private static SetInfo parseSet(Node parent) throws XmlParserException {
String id = "";
String type = "";
String measurementids = null;
NodeList nodes = parent.getChildNodes();
Vector<SetInfo> sets = new Vector<SetInfo>();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
if (element.getTagName().equals("id")) id = element.getTextContent();
else if (element.getTagName().equals("set")) sets.add(parseSet(element));
else if (element.getTagName().equals("type")) type = element.getTextContent();
else if (element.getTagName().equals("measurementids"))
measurementids = element.getTextContent();
}
// create the set
SetInfo set = new SetInfo(id, Integer.parseInt(type));
if (measurementids != null) {
int mids[] = ByteArray.toIntArray(Base64.decode(measurementids), ByteArray.ENDIAN_LITTLE, 32);
for (int mid : mids) set.addMeasurementID(mid);
}
// add the children
for (SetInfo s : sets) set.addChild(s);
return set;
}
private static MeasurementInfo parseMeasurement(Node parent) throws XmlParserException {
String id = "";
String label = "";
String sampleid = "";
Vector<FileInfo> files = null;
Vector<ScanInfo> scans = null;
NodeList nodes = parent.getChildNodes();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
if (element.getTagName().equals("id")) id = element.getTextContent();
else if (element.getTagName().equals("label")) label = element.getTextContent();
else if (element.getTagName().equals("sampleid")) sampleid = element.getTextContent();
else if (element.getTagName().equals("scans")) scans = parseScans(node);
else if (element.getTagName().equals("files")) files = parseFiles(node);
}
MeasurementInfo measurement = new MeasurementInfo(Integer.parseInt(id), sampleid);
measurement.setLabel(label);
measurement.addFileInfos(files);
if (scans != null) measurement.addScanInfos(scans);
return measurement;
}
private static IPeakSet<? extends IPeak> parsePeakSet(Node parent) throws XmlParserException {
// retrieve all the properties
Vector<IPeak> peaks = new Vector<IPeak>();
NodeList nodes = parent.getChildNodes();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
if (element.getTagName().equals("peaks")) {
NodeList nodes2 = node.getChildNodes();
for (int nodeid2 = 0; nodeid2 < nodes2.getLength(); ++nodeid2) {
Node node2 = nodes2.item(nodeid2);
if (node2.getNodeType() != Node.ELEMENT_NODE) continue;
IPeak peak = parseIPeak(node2);
if (peak != null) peaks.add(peak);
}
}
}
// create the bugger
IPeakSet<IPeak> peakset = new IPeakSet<IPeak>(peaks);
parseIPeak(parent, peakset);
return peakset;
}
/**
* Set a property of a resource to a value.
*
* @param name the property name
* @param value the property value
* @exception com.ibm.webdav.WebDAVException
*/
public void setProperty(String name, Element value) throws WebDAVException {
// load the properties
Document propertiesDocument = resource.loadProperties();
Element properties = propertiesDocument.getDocumentElement();
String ns = value.getNamespaceURI();
Element property = null;
if (ns == null) {
property = (Element) ((Element) properties).getElementsByTagName(value.getTagName()).item(0);
} else {
property = (Element) properties.getElementsByTagNameNS(ns, value.getLocalName()).item(0);
}
if (property != null) {
try {
properties.removeChild(property);
} catch (DOMException exc) {
}
}
properties.appendChild(propertiesDocument.importNode(value, true));
// write out the properties
resource.saveProperties(propertiesDocument);
}
/*
* Output this item. Then, if the element has child elements, output each.
*/
private void outputItem(Element e, PrintWriter out) {
int chk = 0;
HashMap collection = new HashMap();
String key = null;
Element collectionElement = null;
log.fine("outputing item for " + e.getAttribute("name") + ": " + e.getAttribute("query"));
out.println("<item>");
out.println("<name>" + e.getAttribute("name") + "</name>");
if (e.getTagName().equalsIgnoreCase("collection")) {
// change made by NETTY (change collectionlist to collection)
out.println(
"<query>collection="
+ e.getAttribute("col_id")
+ "&xsl=metadata_to_html_full</query>");
} else {
out.println(
"<query>owner=" + e.getAttribute("query") + "&xsl=metadata_to_html_full</query>");
}
// now output children
NodeList children = e.getChildNodes();
for (int i = 0; i < children.getLength(); i++) {
Node child = children.item(i);
if (child.getNodeType() == Node.ELEMENT_NODE) {
chk++;
outputItem((Element) child, out);
}
}
out.println("</item>");
}
/*
* If the element contains an attribute 'makeOnly' with a value of 'true',
* create a child element before any existing children which will display a node
* which will display only the elements records.
* Compute the query attribute, which is the appended result of all of the children
* appended to this element name. If noQuery=true. then do not generate a query term
* for this element.
*/
String computeQuery(Element e) {
String query = "";
if (!(e.getAttribute("noQuery").equalsIgnoreCase("true"))) {
query = e.getAttribute("name");
}
String makeOnly = e.getAttribute("makeOnly");
boolean madeOnly = false;
NodeList children = e.getChildNodes();
for (int i = 0; i < children.getLength(); i++) {
Node child = children.item(i);
if (child.getNodeType() == Node.ELEMENT_NODE) {
if (makeOnly.equalsIgnoreCase("true") && !madeOnly) {
// need to make an ...-Only node and populate it
String onlyTagName = e.getTagName() + "-Only";
Element only = ((Document) dom.getNode()).createElement(onlyTagName);
only.setAttribute("name", e.getAttribute("name") + "-Only");
only.setAttribute("query", e.getAttribute("name"));
e.insertBefore(only, child);
i++;
madeOnly = true;
}
if (query.length() > 0) {
query += ",";
}
query += computeQuery((Element) child);
}
}
log.info("setting query for " + e.getNodeName() + " " + query);
e.setAttribute("query", query);
return query;
}
/**
* Unmarshall a Genotype instance from a given XML Element representation. Its population of
* Chromosomes will be unmarshalled from the Chromosome sub-elements.
