Examples with ASTRootNode org.jmathml.ASTRootNode used on opensource projects

Example 1 with ASTRootNode

use of org.jmathml.ASTRootNode in project vcell by virtualcell.

the class SEDMLReader method getSetValueContent.

private SetValue getSetValueContent(SetValue c, Element element) throws DataConversionException {
    List<Element> children = element.getChildren();
    Iterator<Element> iChildren = children.iterator();
    while (iChildren.hasNext()) {
        Element eChild = (Element) iChildren.next();
        if (eChild.getName().equals(SEDMLTags.CHANGE_ATTR_MATH)) {
            ASTNode math = (ASTRootNode) new MathMLReader().parseMathML(eChild);
            c.setMath(math);
        } else if (eChild.getName().equals(SEDMLTags.DATAGEN_ATTR_VARS_LIST)) {
            List<Element> lVariables = eChild.getChildren();
            Iterator<Element> iVariables = lVariables.iterator();
            while (iVariables.hasNext()) {
                Element eVariable = (Element) iVariables.next();
                if (eVariable.getName().equals(SEDMLTags.DATAGEN_ATTR_VARIABLE)) {
                    c.addVariable(createVariable(eVariable, true));
                }
            }
        } else if (eChild.getName().equals(SEDMLTags.DATAGEN_ATTR_PARAMS_LIST)) {
            List<Element> lParameters = eChild.getChildren();
            Iterator<Element> iParameters = lParameters.iterator();
            while (iParameters.hasNext()) {
                Element eParameter = (Element) iParameters.next();
                if (eParameter.getName().equals(SEDMLTags.DATAGEN_ATTR_PARAMETER)) {
                    c.addParameter(createParameter(eParameter));
                }
            }
        } else {
            log.warn("Unexpected " + eChild);
        }
    }
    return c;
}

Example 2 with ASTRootNode

use of org.jmathml.ASTRootNode in project vcell by virtualcell.

the class Libsedml method parseFormulaString.

/**
 * Convenience method to parse free text math into an ASTNode. The style of
 * math is a C-style syntax, e.g.,<br/>
 * . The parsing supports standard arithmetical operations and function
 * calls. E.g.,
 *
 * <ul>
 * <li>4 + 2
 * <li>sin(pi / 2) // or any other trig function
 * <li>log(9,81) // = 2
 * <li>root(4,81) //=3
 * <li>exp(t)
 * </ul>
 * <p>
 * In addition, the strings <code>pi</code>, <code>NaN</code>,
 * <code>infinity</code> and <code>exponentiale</code> are translated into
 * constants.
 * </p>
 *
 * Functions not supported by this library ( see ASTFunctionType for
 * supported functions ) will be parsed into a function call, which will not
 * be evaluable. E.g., <br/>
 *
 * <pre>
 * myfunction(a, b)
 * </pre>
 *
 * can be turned into an ASTNode, but will not be evaluable, unless a symbol
 * definition class is supplied. (See the
 * <code>org.jlibsedml.mathsymbols</code> package for how the SED-ML
 * aggregate functions are supported).
 *
 * @param math
 *            A <code>String</code> of math.
 * @return An {@link ASTNode}. This will be an {@link ASTRootNode} with the
 *         math nodes as children. E.g., the string
 *
 *         <pre>
 * 2 * (4 / 5)
 * </pre>
 *         will return the structure:
 *         <pre>
 *  ASTRootNode
 *       ASTimes
 *            ASTCn(2)
 *            ASTDivide
 *                 ASTCn(4)
 *                 ASTCn(5)
 * </pre>
 *
 *         If <code>math</code> is null or empty, returns <code>null</code>.
 * @throws RuntimeException
 *             if mathString cannot be parsed due to incorrect syntax.
 */
public static ASTNode parseFormulaString(String math) {
    if (math == null || math.length() == 0) {
        return null;
    }
    ASTRootNode rc = new ASTRootNode();
    new TextToASTNodeMathParser2().parseString(math, rc);
    return rc;
}

Example 3 with ASTRootNode

use of org.jmathml.ASTRootNode in project vcell by virtualcell.

the class SEDMLReader method addFunctionalRangeLists.

