public void setValue(String value) {
synchronized (DOMUtils.getDOMLock(elt)) {
{
String oldValue = getValue();
if (oldValue == null ? value == null : oldValue.equals(value)) return;
synchronized (DOMUtils.getDOMLock(elt)) {
// Get rid of any text nodes that are children of the element.
elt.normalize();
}
NodeList nl = elt.getChildNodes();
for (int i = (nl.getLength() - 1); i >= 0; i--) {
Node n = nl.item(i);
if (n.getNodeType() == Node.TEXT_NODE) {
synchronized (DOMUtils.getDOMLock(elt)) {
elt.removeChild(n);
}
IXArch context = getXArch();
if (context != null) {
context.fireXArchEvent(
new XArchEvent(
this,
XArchEvent.CLEAR_EVENT,
XArchEvent.SIMPLE_TYPE_VALUE_CHANGED,
"$SIMPLETYPEVALUE$",
null,
XArchUtils.getDefaultXArchImplementation().isContainedIn(xArch, this),
true));
}
}
}
}
elt.normalize();
Document doc = elt.getOwnerDocument();
Text txt = doc.createTextNode(value);
elt.appendChild(txt);
}
IXArch context = getXArch();
if (context != null) {
context.fireXArchEvent(
new XArchEvent(
this,
XArchEvent.SET_EVENT,
XArchEvent.SIMPLE_TYPE_VALUE_CHANGED,
"$SIMPLETYPEVALUE$",
value,
XArchUtils.getDefaultXArchImplementation().isContainedIn(xArch, this)));
}
}
public static void write() {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
Document doc;
System.out.println("Writing patient data file\n");
try {
DocumentBuilder builder = factory.newDocumentBuilder();
doc = builder.newDocument();
Element root = doc.createElement("patientdata");
root.appendChild(XMLInterface.nl(doc));
// get first PatientData from DataStore
Iterator<PatientDataStore> pdsIt = GlobalVars.pds.iterator();
while (pdsIt.hasNext()) {
PatientDataStore pds = pdsIt.next();
Node n = pds.createXMLNode(doc);
XMLInterface.addNode(doc, root, n, 0);
}
root.normalize();
// create junk to write it out (see java xml tutorial)
TransformerFactory tFactory = TransformerFactory.newInstance();
Transformer transformer = tFactory.newTransformer();
DOMSource src = new DOMSource(root);
StreamResult result = new StreamResult(new File(GlobalVars.XMLDataFile));
transformer.transform(src, result);
} catch (Exception e) {
System.err.println("Error WRITING xml patient data file");
e.printStackTrace();
}
}
public void clearValue() {
synchronized (DOMUtils.getDOMLock(elt)) {
// Get rid of any text nodes that are children of the element.
elt.normalize();
}
NodeList nl = elt.getChildNodes();
for (int i = (nl.getLength() - 1); i >= 0; i--) {
Node n = nl.item(i);
if (n.getNodeType() == Node.TEXT_NODE) {
synchronized (DOMUtils.getDOMLock(elt)) {
elt.removeChild(n);
}
IXArch context = getXArch();
if (context != null) {
context.fireXArchEvent(
new XArchEvent(
this,
XArchEvent.CLEAR_EVENT,
XArchEvent.SIMPLE_TYPE_VALUE_CHANGED,
"$SIMPLETYPEVALUE$",
null,
XArchUtils.getDefaultXArchImplementation().isContainedIn(xArch, this)));
}
}
}
}
public static String textInElement(Element elem) {
StringBuilder buf = new StringBuilder(100);
elem.normalize();
NodeList nlst = elem.getChildNodes();
for (int i = 0, nlen = nlst.getLength(); i < nlen; i++) {
Node n = nlst.item(i);
if (n instanceof Text) {
final String data = ((Text) n).getData();
buf.append(data);
}
}
return buf.toString();
}
public String getValue() {
synchronized (DOMUtils.getDOMLock(elt)) {
elt.normalize();
NodeList nl = elt.getChildNodes();
for (int i = (nl.getLength() - 1); i >= 0; i--) {
Node n = nl.item(i);
if (n.getNodeType() == Node.TEXT_NODE) {
return n.getNodeValue();
}
}
return null;
}
}
/**
* Save the XML description of the circuit
*
* @param output an output stream to write in
* @return true if the dump was successful, false either
*/
public boolean dumpToXml(OutputStream output) {
Document doc;
Element root;
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder;
try {
builder = factory.newDocumentBuilder();
doc = builder.newDocument();
} catch (ParserConfigurationException pce) {
System.err.println("dumpToXmlFile: unable to write XML save file.");
return false;
}
root = doc.createElement("Circuit");
root.setAttribute("name", this.getName());
for (iterNodes = this.nodes.iterator(); iterNodes.hasNext(); )
iterNodes.next().dumpToXml(doc, root);
root.normalize();
doc.appendChild(root);
try {
TransformerFactory tffactory = TransformerFactory.newInstance();
Transformer transformer = tffactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
DOMSource source = new DOMSource(doc);
StreamResult result = new StreamResult(output);
transformer.transform(source, result);
} catch (TransformerConfigurationException tce) {
System.err.println("dumpToXmlFile: Configuration Transformer exception.");
return false;
} catch (TransformerException te) {
System.err.println("dumpToXmlFile: Transformer exception.");
return false;
}
return true;
}
/**
* Unmarshall a Chromosome instance from a given XML Element representation.