*
* @param a_activeConfiguration the current active Configuration object that is to be used during
* construction of the Genotype and Chromosome instances
* @param a_xmlElement the XML Element representation of the Genotype
* @return a new Genotype instance, complete with a population of Chromosomes, setup with the data
* from the XML Element representation
* @throws ImproperXMLException if the given Element is improperly structured or missing data
* @throws InvalidConfigurationException if the given Configuration is in an inconsistent state
* @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
* @author Klaus Meffert
* @since 1.0
*/
public static Genotype getGenotypeFromElement(
Configuration a_activeConfiguration, Element a_xmlElement)
throws ImproperXMLException, InvalidConfigurationException,
UnsupportedRepresentationException, GeneCreationException {
// Sanity check. Make sure the XML element isn't null and that it
// actually represents a genotype.
if (a_xmlElement == null || !(a_xmlElement.getTagName().equals(GENOTYPE_TAG))) {
throw new ImproperXMLException(
"Unable to build Genotype instance from XML Element: "
+ "given Element is not a 'genotype' element.");
}
// Fetch all of the nested chromosome elements and convert them
// into Chromosome instances.
// ------------------------------------------------------------
NodeList chromosomes = a_xmlElement.getElementsByTagName(CHROMOSOME_TAG);
int numChromosomes = chromosomes.getLength();
Population population = new Population(a_activeConfiguration, numChromosomes);
for (int i = 0; i < numChromosomes; i++) {
population.addChromosome(
getChromosomeFromElement(a_activeConfiguration, (Element) chromosomes.item(i)));
}
// Construct a new Genotype with the chromosomes and return it.
// ------------------------------------------------------------
return new Genotype(a_activeConfiguration, population);
}
/**
* Unmarshall a Chromosome instance from a given XML Element representation.
*
* @param a_activeConfiguration the current active Configuration object that is to be used during
* construction of the Chromosome
* @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 InvalidConfigurationException if the given Configuration is in an inconsistent state
* @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 Chromosome getChromosomeFromElement(
Configuration a_activeConfiguration, Element a_xmlElement)
throws ImproperXMLException, InvalidConfigurationException,
UnsupportedRepresentationException, GeneCreationException {
// Do some sanity checking. Make sure the XML Element isn't null and
// that in fact represents a chromosome.
// -----------------------------------------------------------------
if (a_xmlElement == null || !(a_xmlElement.getTagName().equals(CHROMOSOME_TAG))) {
throw new ImproperXMLException(
"Unable to build Chromosome instance from XML Element: "
+ "given Element is not a 'chromosome' element.");
}
// Extract the nested genes element and make sure it exists.
// ---------------------------------------------------------
Element genesElement = (Element) a_xmlElement.getElementsByTagName(GENES_TAG).item(0);
if (genesElement == null) {
throw new ImproperXMLException(
"Unable to build Chromosome instance from XML Element: "
+ "'genes' sub-element not found.");
}
// Construct the genes from their representations.
// -----------------------------------------------
Gene[] geneAlleles = getGenesFromElement(a_activeConfiguration, genesElement);
// Construct the new Chromosome with the genes and return it.
// ----------------------------------------------------------
return new Chromosome(a_activeConfiguration, geneAlleles);
}
/**
* @param sourceFile File to read from
* @return List of String objects with the shas
*/
public static FileRequestFileContent readRequestFile(final File sourceFile) {
if (!sourceFile.isFile() || !(sourceFile.length() > 0)) {
return null;
}
Document d = null;
try {
d = XMLTools.parseXmlFile(sourceFile.getPath());
} catch (final Throwable t) {
logger.log(Level.SEVERE, "Exception in readRequestFile, during XML parsing", t);
return null;
}
if (d == null) {
logger.log(Level.SEVERE, "Could'nt parse the request file");
return null;
}
final Element rootNode = d.getDocumentElement();
if (rootNode.getTagName().equals(TAG_FrostFileRequestFile) == false) {
logger.severe(
"Error: xml request file does not contain the root tag '"
+ TAG_FrostFileRequestFile
+ "'");
return null;
}
final String timeStampStr = XMLTools.getChildElementsTextValue(rootNode, TAG_timestamp);
if (timeStampStr == null) {
logger.severe("Error: xml file does not contain the tag '" + TAG_timestamp + "'");
return null;
}
final long timestamp = Long.parseLong(timeStampStr);
final List<Element> nodelist = XMLTools.getChildElementsByTagName(rootNode, TAG_shaList);
if (nodelist.size() != 1) {
logger.severe("Error: xml request files must contain only one element '" + TAG_shaList + "'");
return null;
}
final Element rootShaNode = nodelist.get(0);
final List<String> shaList = new LinkedList<String>();
final List<Element> xmlKeys = XMLTools.getChildElementsByTagName(rootShaNode, TAG_sha);
for (final Element el : xmlKeys) {
final Text txtname = (Text) el.getFirstChild();
if (txtname == null) {
continue;
}
final String sha = txtname.getData();
shaList.add(sha);
}
final FileRequestFileContent content = new FileRequestFileContent(timestamp, shaList);
return content;
}
/**
* ** Gets a virtual DBRecord from the specified remote service ** @param servReq The remote web
* service ** @return The virtual DBRecord (cannot be saved or reloaded)
*/
@SuppressWarnings("unchecked")
public gDBR getVirtualDBRecord(final ServiceRequest servReq) throws DBException {
String CMD_dbget = DBFactory.CMD_dbget;
String TAG_Response = servReq.getTagResponse();
String TAG_Record = DBFactory.TAG_Record;
String ATTR_command = servReq.getAttrCommand();
String ATTR_result = servReq.getAttrResult();
/* send request / get response */
Document xmlDoc = null;
try {
xmlDoc =
servReq.sendRequest(
CMD_dbget,
new ServiceRequest.RequestBody() {
public StringBuffer appendRequestBody(StringBuffer sb, int indent) {
return DBRecordKey.this.toRequestXML(sb, indent);
}
});
} catch (IOException ioe) {
Print.logException("Error", ioe);
