {
        // check if its value is assigned to another variable (i.e. A = B)
        @SuppressWarnings("unchecked") ArrayList<Element> list = new ArrayList<Element>(parent.getChildren(MathMLTags.IDENTIFIER, mathns));
        if (list.size() == 2) {
            expStr = (list.get(1)).getTextTrim();
        }
        if (expStr == null || expStr.length() == 0) {
            expStr = parent.getChildText(MathMLTags.CONSTANT, mathns);
        }
        if (expStr == null || expStr.length() == 0) {
            // check if 'piecewise'
            sibling = parent.getChild(MathMLTags.PIECEWISE, mathns);
        }
        if (expStr != null) {
            try {
                exp = new Expression(expStr);
                exp = processMathExp(comp, exp);
                nl.mangleString(expStr);
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException(e.getMessage());
            }
        }
    }
    if (sibling != null) {
        Element trimmedMath = new Element(CELLMLTags.MATH, mathns).addContent(sibling.detach());
        fixMathMLBug(trimmedMath);
        try {
            exp = (new ExpressionMathMLParser(null)).fromMathML(trimmedMath);
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException(e.getMessage());
        }
        exp = processMathExp(comp, exp);
        expStr = exp.infix();
        nl.mangleString(expStr);
    }
    Domain domain = null;
    return new Function(mangledName, exp, domain);
}

Example 63 with Expression

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

the class SBPAXHMMIrrevLawBuilder method addKinetics.

public void addKinetics(KineticContext context) {
    try {
        ReactionStep reaction = context.getReaction();
        HMM_IRRKinetics kinetics = new HMM_IRRKinetics((SimpleReaction) reaction);
        NameScope modelScope = reaction.getModel().getNameScope();
        ModelParameter kMichaelis = context.getParameter(SBOList.MICHAELIS_CONST_FORW);
        if (kMichaelis != null) {
            KineticsParameter kmParameter = kinetics.getKmParameter();
            kmParameter.setExpression(new Expression(kMichaelis, modelScope));
            kmParameter.setUnitDefinition(kMichaelis.getUnitDefinition());
        }
        ModelParameter kcat = context.getParameter(SBOList.CATALYTIC_RATE_CONST_FORW);
        if (kcat != null && context.getCatalysts().size() == 1) {
            KineticsParameter vmaxParameter = kinetics.getVmaxParameter();
            Catalyst catalyst = context.getCatalysts().iterator().next();
            vmaxParameter.setExpression(Expression.mult(new Expression(kcat, modelScope), new Expression(catalyst.getSpeciesContext(), modelScope)));
        // vmaxParameter.setUnitDefinition(vMax.getUnitDefinition());
        } else {
            ModelParameter vMax = context.getParameter(SBOList.MAXIMAL_VELOCITY_FORW);
            if (vMax != null) {
                KineticsParameter vmaxParameter = kinetics.getVmaxParameter();
                vmaxParameter.setExpression(new Expression(vMax, modelScope));
                vmaxParameter.setUnitDefinition(vMax.getUnitDefinition());
            }
        }
    } catch (ExpressionException e) {
        e.printStackTrace();
    }
}

Example 64 with Expression

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

the class SBPAXKineticsExtractor method setKForwardParam.

private static void setKForwardParam(ReactionStep reaction, SBOParam kForward, Kinetics kinetics) throws ExpressionException, PropertyVetoException {
    if (kForward != null) {
        KineticsParameter fwdParam = ((MassActionKinetics) kinetics).getForwardRateParameter();
        kinetics.setParameterValue(fwdParam, new Expression(kForward.getNumber()));
        String unitF = SBOParam.formatUnit(kForward.getUnit());
        VCUnitDefinition fwdUnit = reaction.getModel().getUnitSystem().getInstance(unitF);
        fwdParam.setUnitDefinition(fwdUnit);
    }
}

Example 65 with Expression

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

the class SBPAXKineticsExtractor method setKReverseParam.

private static void setKReverseParam(ReactionStep reaction, SBOParam kReverse, Kinetics kinetics) throws ExpressionException, PropertyVetoException {
    if (kReverse != null) {
        KineticsParameter revParam = ((MassActionKinetics) kinetics).getReverseRateParameter();
        kinetics.setParameterValue(revParam, new Expression(kReverse.getNumber()));
        String unitR = SBOParam.formatUnit(kReverse.getUnit());
        VCUnitDefinition revUnit = reaction.getModel().getUnitSystem().getInstance(unitR);
        revParam.setUnitDefinition(revUnit);
    }
}