private void addFunctionalRangeLists(Range r, Element element) throws DataConversionException {
    String childName = null;
    List<Element> children = element.getChildren();
    Iterator<Element> iChildren = children.iterator();
    while (iChildren.hasNext()) {
        Element eChild = (Element) iChildren.next();
        childName = eChild.getName();
        if (eChild.getName().equals(SEDMLTags.FUNCTIONAL_RANGE_VAR_LIST)) {
            addFunctionalRangeVariable(r, eChild);
        } else if (eChild.getName().equals(SEDMLTags.FUNCTIONAL_RANGE_PAR_LIST)) {
            addFunctionalRangeParameter(r, eChild);
        } else if (eChild.getName().equals(SEDMLTags.FUNCTION_MATH_TAG)) {
            ASTNode math = (ASTRootNode) new MathMLReader().parseMathML(eChild);
            log.debug("r      " + math.toString());
            ((FunctionalRange) r).setMath(math);
        } else {
            log.warn("Unexpected " + eChild);
        }
    }
}

Example 4 with ASTRootNode

use of org.jmathml.ASTRootNode in project vcell by virtualcell.

the class SEDMLReader method getChange.

Change getChange(Element aChange) throws DataConversionException {
    Change rc = null;
    if (aChange.getName().equals(SEDMLTags.CHANGE_ATTRIBUTE)) {
        rc = new ChangeAttribute(new XPathTarget(aChange.getAttributeValue(SEDMLTags.CHANGE_ATTR_TARGET)), aChange.getAttributeValue(SEDMLTags.CHANGE_ATTR_NEWVALUE));
    } else if (aChange.getName().equals(SEDMLTags.CHANGE_XML) || aChange.getName().equals(SEDMLTags.ADD_XML)) {
        Iterator<Element> changeChildren = aChange.getChildren().iterator();
        while (changeChildren.hasNext()) {
            Element el = (Element) changeChildren.next();
            if (el.getName().equals(SEDMLTags.NEW_XML)) {
                List<Element> xml = getNewXML(el);
                NewXML newxml = new NewXML(xml);
                if (aChange.getName().equals(SEDMLTags.CHANGE_XML))
                    rc = new ChangeXML(new XPathTarget(aChange.getAttributeValue(SEDMLTags.CHANGE_ATTR_TARGET)), newxml);
                else
                    rc = new AddXML(new XPathTarget(aChange.getAttributeValue(SEDMLTags.CHANGE_ATTR_TARGET)), newxml);
            }
        }
    } else if (aChange.getName().equals(SEDMLTags.REMOVE_XML)) {
        rc = new RemoveXML(new XPathTarget(aChange.getAttributeValue(SEDMLTags.CHANGE_ATTR_TARGET)));
    } else if (aChange.getName().equals(SEDMLTags.COMPUTE_CHANGE)) {
        ASTRootNode math = null;
        Element toAdd = null;
        List<Variable> vars = new ArrayList<Variable>();
        List<Parameter> params = new ArrayList<Parameter>();
        Iterator<Element> changeChildren = aChange.getChildren().iterator();
        while (changeChildren.hasNext()) {
            Element el = (Element) changeChildren.next();
            if (el.getName().equals(SEDMLTags.CHANGE_ATTR_MATH)) {
                math = (ASTRootNode) new MathMLReader().parseMathML(el);
            } else if (el.getName().equals(SEDMLTags.DATAGEN_ATTR_VARS_LIST)) {
                List<Element> lVariables = el.getChildren();
                Iterator<Element> iVariables = lVariables.iterator();
                while (iVariables.hasNext()) {
                    Element eVariable = (Element) iVariables.next();
                    if (eVariable.getName().equals(SEDMLTags.DATAGEN_ATTR_VARIABLE)) {
                        vars.add(createVariable(eVariable, true));
                    }
                }
            } else if (el.getName().equals(SEDMLTags.DATAGEN_ATTR_PARAMS_LIST)) {
                List<Element> lParameters = el.getChildren();
                Iterator<Element> iParameters = lParameters.iterator();
                while (iParameters.hasNext()) {
                    Element eParameter = (Element) iParameters.next();
                    if (eParameter.getName().equals(SEDMLTags.DATAGEN_ATTR_PARAMETER)) {
                        params.add(createParameter(eParameter));
                    }
                }
            }
        // TODO: variable and parameter need to be also
        // loaded here
        }
        ComputeChange cc = new ComputeChange(new XPathTarget(aChange.getAttributeValue(SEDMLTags.CHANGE_ATTR_TARGET)), math);
        cc.setListOfParameters(params);
        cc.setListOfVariables(vars);
        rc = cc;
    }
    addNotesAndAnnotation(rc, aChange);
    return rc;
}