throw new DBException("Request read error", ioe);
}
/* parse 'GTSResponse' */
Element gtsResponse = xmlDoc.getDocumentElement();
if (!gtsResponse.getTagName().equalsIgnoreCase(TAG_Response)) {
Print.logError("Request XML does not start with '%s'", TAG_Response);
throw new DBException("Response XML does not begin eith '" + TAG_Response + "'");
}
/* request command/argument */
String cmd = StringTools.trim(gtsResponse.getAttribute(ATTR_command));
String result = StringTools.trim(gtsResponse.getAttribute(ATTR_result));
if (StringTools.isBlank(result)) {
result = StringTools.trim(gtsResponse.getAttribute("type"));
}
if (!result.equalsIgnoreCase("success")) {
Print.logError("Response indicates failure");
throw new DBException("Response does not indicate 'success'");
}
/* Record */
NodeList rcdList = XMLTools.getChildElements(gtsResponse, TAG_Record);
if (rcdList.getLength() <= 0) {
Print.logError("No 'Record' tags");
throw new DBException("GTSResponse does not contain any 'Record' tags");
}
Element rcdElem = (Element) rcdList.item(0);
/* return DBRecord */
gDBR dbr = (gDBR) DBFactory.parseXML_DBRecord(rcdElem);
dbr.setVirtual(true);
return dbr;
}
private static Header parseHeader(Node parent) throws XmlParserException {
Header header = new Header();
NodeList nodes = parent.getChildNodes();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
try {
if (element.getTagName().equals("nrpeaks"))
header.setNrPeaks(Integer.parseInt(element.getTextContent()));
else if (element.getTagName().equals("date")) header.setDate(element.getTextContent());
else if (element.getTagName().equals("owner")) header.setOwner(element.getTextContent());
else if (element.getTagName().equals("description"))
header.setDescription(element.getTextContent());
else if (element.getTagName().equals("sets")) header.addSetInfos(parseSets(element));
else if (element.getTagName().equals("measurements"))
header.addMeasurementInfos(parseMeasurements(element));
else if (element.getTagName().equals("annotations")) {
Vector<Annotation> annotations = parseAnnotations(element);
if (annotations != null)
for (Annotation annotation : annotations) header.addAnnotation(annotation);
}
} catch (Exception e) {
throw new XmlParserException(
"Invalid value in header (" + element.getTagName() + "): '" + e.getMessage() + "'.");
}
}
return header;
}
private static Vector<Annotation> parseAnnotations(Node parent) throws XmlParserException {
Vector<Annotation> annotations = new Vector<Annotation>();
NodeList nodes = parent.getChildNodes();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
if (element.getTagName().equals("annotation")) {
String label = null, value = null, valuetype = null, unit = null;
NodeList annotation_nodes = element.getChildNodes();
for (int annotationid = 0; annotationid < annotation_nodes.getLength(); ++annotationid) {
Node annotation_node = annotation_nodes.item(annotationid);
if (annotation_node.getNodeType() != Node.ELEMENT_NODE) continue;
Element annotation_element = (Element) annotation_node;
if (annotation_element.getTagName().equals("label"))
label = annotation_element.getTextContent();
else if (annotation_element.getTagName().equals("value"))
value = annotation_element.getTextContent();
else if (annotation_element.getTagName().equals("valuetype"))
valuetype = annotation_element.getTextContent();
}
if (label == null || value == null || valuetype == null)
throw new XmlParserException("Annotation is missing either: label, value or valuetype");
Annotation annotation =
new Annotation(label, value, Annotation.ValueType.valueOf(valuetype));
annotation.setUnit(unit);
if (annotation.getValueType() == Annotation.ValueType.ONTOLOGY)
annotation.setOntologyRef(element.getAttribute("ontologyref"));
if (element.getAttribute("unit") != null) annotation.setUnit(element.getAttribute("unit"));
annotations.add(annotation);
}
}
return annotations;
}
private static ScanInfo parseScan(Node parent) throws XmlParserException {
double retentiontime = 0;
Polarity polarity = Polarity.NEUTRAL;
Vector<Annotation> annotations = null;
NodeList nodes = parent.getChildNodes();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
if (element.getTagName().equals("polarity"))
polarity = Polarity.valueOf(element.getTextContent());
else if (element.getTagName().equals("retentiontime"))
retentiontime = Double.parseDouble(element.getTextContent());
else if (element.getTagName().equals("annotations")) annotations = parseAnnotations(element);
}
ScanInfo scan = new ScanInfo(retentiontime, polarity);
if (annotations != null) scan.addAnnotations(annotations);
return scan;
}
private static FileInfo parseFile(Node parent) throws XmlParserException {
String label = "";
String name = "";
String location = "";
Vector<Annotation> annotations = null;
NodeList nodes = parent.getChildNodes();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
if (element.getTagName().equals("label")) label = element.getTextContent();
else if (element.getTagName().equals("name")) name = element.getTextContent();
else if (element.getTagName().equals("location")) location = element.getTextContent();
else if (element.getTagName().equals("annotations")) annotations = parseAnnotations(node);
}
FileInfo file = new FileInfo(label, name, location);
if (annotations != null) file.addAnnotations(annotations);
return file;
}
public void load(InputStream is) throws IOException, ParserConfigurationException, SAXException {
doc = db.parse(is);
docElt = doc.getDocumentElement();
if (docElt.getTagName().equals(docElementName)) {
NodeList nl = docElt.getElementsByTagName(trackElementName);
for (int i = 0; i < nl.getLength(); i++) {
Element elt = (Element) nl.item(i);
Track track = new Track(elt);
tracks.add(track);
hash.put(track.getKey(), track);
}
}
}
private static Vector<FileInfo> parseFiles(Node parent) throws XmlParserException {
Vector<FileInfo> files = new Vector<FileInfo>();
NodeList nodes = parent.getChildNodes();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
if (element.getTagName().equals("file")) files.add(parseFile(node));
}
return files;
}
/**
* Unmarshall a Chromosome instance from a given XML Document representation. Its genes will be
* unmarshalled from the gene sub-elements.
