Examples with FastRate cbit.vcell.math.FastRate used on opensource projects

Example 11 with FastRate

use of cbit.vcell.math.FastRate in project vcell by virtualcell.

the class FastSystemAnalyzer method refreshFastVarList.

/**
 * @return java.util.Vector
 */
private void refreshFastVarList() throws MathException, ExpressionException {
    fastVarList.clear();
    // 
    // get list of unique (VolVariables and MemVariables) in fastRate expressions
    // 
    Enumeration<FastRate> fastRatesEnum = fastSystem.getFastRates();
    while (fastRatesEnum.hasMoreElements()) {
        FastRate fr = fastRatesEnum.nextElement();
        Expression exp = fr.getFunction();
        Enumeration<Variable> enum1 = MathUtilities.getRequiredVariables(exp, this);
        while (enum1.hasMoreElements()) {
            Variable var = enum1.nextElement();
            if (var instanceof VolVariable || var instanceof MemVariable) {
                if (!fastVarList.contains(var)) {
                    fastVarList.addElement(var);
                // System.out.println("FastSystemImplicit.refreshFastVarList(), FAST RATE VARIABLE: "+var.getName());
                }
            }
        }
    }
    // 
    // get list of all variables used in invariant expressions that are not used in fast rates
    // 
    Enumeration<FastInvariant> fastInvariantsEnum = fastSystem.getFastInvariants();
    while (fastInvariantsEnum.hasMoreElements()) {
        FastInvariant fi = (FastInvariant) fastInvariantsEnum.nextElement();
        Expression exp = fi.getFunction();
        // System.out.println("FastSystemImplicit.refreshFastVarList(), ORIGINAL FAST INVARIANT: "+exp);
        Enumeration<Variable> enum1 = MathUtilities.getRequiredVariables(exp, this);
        while (enum1.hasMoreElements()) {
            Variable var = enum1.nextElement();
            if (var instanceof VolVariable || var instanceof MemVariable) {
                if (!fastVarList.contains(var)) {
                    fastVarList.addElement(var);
                }
            }
        }
    }
    // 
    // verify that there are N equations (rates+invariants) and N unknowns (fastVariables)
    // 
    int numBoundFunctions = fastSystem.getNumFastInvariants() + fastSystem.getNumFastRates();
    if (fastVarList.size() != numBoundFunctions) {
        throw new MathException("FastSystem.checkDimension(), there are " + fastVarList.size() + " variables and " + numBoundFunctions + " FastInvariant's & FastRates");
    }
}

Example 12 with FastRate

use of cbit.vcell.math.FastRate in project vcell by virtualcell.

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a FastSystemImplicit object.
 * Creation date: (3/2/2001 4:05:28 PM)
 * @return Element
 * @param param cbit.vcell.math.FastSystemImplicit
 */
private Element getXML(FastSystem param) {
    Element fastsystem = new Element(XMLTags.FastSystemTag);
    // Add Fast Invariant subelements
    Element fastinvariant;
    Enumeration<FastInvariant> enum_fi = param.getFastInvariants();
    while (enum_fi.hasMoreElements()) {
        fastinvariant = new Element(XMLTags.FastInvariantTag);
        FastInvariant fi = enum_fi.nextElement();
        fastinvariant.addContent(mangleExpression(fi.getFunction()));
        fastsystem.addContent(fastinvariant);
    }
    // Add FastRate subelements
    Element fastrate;
    Enumeration<FastRate> enum_fr = param.getFastRates();
    while (enum_fr.hasMoreElements()) {
        FastRate fr = (FastRate) enum_fr.nextElement();
        fastrate = new Element(XMLTags.FastRateTag);
        fastrate.addContent(mangleExpression(fr.getFunction()));
        fastsystem.addContent(fastrate);
    }
    return fastsystem;
}

Example 13 with FastRate

use of cbit.vcell.math.FastRate in project vcell by virtualcell.

the class ITextWriter method writeFastSystem.

protected void writeFastSystem(Section container, FastSystem fs) throws DocumentException {
    Table eqTable = getTable(2, 100, 1, 2, 2);
    eqTable.addCell(createCell(VCML.FastSystem, getBold(DEF_HEADER_FONT_SIZE), 2, 1, Element.ALIGN_CENTER, true));
    eqTable.endHeaders();
    Enumeration<FastInvariant> enum_fi = fs.getFastInvariants();
    while (enum_fi.hasMoreElements()) {
        FastInvariant fi = enum_fi.nextElement();
        eqTable.addCell(createCell(VCML.FastInvariant, getFont()));
        eqTable.addCell(createCell(fi.getFunction().infix(), getFont()));
    }
    Enumeration<FastRate> enum_fr = fs.getFastRates();
    while (enum_fr.hasMoreElements()) {
        FastRate fr = enum_fr.nextElement();
        eqTable.addCell(createCell(VCML.FastRate, getFont()));
        eqTable.addCell(createCell(fr.getFunction().infix(), getFont()));
    }
    container.add(eqTable);
}