Examples with JDOMTreeWalker cbit.util.xml.JDOMTreeWalker used on opensource projects

Example 1 with JDOMTreeWalker

use of cbit.util.xml.JDOMTreeWalker in project vcell by virtualcell.

the class CellQuanVCTranslator method isTimeVar.

private boolean isTimeVar(String varName) {
    boolean flag = false;
    JDOMTreeWalker walker = new JDOMTreeWalker(sRoot, new ElementFilter(MathMLTags.BVAR));
    while (walker.hasNext()) {
        Element bvar = (Element) walker.next();
        String timeVar = bvar.getChildText(MathMLTags.IDENTIFIER, mathns);
        if (varName.trim().equals(timeVar.trim())) {
            flag = true;
            break;
        }
    }
    return flag;
}

Example 2 with JDOMTreeWalker

use of cbit.util.xml.JDOMTreeWalker in project vcell by virtualcell.

the class CellQuanVCTranslator method addVarsAndConns.

// add all the components and variables to the name manager, and resolve all connections
protected void addVarsAndConns() {
    JDOMTreeWalker walker = new JDOMTreeWalker(sRoot, new ElementFilter(CELLMLTags.VARIABLE));
    Element temp;
    String firstKey, secondKey;
    while (walker.hasNext()) {
        temp = (Element) walker.next();
        firstKey = ((Element) temp.getParent()).getAttributeValue(CELLMLTags.name, sAttNamespace);
        secondKey = temp.getAttributeValue(CELLMLTags.name, sAttNamespace);
        nm.add(firstKey, secondKey);
    }
    walker = new JDOMTreeWalker(sRoot, new ElementFilter(CELLMLTags.CONNECTION));
    Element mapComp, mapVar;
    String comp1, comp2, var1, var2;
    boolean flag;
    while (walker.hasNext()) {
        temp = (Element) walker.next();
        Vector<String> vars1_vect = new Vector<String>();
        Vector<String> vars2_vect = new Vector<String>();
        mapComp = temp.getChild(CELLMLTags.MAP_COMP, sNamespace);
        comp1 = mapComp.getAttributeValue(CELLMLTags.comp1, sAttNamespace);
        comp2 = mapComp.getAttributeValue(CELLMLTags.comp2, sAttNamespace);
        @SuppressWarnings("unchecked") Iterator<Element> i = temp.getChildren(CELLMLTags.MAP_VAR, sNamespace).iterator();
        while (i.hasNext()) {
            mapVar = i.next();
            var1 = mapVar.getAttributeValue(CELLMLTags.var1, sAttNamespace);
            var2 = mapVar.getAttributeValue(CELLMLTags.var2, sAttNamespace);
            flag = isVisible(comp1, var1);
            boolean connected;
            if (flag) {
                // component1/variable1 is the "output" variable so connect component2/variable2 to it
                connected = nm.connect(comp2, var2, comp1, var1);
            } else {
                // connect to component2/variable2 if its the output
                flag = isVisible(comp2, var2);
                if (flag) {
                    connected = nm.connect(comp1, var1, comp2, var2);
                } else {
                    // or allow connections to remain chained (in case the model defines groups)
                    flag = isMiddleComp(comp1, var1);
                    if (flag) {
                        connected = nm.connect(comp2, var2, comp1, var1);
                    } else {
                        connected = nm.connect(comp1, var1, comp2, var2);
                    }
                }
            }
            if (!connected) {
                System.err.println("Error: Unable to connect variables: " + comp1 + " " + var1 + ", " + comp2 + " " + var2);
            } else {
                // they are connected; add vars to vars_vectors
                vars1_vect.add(var1);
                vars2_vect.add(var2);
            }
        }
        CellmlConnection newConnection = new CellmlConnection(comp1, comp2, vars1_vect, vars2_vect);
        connectionsVector.add(newConnection);
    }
    nm.generateMangledNames();
}

Example 3 with JDOMTreeWalker

use of cbit.util.xml.JDOMTreeWalker in project vcell by virtualcell.

the class CellQuanVCTranslator method getInitial.

private String getInitial(Element comp, String variableName) {
    String initial = "0.0";
    Element temp;
    JDOMTreeWalker walker = new JDOMTreeWalker(comp, new ElementFilter(CELLMLTags.VARIABLE));
    temp = walker.getMatchingElement(CELLMLTags.name, sAttNamespace, variableName);
    if (temp != null) {
        initial = temp.getAttributeValue(CELLMLTags.initial_value, sAttNamespace);
        if (initial == null || initial.length() == 0)
            initial = "0.0";
    }
    return initial;
}

Example 4 with JDOMTreeWalker

use of cbit.util.xml.JDOMTreeWalker in project vcell by virtualcell.

the class CellQuanVCTranslator method isMiddleComp.

private boolean isMiddleComp(String comp, String var) {
    boolean flag = false;
    String privateInterface;
    JDOMTreeWalker walker = new JDOMTreeWalker(sRoot, new ElementFilter(CELLMLTags.COMPONENT));
    Element matchingComp = walker.getMatchingElement(CELLMLTags.name, sAttNamespace, comp);
    if (matchingComp != null) {
        walker = new JDOMTreeWalker(matchingComp, new ElementFilter(CELLMLTags.VARIABLE));
        Element matchingVar = walker.getMatchingElement(CELLMLTags.name, sAttNamespace, var);
        if (matchingVar != null) {
            privateInterface = matchingVar.getAttributeValue(CELLMLTags.private_interface, sAttNamespace);
            if (CELLMLTags.outInterface.equals(privateInterface))
                flag = true;
        }
    }
    return flag;
}

Example 5 with JDOMTreeWalker

use of cbit.util.xml.JDOMTreeWalker in project vcell by virtualcell.

the class CellQuanVCTranslator method getMatchingVarRef.

private Element getMatchingVarRef(Element comp, String varName) {
    JDOMTreeWalker walker = new JDOMTreeWalker(comp, new ElementFilter(CELLMLTags.ROLE));
    Element temp = walker.getMatchingElement(CELLMLTags.delta_variable, sAttNamespace, varName);
    if (temp != null) {
        return (Element) temp.getParent();
    } else {
        return null;
    }
}