*
* @param a_activeConfiguration the current active Configuration object that is to be used during
* construction of the Chromosome instances
* @param a_xmlDocument the XML Document representation of the Chromosome
* @return a new Chromosome instance setup with the data from the XML Document representation
* @throws ImproperXMLException if the given Document is improperly structured or missing data
* @throws InvalidConfigurationException if the given Configuration is in an inconsistent state
* @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 Chromosome getChromosomeFromDocument(
Configuration a_activeConfiguration, Document a_xmlDocument)
throws ImproperXMLException, InvalidConfigurationException,
UnsupportedRepresentationException, GeneCreationException {
// Extract the root element, which should be a chromosome element.
// After verifying that the root element is not null and that it
// in fact is a chromosome element, then convert it into a Chromosome
// instance.
// ------------------------------------------------------------------
Element rootElement = a_xmlDocument.getDocumentElement();
if (rootElement == null || !(rootElement.getTagName().equals(CHROMOSOME_TAG))) {
throw new ImproperXMLException(
"Unable to build Chromosome instance from XML Document: "
+ "'chromosome' element must be at root of Document.");
}
return getChromosomeFromElement(a_activeConfiguration, rootElement);
}
private static void parseIPeak(Node parent, IPeak peak) throws XmlParserException {
// retrieve all the properties
int scan = -1;
double retentiontime = -1;
double mass = -1;
double intensity = -1;
int patternid = -1;
int measurementid = -1;
// String sha1 = null;
Vector<Annotation> annotations = null;
NodeList nodes = parent.getChildNodes();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
if (element.getTagName().equals("patternid"))
patternid = Integer.parseInt(element.getTextContent());
else if (element.getTagName().equals("measurementid"))
measurementid = Integer.parseInt(element.getTextContent());
else if (element.getTagName().equals("annotations")) annotations = parseAnnotations(element);
else if (element.getTagName().equals("scan"))
scan = Integer.parseInt(element.getTextContent());
else if (element.getTagName().equals("retentiontime"))
retentiontime = Double.parseDouble(element.getTextContent());
else if (element.getTagName().equals("mass"))
mass = Double.parseDouble(element.getTextContent());
else if (element.getTagName().equals("intensity"))
intensity = Double.parseDouble(element.getTextContent());
// else if (element.getTagName().equals("sha1sum"))
// sha1 = element.getTextContent();
}
// check whether obligatory values are missing
if (mass == -1 || intensity == -1)
throw new XmlParserException("Mass and/or intensity information is missing for IPeak.");
peak.setScanID(scan);
peak.setRetentionTime(retentiontime);
peak.setMass(mass);
peak.setIntensity(intensity);
peak.setPatternID(patternid);
peak.setMeasurementID(measurementid);
if (annotations != null)
for (Annotation annotation : annotations) peak.addAnnotation(annotation);
// check whether
// if (sha1!=null && !sha1.equals(peak.sha1()))
// throw new XmlParserException("SHA1-sum for individual ipeak element does not match.");
}
@SuppressWarnings("unchecked")
private static BackgroundIon<? extends Peak> parseBackgroundIon(Node parent)
throws XmlParserException {
// retrieve the separate peaks
PeakData<? extends Peak> peakdata = null;
NodeList nodes = parent.getChildNodes();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
if (element.getTagName().equals("peakdata")) {
peakdata = parsePeakData(element);
}
}
// create the bugger
BackgroundIon<? extends Peak> backgroundion = null;
if (peakdata.getFactory().getPeakClass().equals(Centroid.class))
backgroundion = new BackgroundIon<Centroid>((PeakData<Centroid>) peakdata);
parseIPeak(parent, backgroundion);
return backgroundion;
}
/**
* 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()]);
}
/**
* Edit the properties of a resource. The updates must refer to a Document containing a WebDAV
* propertyupdates element as the document root.
*
* @param updates an XML Document containing propertyupdate elements
* @return the result of making the updates describing the edits to be made.
* @exception com.ibm.webdav.WebDAVException
*/
public MultiStatus setProperties(Document propertyUpdates) throws WebDAVException {
// create a MultiStatus to hold the results. It will hold a MethodResponse
// for each update, and one for the method as a whole
MultiStatus multiStatus = new MultiStatus();
boolean errorsOccurred = false;
// first, load the properties so they can be edited
Document propertiesDocument = resource.loadProperties();
Element properties = (Element) propertiesDocument.getDocumentElement();
// be sure the updates have at least one update
Element propertyupdate = (Element) propertyUpdates.getDocumentElement();
String tagName = propertyupdate.getNamespaceURI() + propertyupdate.getLocalName();
if (!tagName.equals("DAV:propertyupdate")) {
throw new WebDAVException(
WebDAVStatus.SC_UNPROCESSABLE_ENTITY, "missing propertyupdate element");
}
NodeList updates = propertyupdate.getChildNodes();
if (updates.getLength() == 0) {
throw new WebDAVException(WebDAVStatus.SC_UNPROCESSABLE_ENTITY, "no updates in request");
}
Vector propsGood = new Vector(); // a list of properties that
// were patched correctly or would have been if another
// property hadn't gone bad.
