public ActionDescriptor getAction(int id) {
// check global actions
for (Iterator iterator = globalActions.iterator(); iterator.hasNext(); ) {
ActionDescriptor actionDescriptor = (ActionDescriptor) iterator.next();
if (actionDescriptor.getId() == id) {
return actionDescriptor;
}
}
// check steps
for (Iterator iterator = steps.iterator(); iterator.hasNext(); ) {
StepDescriptor stepDescriptor = (StepDescriptor) iterator.next();
ActionDescriptor actionDescriptor = stepDescriptor.getAction(id);
if (actionDescriptor != null) {
return actionDescriptor;
}
}
// check initial actions, which we now must have unique id's
for (Iterator iterator = initialActions.iterator(); iterator.hasNext(); ) {
ActionDescriptor actionDescriptor = (ActionDescriptor) iterator.next();
if (actionDescriptor.getId() == id) {
return actionDescriptor;
}
}
return null;
}
/**
* This will invoke the <code>startElement</code> callback in the <code>ContentHandler</code>.
*
* @param element <code>Element</code> used in callbacks.
* @param nsAtts <code>List</code> of namespaces to declare with the element or <code>null</code>.
*/
private void startElement(Element element, Attributes nsAtts) throws JDOMException {
String namespaceURI = element.getNamespaceURI();
String localName = element.getName();
String rawName = element.getQualifiedName();
// Allocate attribute list.
AttributesImpl atts = (nsAtts != null) ? new AttributesImpl(nsAtts) : new AttributesImpl();
List attributes = element.getAttributes();
Iterator i = attributes.iterator();
while (i.hasNext()) {
Attribute a = (Attribute) i.next();
atts.addAttribute(
a.getNamespaceURI(),
a.getName(),
a.getQualifiedName(),
getAttributeTypeName(a.getAttributeType()),
a.getValue());
}
try {
contentHandler.startElement(namespaceURI, localName, rawName, atts);
} catch (SAXException se) {
throw new JDOMException("Exception in startElement", se);
}
}
public AlbumBean[] getResult() {
synchronized (libraryList) {
AlbumBean[] res;
res = libraryList.toArray(new AlbumBean[libraryList.size()]);
return res;
}
}
@Override
public void processingInstruction(String target, String data) throws SAXException {
_logger.fine("Processing Instruction " + target);
_logger.fine("Processing Instruction data: " + data);
if (target.equals("assemble")) {
if (!_stack.isEmpty()) {
ElementInfo element = _stack.get(_stack.size() - 1);
Matcher matcher = PROCESSING_INSTRUCTION.matcher(data);
while (matcher.find()) {
if (matcher.groupCount() == 2) {
String name = matcher.group(1);
if (name.charAt(0) == '@') {
element.inst.put(name, matcher.group(2));
} else {
element.args.add(guessUntypedValue(name, matcher.group(2)));
}
_logger.fine(
"Processing Instruction for "
+ element.data.getClass()
+ "\n\ttarget = "
+ target
+ "\n\t"
+ name
+ "="
+ matcher.group(2));
}
}
}
}
}
private LinkedHashMap[] obtenerMapeos(CliGol cliGol, NodeList variables, String[] excluye) {
LinkedHashMap<String, Object> mapa = new LinkedHashMap<String, Object>();
LinkedHashMap<String, String> puntos = new LinkedHashMap<String, String>();
List<String> ex = Arrays.asList(excluye);
for (int i = 0; i < variables.getLength(); i++) {
String nom = variables.item(i).getNodeName();
if (!ex.contains(nom)) {
String golMapdijo = GolMap.xmlGol(nom);
String val = null;
if (golMapdijo != null) {
val = buscaValEnCli(golMapdijo, cliGol);
mapa.put(nom, val);
puntos.put(nom, variables.item(i).getTextContent());
}
}
}
return new LinkedHashMap[] {mapa, puntos};
}
/**
* This will take the supplied <code>{@link Element}</code> and transfer its namespaces to the
* global namespace storage.
*
* @param element <code>Element</code> to read namespaces from.