*
* @param a_activeConfiguration current Configuration object
* @param a_xmlElement the XML Element representation of the Chromosome
* @return a new Chromosome instance setup with the data from the XML Element representation
* @throws ImproperXMLException if the given Element is improperly structured or missing data
* @throws UnsupportedRepresentationException if the actively configured Gene implementation does
* not support the string representation of the alleles used in the given XML document
* @throws GeneCreationException if there is a problem creating or populating a Gene instance
* @author Neil Rotstan
* @since 1.0
*/
public static Gene[] getGenesFromElement(
Configuration a_activeConfiguration, Element a_xmlElement)
throws ImproperXMLException, UnsupportedRepresentationException, GeneCreationException {
// Do some sanity checking. Make sure the XML Element isn't null and
// that it in fact represents a set of genes.
// -----------------------------------------------------------------
if (a_xmlElement == null || !(a_xmlElement.getTagName().equals(GENES_TAG))) {
throw new ImproperXMLException(
"Unable to build Chromosome instance from XML Element: "
+ "given Element is not a 'genes' element.");
}
List genes = Collections.synchronizedList(new ArrayList());
// Extract the nested gene elements.
// ---------------------------------
NodeList geneElements = a_xmlElement.getElementsByTagName(GENE_TAG);
if (geneElements == null) {
throw new ImproperXMLException(
"Unable to build Gene instances from XML Element: "
+ "'"
+ GENE_TAG
+ "'"
+ " sub-elements not found.");
}
// For each gene, get the class attribute so we know what class
// to instantiate to represent the gene instance, and then find
// the child text node, which is where the string representation
// of the allele is located, and extract the representation.
// -------------------------------------------------------------
int numberOfGeneNodes = geneElements.getLength();
for (int i = 0; i < numberOfGeneNodes; i++) {
Element thisGeneElement = (Element) geneElements.item(i);
thisGeneElement.normalize();
// Fetch the class attribute and create an instance of that
// class to represent the current gene.
// --------------------------------------------------------
String geneClassName = thisGeneElement.getAttribute(CLASS_ATTRIBUTE);
Gene thisGeneObject;
Class geneClass = null;
try {
geneClass = Class.forName(geneClassName);
try {
Constructor constr = geneClass.getConstructor(new Class[] {Configuration.class});
thisGeneObject = (Gene) constr.newInstance(new Object[] {a_activeConfiguration});
} catch (NoSuchMethodException nsme) {
// Try it by calling method newGeneInternal.
// -----------------------------------------
Constructor constr = geneClass.getConstructor(new Class[] {});
thisGeneObject = (Gene) constr.newInstance(new Object[] {});
thisGeneObject =
(Gene)
PrivateAccessor.invoke(
thisGeneObject, "newGeneInternal", new Class[] {}, new Object[] {});
}
} catch (Throwable e) {
throw new GeneCreationException(geneClass, e);
}
// Find the text node and fetch the string representation of
// the allele.
// ---------------------------------------------------------
NodeList children = thisGeneElement.getChildNodes();
int childrenSize = children.getLength();
String alleleRepresentation = null;
for (int j = 0; j < childrenSize; j++) {
Element alleleElem = (Element) children.item(j);
if (alleleElem.getTagName().equals(ALLELE_TAG)) {
alleleRepresentation = alleleElem.getAttribute("value");
}
if (children.item(j).getNodeType() == Node.TEXT_NODE) {
// We found the text node. Extract the representation.
// ---------------------------------------------------
alleleRepresentation = children.item(j).getNodeValue();
break;
}
}
// Sanity check: Make sure the representation isn't null.
// ------------------------------------------------------
if (alleleRepresentation == null) {
throw new ImproperXMLException(
"Unable to build Gene instance from XML Element: "
+ "value (allele) is missing representation.");
}
// Now set the value of the gene to that reflect the
// string representation.
// -------------------------------------------------
try {
thisGeneObject.setValueFromPersistentRepresentation(alleleRepresentation);
} catch (UnsupportedOperationException e) {
throw new GeneCreationException(
"Unable to build Gene because it does not support the "
+ "setValueFromPersistentRepresentation() method.");
}
// Finally, add the current gene object to the list of genes.
// ----------------------------------------------------------
genes.add(thisGeneObject);
}
return (Gene[]) genes.toArray(new Gene[genes.size()]);
}