// apply the updates
Node temp = null;
for (int i = 0; i < updates.getLength(); i++) {
temp = updates.item(i);
// skip any ignorable TXText elements
if (!(temp.getNodeType() == Node.ELEMENT_NODE)) {
continue;
}
Element update = (Element) temp;
int updateCommand = -1;
tagName = update.getNamespaceURI() + update.getLocalName();
if (tagName.equals("DAV:set")) {
updateCommand = set;
} else if (tagName.equals("DAV:remove")) {
updateCommand = remove;
} else {
throw new WebDAVException(
WebDAVStatus.SC_UNPROCESSABLE_ENTITY,
update.getTagName() + " is not a valid property update request");
}
// iterate through the props in the set or remove element and update the
// properties as directed
Element prop = (Element) update.getElementsByTagNameNS("DAV:", "prop").item(0);
if (prop == null) {
throw new WebDAVException(
WebDAVStatus.SC_UNPROCESSABLE_ENTITY, "no propeprties in update request");
}
NodeList propsToUpdate = prop.getChildNodes();
for (int j = 0; j < propsToUpdate.getLength(); j++) {
temp = propsToUpdate.item(j);
// skip any TXText elements??
if (!(temp.getNodeType() == Node.ELEMENT_NODE)) {
continue;
}
Element propToUpdate = (Element) temp;
// find the property in the properties element
Element property = null;
PropertyName propertyName = new PropertyName(propToUpdate);
if (((Element) propToUpdate).getNamespaceURI() != null) {
property =
(Element)
properties
.getElementsByTagNameNS(
propToUpdate.getNamespaceURI(), propToUpdate.getLocalName())
.item(0);
} else {
property = (Element) properties.getElementsByTagName(propToUpdate.getTagName()).item(0);
}
boolean liveone = isLive(propertyName.asExpandedString());
if (liveone) {
errorsOccurred = true;
PropertyResponse response = new PropertyResponse(resource.getURL().toString());
response.addProperty(propertyName, propToUpdate, WebDAVStatus.SC_FORBIDDEN);
multiStatus.addResponse(response);
}
// do the update
if (updateCommand == set) {
if (property != null) {
try {
properties.removeChild(property);
} catch (DOMException exc) {
}
}
if (!liveone) {
// I don't think we're allowed to update live properties
// here. Doing so effects the cache. A case in
// point is the lockdiscoveryproperty. properties
// is actually the properites cache "document" of this
// resource. Even though we don't "save" the request
// if it includes live properties, we don't remove
// it from the cache after we'd set it here, so it
// can affect other queries. (jlc 991002)
properties.appendChild(propertiesDocument.importNode(propToUpdate, true));
propsGood.addElement(propToUpdate);
}
} else if (updateCommand == remove) {
try {
if (property != null) {
properties.removeChild(property);
propsGood.addElement(propToUpdate);
}
} catch (DOMException exc) {
}
}
}
}
{
Enumeration els = propsGood.elements();
for (; els.hasMoreElements(); ) {
Object ob1 = els.nextElement();
Element elProp = (Element) ob1;
PropertyName pn = new PropertyName(elProp);
PropertyResponse response = new PropertyResponse(resource.getURL().toString());
response.addProperty(
pn,
(Element) elProp.cloneNode(false),
(errorsOccurred ? WebDAVStatus.SC_FAILED_DEPENDENCY : WebDAVStatus.SC_OK));
// todo: add code for responsedescription
multiStatus.addResponse(response);
}
}
// write out the properties
if (!errorsOccurred) {
resource.saveProperties(propertiesDocument);
}
return multiStatus;
}
/**
* Reads an XML element into a bean property by first locating the XML element corresponding to
* this property.
*
* @param ob The bean whose property is being set
* @param desc The property that will be set
* @param nodes The list of XML items that may contain the property
* @throws IOException If there is an error reading the document
*/
public void readProperty(Object ob, PropertyDescriptor desc, NodeList nodes, NamedNodeMap attrs)
throws IOException {
int numAttrs = attrs.getLength();
for (int i = 0; i < numAttrs; i++) {
// See if the attribute name matches the property name
if (namesMatch(desc.getName(), attrs.item(i).getNodeName())) {
// Get the method used to set this property
Method setter = desc.getWriteMethod();
// If this object has no setter, don't bother writing it
if (setter == null) continue;
// Get the value of the property
Object obValue = getObjectValue(desc, attrs.item(i).getNodeValue());
if (obValue != null) {
try {
// Set the property value
setter.invoke(ob, new Object[] {obValue});
} catch (InvocationTargetException exc) {
throw new IOException(
"Error setting property " + desc.getName() + ": " + exc.toString());
} catch (IllegalAccessException exc) {
throw new IOException(
"Error setting property " + desc.getName() + ": " + exc.toString());
}
}
return;
}
}
int numNodes = nodes.getLength();
Vector arrayBuild = null;
for (int i = 0; i < numNodes; i++) {
Node node = nodes.item(i);
// If this node isn't an element, skip it
if (!(node instanceof Element)) continue;
Element element = (Element) node;
// See if the tag name matches the property name
if (namesMatch(desc.getName(), element.getTagName())) {
// Get the method used to set this property
Method setter = desc.getWriteMethod();
// If this object has no setter, don't bother writing it
if (setter == null) continue;
// Get the value of the property
Object obValue = getObjectValue(desc, element);
// 070201 MAW: Modified from change submitted by Steve Poulson
if (setter.getParameterTypes()[0].isArray()) {
if (arrayBuild == null) {
arrayBuild = new Vector();
}
arrayBuild.addElement(obValue);
// 070201 MAW: Go ahead and read through the rest of the nodes in case
// another one matches the array. This has the effect of skipping
// over the "return" statement down below
continue;
}