*/
private void transferNamespaces(Element element) {
Iterator i = declaredNamespaces.iterator();
while (i.hasNext()) {
Namespace ns = (Namespace) i.next();
if (ns != element.getNamespace()) {
element.addNamespaceDeclaration(ns);
}
}
declaredNamespaces.clear();
}
// returns list of statements
protected static void replaceMultSPO(
Statement st, NodeFactory f, Map o2n, Collection result, RDFNode toReplace, int position)
throws ModelException {
Collection replacements;
if (toReplace instanceof Statement) {
List l = new ArrayList();
replaceMult((Statement) toReplace, f, o2n, l);
if (l.size() == 1 && toReplace == l.get(0)) {
result.add(st);
return; // keep the same
} else replacements = l;
} else {
Object ro = o2n.get(toReplace);
if (ro instanceof Collection) replacements = (Collection) ro;
else if (ro != null) {
replacements = new ArrayList();
replacements.add(ro);
} else { // no replacement needed
result.add(st); // keep the same statement
return;
}
}
for (Iterator it = replacements.iterator(); it.hasNext(); ) {
Statement rs = null;
Object rr = it.next();
switch (position) {
case 0:
rs = f.createStatement((Resource) rr, st.predicate(), st.object());
break;
case 1:
rs = f.createStatement(st.subject(), (Resource) rr, st.object());
break;
case 2:
rs = f.createStatement(st.subject(), st.predicate(), (RDFNode) rr);
break;
}
result.add(rs);
}
}
public static List getObjects(Model m, Resource subject, Resource predicate)
throws ModelException {
List result = new ArrayList();
if (m == null || m.size() == 0) return result;
for (Enumeration en = m.find(subject, predicate, null).elements(); en.hasMoreElements(); ) {
Statement st = (Statement) en.nextElement();
result.add(st.object());
}
return result;
}
public void updateBean(AlbumBean newBean, AlbumBean oldBean) throws LibraryException {
synchronized (libraryList) {
// Find the bean
int index = libraryList.indexOf(oldBean);
if (index == -1) {
LibraryException le = new LibraryException(Utils.getResourceString(ERROR_BEAN_NOT_FOUND));
throw le;
}
// Set the new bean
libraryList.set(index, newBean);
setChanged();
fireLibraryChangeEvent(
new LibraryChangeEvent(this, new AlbumBean[] {oldBean}, LibraryChangeEvent.UPDATE));
}
}
private AlbumBean addOrUpdateAlbum(
Map<Integer, AlbumBean> map, SongBean song, boolean albumOnly) {
// Add an album bean
if (song != null && song.getAlbum() != null) {
int hashCode = (song.getAlbum() + (albumOnly ? "" : '\uFFFF' + song.getArtist())).hashCode();
// Check if the album beam already exists
AlbumBean album = map.get(hashCode);
if (album == null) {
album = new AlbumBean();
album.setAlbum(song.getAlbum());
map.put(hashCode, album);
}
// Update the album properties
try {
// Add the track id to the album bean
album.addSong(song);
album.incTracks();
album.setArtist(song.getArtist());
album.setGenre(song.getGenre());
album.setDisc_Count(song.getDisc_Count());
} catch (LibraryException le) {
// There was an error adding the song to this album, remove it
map.remove(hashCode);
// Add to warning message
warningList.add(song.getName() + " " + le);
}
return album;
}
return null;
}
private void guardarEnListas(String nodeName, String informacion) {
System.out.println(informacion);
if (nodeName.equals("NoHit")) {
NoHit.add(informacion);
return;
}
if (nodeName.equals("Hit")) {
Hit.add(informacion);
return;
}
if (nodeName.equals("Buro")) {
Buro.add(informacion);
return;
}
}
public void startElement(String uri, String localName, String qName, Attributes atts) {
logger.log(
LogService.LOG_DEBUG,
"Here is OcdHandler:startElement():" //$NON-NLS-1$
+ qName);
if (!_isParsedDataValid) return;
String name = getName(localName, qName);
if (name.equalsIgnoreCase(AD)) {
AttributeDefinitionHandler attributeDefHandler = new AttributeDefinitionHandler(this);
attributeDefHandler.init(name, atts, _ad_vector);
} else if (name.equalsIgnoreCase(ICON)) {
IconHandler iconHandler = new IconHandler(this);
iconHandler.init(name, atts);
if (iconHandler._isParsedDataValid) icons.add(iconHandler._icon);
} else {
logger.log(
LogService.LOG_WARNING,
NLS.bind(
MetaTypeMsg.UNEXPECTED_ELEMENT,
new Object[] {
name,
atts.getValue(ID),
_dp_url,
_dp_bundle.getBundleId(),
_dp_bundle.getSymbolicName()
}));
}
}
/** @deprecated use immediateChildrenByTagName( Element parent, String tagName ) */
public static NodeList getImmediateChildElementsByTagName(Element parent, String tagName)
throws DOMException {
final List nodes = new ArrayList();
for (Node child = parent.getFirstChild(); child != null; child = child.getNextSibling())
if (child instanceof Element && ((Element) child).getTagName().equals(tagName))
nodes.add(child);
return new NodeList() {
public int getLength() {
return nodes.size();
}
public Node item(int i) {
return (Node) nodes.get(i);
}
};
}
/**
* This will add the prefix mapping to the JDOM <code>Document</code> object.