if (obValue != null) {
try {
// Set the property value
setter.invoke(ob, new Object[] {obValue});
} catch (InvocationTargetException exc) {
throw new IOException(
"Error setting property " + desc.getName() + ": " + exc.toString());
} catch (IllegalAccessException exc) {
throw new IOException(
"Error setting property " + desc.getName() + ": " + exc.toString());
}
}
return;
}
}
// If we build a vector of array members, convert the vector into
// an array and save it in the property
if (arrayBuild != null) {
// Get the method used to set this property
Method setter = desc.getWriteMethod();
if (setter == null) return;
Object[] obValues = (Object[]) Array.newInstance(desc.getPropertyType(), arrayBuild.size());
arrayBuild.copyInto(obValues);
try {
setter.invoke(ob, new Object[] {obValues});
} catch (InvocationTargetException exc) {
throw new IOException("Error setting property " + desc.getName() + ": " + exc.toString());
} catch (IllegalAccessException exc) {
throw new IOException("Error setting property " + desc.getName() + ": " + exc.toString());
}
return;
}
}
/**
* ** Returns a ReverseGeocode instance containing address information ** @param gp The GeoPoint
* ** @return The ReverseGeocode instance
*/
private ReverseGeocode getAddressReverseGeocode(GeoPoint gp, String localeStr) {
/* URL */
String url = this.getAddressReverseGeocodeURL(gp);
Print.logInfo("Address URL: " + url);
/* create XML document */
Document xmlDoc = GetXMLDocument(url);
if (xmlDoc == null) {
return null;
}
/* create ReverseGeocode response */
Element reversegeocode = xmlDoc.getDocumentElement();
if (!reversegeocode.getTagName().equalsIgnoreCase(TAG_reversegeocode)) {
return null;
}
/* init */
String address_val = null; // null address
String house_val = null; // house number
String road_val = null; // street name
String city_val = null; // city name
String county_val = null; // county name
String state_val = null; // state/province
String postcode_val = null; // postal code
String country_name_val = null; // country name
String country_code_val = null; // country code
// full address
NodeList resultList = XMLTools.getChildElements(reversegeocode, TAG_result);
for (int r = 0; r < resultList.getLength(); r++) {
Element result = (Element) resultList.item(r);
// String osmType = XMLTools.getAttribute(result, ATTR_osm_type, null, false);
address_val = XMLTools.getNodeText(result, " ", false);
break; // only the first element
}
// address components
NodeList addresspartsList = XMLTools.getChildElements(reversegeocode, TAG_addressparts);
for (int a = 0; (a < addresspartsList.getLength()); a++) {
Element addressparts = (Element) addresspartsList.item(a);
NodeList addresspartsChildren = addressparts.getChildNodes();
for (int ac = 0; ac < addresspartsChildren.getLength(); ac++) {
Node child = addresspartsChildren.item(ac);
if (!(child instanceof Element)) {
continue;
}
Element elem = (Element) child;
String elemName = elem.getNodeName();
if (elemName.equalsIgnoreCase(TAG_house)) {
house_val = XMLTools.getNodeText(elem, " ", false);
} else if (elemName.equalsIgnoreCase(TAG_tram)) {
// ignore
} else if (elemName.equalsIgnoreCase(TAG_road)) {
road_val = XMLTools.getNodeText(elem, " ", false);
} else if (elemName.equalsIgnoreCase(TAG_residential)) {
// ignore
} else if (elemName.equalsIgnoreCase(TAG_village)) {
// ignore
} else if (elemName.equalsIgnoreCase(TAG_town)) {
if (StringTools.isBlank(city_val)) {
city_val = XMLTools.getNodeText(elem, " ", false);
}
} else if (elemName.equalsIgnoreCase(TAG_city)) {
city_val = XMLTools.getNodeText(elem, " ", false);
} else if (elemName.equalsIgnoreCase(TAG_county)) {
county_val = XMLTools.getNodeText(elem, " ", false);
} else if (elemName.equalsIgnoreCase(TAG_postcode)) {
postcode_val = XMLTools.getNodeText(elem, " ", false);
} else if (elemName.equalsIgnoreCase(TAG_state)) {
state_val = XMLTools.getNodeText(elem, " ", false);
} else if (elemName.equalsIgnoreCase(TAG_country)) {
country_name_val = XMLTools.getNodeText(elem, " ", false);
} else if (elemName.equalsIgnoreCase(TAG_country_code)) {
country_code_val = StringTools.trim(XMLTools.getNodeText(elem, " ", false)).toUpperCase();
} else {
// elemName unrecognized
}
}
break; // only the first element
}
/* populate ReverseGeocode instance */
ReverseGeocode rg = new ReverseGeocode();
StringBuffer addr = new StringBuffer();
// house number /road
if (!StringTools.isBlank(house_val)) {
addr.append(house_val);
if (!StringTools.isBlank(road_val)) {
addr.append(" ");
addr.append(road_val);
rg.setStreetAddress(house_val + " " + road_val);
} else {
rg.setStreetAddress(house_val);
}
} else if (!StringTools.isBlank(road_val)) {
addr.append(road_val);
rg.setStreetAddress(road_val);
}
// city/county
if (!StringTools.isBlank(city_val)) {
if (addr.length() > 0) {
addr.append(", ");
}
addr.append(city_val);
rg.setCity(city_val);
}
if (!StringTools.isBlank(county_val)) {
if (StringTools.isBlank(city_val)) {
// "city" not provided, at least include the "county"
if (addr.length() > 0) {
addr.append(", ");
}
addr.append("[").append(county_val).append("]");
}
// rg.setCounty(county_val);
}
// state/province
if (!StringTools.isBlank(state_val)) {
if (addr.length() > 0) {
addr.append(", ");
}
addr.append(state_val);
rg.setStateProvince(state_val);
if (!StringTools.isBlank(postcode_val)) {
addr.append(" ").append(postcode_val);
rg.setPostalCode(postcode_val);
}
} else {
if (!StringTools.isBlank(postcode_val)) {
if (addr.length() > 0) {
addr.append(", ");
}
addr.append(postcode_val);
rg.setPostalCode(postcode_val);
}
}
// country
if (!StringTools.isBlank(country_code_val)) {
if (country_code_val.equalsIgnoreCase("US")) {
// if (addr.length() > 0) { addr.append(", "); }
// addr.append("USA");
} else if (!StringTools.isBlank(country_name_val)) {
if (addr.length() > 0) {
addr.append(", ");
}
addr.append(country_name_val);
} else {
if (addr.length() > 0) {
addr.append(", ");
}
addr.append(country_code_val);
}
rg.setCountryCode(country_code_val);
}
// full address
rg.setFullAddress(addr.toString());
return rg;
}
// http://code.google.com/apis/maps/documentation/geocoding/index.html
public GeoPoint getGeocode(String address, String country) {
/* URL */
String url = this.getGeoPointGeocodeURL(address, country);
Print.logDebug("Google GC URL: " + url);
/* create XML document */
Document xmlDoc = GetXMLDocument(url, this.getGeocodeTimeout());
if (xmlDoc == null) {
return null;
}
/* vars */
String errCode = null;
GeoPoint geoPoint = null;
/* parse "xml" */
Element kml = xmlDoc.getDocumentElement();
if (kml.getTagName().equalsIgnoreCase(TAG_kml)) {
NodeList ResponseList = XMLTools.getChildElements(kml, TAG_Response);
for (int g = 0; (g < ResponseList.getLength()); g++) {
Element response = (Element) ResponseList.item(g);
NodeList responseNodes = response.getChildNodes();
for (int n = 0; n < responseNodes.getLength(); n++) {
Node responseNode = responseNodes.item(n);
if (!(responseNode instanceof Element)) {
continue;
}
Element responseElem = (Element) responseNode;
String responseNodeName = responseElem.getNodeName();
if (responseNodeName.equalsIgnoreCase(TAG_name)) {
// <name>1600 Amphitheatre Parkway, Mountain View, CA</name>
} else if (responseNodeName.equalsIgnoreCase(TAG_Status)) {
// <Status> ... </Status>
NodeList statusNodes = responseElem.getChildNodes();
for (int st = 0; st < statusNodes.getLength(); st++) {
Node statusNode = statusNodes.item(st);
if (!(statusNode instanceof Element)) {
continue;
}
Element statusElem = (Element) statusNode;
String statusNodeName = statusElem.getNodeName();
if (statusNodeName.equalsIgnoreCase(TAG_code)) {
errCode = StringTools.trim(GoogleGeocodeV2.GetNodeText(statusElem)); // expect "200"
break; // we only care about the 'code'
}
}
} else if (responseNodeName.equalsIgnoreCase(TAG_Placemark)) {
// <Placemark> ... </Placemark>
String id = responseElem.getAttribute(ATTR_id);
if ((id != null) && id.equals("p1")) {
NodeList placemarkNodes = responseElem.getChildNodes();
for (int pm = 0; (geoPoint == null) && (pm < placemarkNodes.getLength()); pm++) {
Node placemarkNode = placemarkNodes.item(pm);
if (!(placemarkNode instanceof Element)) {
continue;
}
Element placemarkElem = (Element) placemarkNode;
String placemarkNodeName = placemarkElem.getNodeName();
if (placemarkNodeName.equalsIgnoreCase(TAG_Point)) {
NodeList pointNodes = placemarkElem.getChildNodes();
for (int ptn = 0; (geoPoint == null) && (ptn < pointNodes.getLength()); ptn++) {
Node pointNode = pointNodes.item(ptn);
if (!(pointNode instanceof Element)) {
continue;
}
Element pointElem = (Element) pointNode;
String pointNodeName = pointElem.getNodeName();
if (pointNodeName.equalsIgnoreCase(TAG_coordinates)) {
String ll[] = StringTools.split(GoogleGeocodeV2.GetNodeText(pointElem), ',');
if (ll.length >= 2) {
double lon = StringTools.parseDouble(ll[0], 0.0); // longitude is first
double lat = StringTools.parseDouble(ll[1], 0.0);
if (GeoPoint.isValid(lat, lon)) {
geoPoint = new GeoPoint(lat, lon);
break; // we only care about the 'GeoPoint'
}
}
}
}
}
}
} else {
// Print.logInfo("Skipping Placemark ID = %s", id);
}
}
}
}
}
/* create address */
if (geoPoint != null) {
// GeoPoint found
return geoPoint;
}
/* check for Google reverse-geocode limit exceeded */
if ((errCode != null) && errCode.equals("620")) {
Print.logError("!!!! Google Reverse-Geocode Limit Exceeded [Error 620] !!!!");
}
/* no reverse-geocode available */
return null;
}
/* return reverse-geocode using nearest address */
public ReverseGeocode getAddressReverseGeocode(GeoPoint gp, String localeStr, boolean cache) {
/* check for failover mode */
if (this.isReverseGeocodeFailoverMode()) {
ReverseGeocodeProvider frgp = this.getFailoverReverseGeocodeProvider();
return frgp.getReverseGeocode(gp, localeStr, cache);
}
/* URL */
String url = this.getAddressReverseGeocodeURL(gp, localeStr);
Print.logDebug("Google RG URL: " + url);
// byte xmlBytes[] = HTMLTools.readPage(url);
/* create XML document */
Document xmlDoc = GetXMLDocument(url, this.getReverseGeocodeTimeout());
if (xmlDoc == null) {
return null;
}
/* vars */
String errCode = null;
String address = null;
/* parse "xml" */
Element kml = xmlDoc.getDocumentElement();
if (kml.getTagName().equalsIgnoreCase(TAG_kml)) {
NodeList ResponseList = XMLTools.getChildElements(kml, TAG_Response);
for (int g = 0; (g < ResponseList.getLength()); g++) {
Element response = (Element) ResponseList.item(g);
NodeList responseNodes = response.getChildNodes();
for (int n = 0; n < responseNodes.getLength(); n++) {
Node responseNode = responseNodes.item(n);
if (!(responseNode instanceof Element)) {
continue;
}
Element responseElem = (Element) responseNode;
String responseNodeName = responseElem.getNodeName();
if (responseNodeName.equalsIgnoreCase(TAG_name)) {
// <name>40.479581,-117.773438</name>
} else if (responseNodeName.equalsIgnoreCase(TAG_Status)) {
// <Status> ... </Status>
NodeList statusNodes = responseElem.getChildNodes();
for (int st = 0; st < statusNodes.getLength(); st++) {
Node statusNode = statusNodes.item(st);
if (!(statusNode instanceof Element)) {
continue;
}
Element statusElem = (Element) statusNode;
String statusNodeName = statusElem.getNodeName();
if (statusNodeName.equalsIgnoreCase(TAG_code)) {
errCode = StringTools.trim(GoogleGeocodeV2.GetNodeText(statusElem)); // expect "200"
break; // we only care about the 'code'
}
}
} else if (responseNodeName.equalsIgnoreCase(TAG_Placemark)) {
// <Placemark> ... </Placemark>
String id = responseElem.getAttribute(ATTR_id);
if ((id != null) && id.equals("p1")) {
NodeList placemarkNodes = responseElem.getChildNodes();
for (int pm = 0; pm < placemarkNodes.getLength(); pm++) {
Node placemarkNode = placemarkNodes.item(pm);
if (!(placemarkNode instanceof Element)) {
continue;
}
Element placemarkElem = (Element) placemarkNode;
String placemarkNodeName = placemarkElem.getNodeName();
if (placemarkNodeName.equalsIgnoreCase(TAG_address)) {
address = GoogleGeocodeV2.GetNodeText(placemarkElem);
break; // we only care about the 'address'
}
}
} else {
// Print.logInfo("Skipping Placemark ID = %s", id);
}
}
}
}
}
/* create address */
if (FAILOVER_DEBUG) {
errCode = "620";
} else if (!StringTools.isBlank(address)) {
// address found
ReverseGeocode rg = new ReverseGeocode();
rg.setFullAddress(address);
return rg;
}
/* check for Google reverse-geocode limit exceeded */
if ((errCode != null) && errCode.equals("620")) {
Print.logError("!!!! Google Reverse-Geocode Limit Exceeded [Error 620] !!!!");
if (this.hasFailoverReverseGeocodeProvider()) {
this.startReverseGeocodeFailoverMode();
ReverseGeocodeProvider frgp = this.getFailoverReverseGeocodeProvider();
Print.logWarn("Failing over to '" + frgp.getName() + "'");
return frgp.getReverseGeocode(gp, localeStr, cache);
}
}
/* no reverse-geocode available */
return null;
}
/**
* Reads XML element(s) into an indexed bean property by first locating the XML element(s)
* corresponding to this property.
*
* @param ob The bean whose property is being set
* @param desc The property that will be set
* @param nodes The list of XML items that may contain the property
* @throws IOException If there is an error reading the document
*/
public void readIndexedProperty(
Object ob, IndexedPropertyDescriptor desc, NodeList nodes, NamedNodeMap attrs)
throws IOException {
// Create a vector to hold the property values
Vector v = new Vector();
int numAttrs = attrs.getLength();
for (int i = 0; i < numAttrs; i++) {
// See if this attribute matches the property name
if (namesMatch(desc.getName(), attrs.item(i).getNodeName())) {
// Get the property value
Object obValue = getObjectValue(desc, attrs.item(i).getNodeValue());
if (obValue != null) {
// Add the value to the list of values to be set
v.addElement(obValue);
}
}
}
int numNodes = nodes.getLength();
for (int i = 0; i < numNodes; i++) {
Node node = nodes.item(i);
// Skip non-element nodes
if (!(node instanceof Element)) continue;
Element element = (Element) node;
// See if this element tag matches the property name
if (namesMatch(desc.getName(), element.getTagName())) {
// Get the property value
Object obValue = getObjectValue(desc, element);
if (obValue != null) {
// Add the value to the list of values to be set
v.addElement(obValue);
}
}
}
// Get the method used to set the property value
Method setter = desc.getWriteMethod();
// If this property has no setter, don't write it
if (setter == null) return;
// Create a new array of property values
Object propArray = Array.newInstance(desc.getPropertyType().getComponentType(), v.size());
// Copy the vector into the array
v.copyInto((Object[]) propArray);
try {
// Store the array of property values
setter.invoke(ob, new Object[] {propArray});
} catch (InvocationTargetException exc) {
throw new IOException("Error setting property " + desc.getName() + ": " + exc.toString());
} catch (IllegalAccessException exc) {
throw new IOException("Error setting property " + desc.getName() + ": " + exc.toString());
}
}
private static PeakData<? extends Peak> parsePeakData(Node parent) throws XmlParserException {
// get the attributes
Node typeattribute = parent.getAttributes().getNamedItem(PeakMLWriter.TYPE);
if (typeattribute == null) throw new XmlParserException("Failed to locate a type attribute.");
Node sizeattribute = parent.getAttributes().getNamedItem(PeakMLWriter.SIZE);
if (sizeattribute == null) throw new XmlParserException("Failed to locate a size attribute.");
int size = Integer.parseInt(sizeattribute.getNodeValue());
String type = typeattribute.getNodeValue();
// create the arrays
int scanids[] = null;
int patternids[] = null;
int measurementids[] = null;
double masses[] = null;
double intensities[] = null;
double retentiontimes[] = null;
// retrieve all the data
NodeList nodes = parent.getChildNodes();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
if (element.getTagName().equals("scanids"))
scanids =
ByteArray.toIntArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
else if (element.getTagName().equals("patternids"))
patternids =
ByteArray.toIntArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
else if (element.getTagName().equals("measurementids"))
measurementids =
ByteArray.toIntArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
else if (element.getTagName().equals("masses"))
masses =
ByteArray.toDoubleArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
else if (element.getTagName().equals("intensities"))
intensities =
ByteArray.toDoubleArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
else if (element.getTagName().equals("retentiontimes"))
retentiontimes =
ByteArray.toDoubleArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
}
// create the PeakData instance
if (type.equals("centroid"))
return new PeakData<Centroid>(
Centroid.factory,
size,
scanids,
patternids,
measurementids,
masses,
intensities,
retentiontimes);
return null;
}