*
* @param prefix <code>String</code> namespace prefix.
* @param uri <code>String</code> namespace URI.
*/
public void startPrefixMapping(String prefix, String uri) throws SAXException {
if (suppress) return;
Namespace ns = Namespace.getNamespace(prefix, uri);
declaredNamespaces.add(ns);
}
/**
* Add a step
*
* @param descriptor The step descriptor to add
* @throws IllegalArgumentException if the descriptor's ID already exists in the workflow
*/
public void addStep(StepDescriptor descriptor) {
if (getStep(descriptor.getId()) != null) {
throw new IllegalArgumentException("Step with id " + descriptor.getId() + " already exists");
}
steps.add(descriptor);
}
/**
* Add a join
*
* @param descriptor The join descriptor to add
* @throws IllegalArgumentException if the descriptor's ID already exists in the workflow
*/
public void addJoin(JoinDescriptor descriptor) {
if (getJoin(descriptor.getId()) != null) {
throw new IllegalArgumentException("Join with id " + descriptor.getId() + " already exists");
}
joins.add(descriptor);
}
/**
* Add a split
*
* @param descriptor The split descriptor to add
* @throws IllegalArgumentException if the descriptor's ID already exists in the workflow
*/
public void addSplit(SplitDescriptor descriptor) {
if (getSplit(descriptor.getId()) != null) {
throw new IllegalArgumentException("Split with id " + descriptor.getId() + " already exists");
}
splits.add(descriptor);
}
private QueryResult gatherResultInfoForSelectQuery(
String queryString, int queryNr, boolean sorted, Document doc, String[] rows) {
Element root = doc.getRootElement();
// Get head information
Element child =
root.getChild("head", Namespace.getNamespace("http://www.w3.org/2005/sparql-results#"));
// Get result rows (<head>)
List headChildren =
child.getChildren(
"variable", Namespace.getNamespace("http://www.w3.org/2005/sparql-results#"));
Iterator it = headChildren.iterator();
ArrayList<String> headList = new ArrayList<String>();
while (it.hasNext()) {
headList.add(((Element) it.next()).getAttributeValue("name"));
}
List resultChildren =
root.getChild("results", Namespace.getNamespace("http://www.w3.org/2005/sparql-results#"))
.getChildren(
"result", Namespace.getNamespace("http://www.w3.org/2005/sparql-results#"));
int nrResults = resultChildren.size();
QueryResult queryResult = new QueryResult(queryNr, queryString, nrResults, sorted, headList);
it = resultChildren.iterator();
while (it.hasNext()) {
Element resultElement = (Element) it.next();
String result = "";
// get the row values and paste it together to one String
for (int i = 0; i < rows.length; i++) {
List bindings =
resultElement.getChildren(
"binding", Namespace.getNamespace("http://www.w3.org/2005/sparql-results#"));
String rowName = rows[i];
for (int j = 0; j < bindings.size(); j++) {
Element binding = (Element) bindings.get(j);
if (binding.getAttributeValue("name").equals(rowName))
if (result.equals(""))
result +=
rowName + ": " + ((Element) binding.getChildren().get(0)).getTextNormalize();
else
result +=
"\n"
+ rowName
+ ": "
+ ((Element) binding.getChildren().get(0)).getTextNormalize();
}
}
queryResult.addResult(result);
}
return queryResult;
}
/**
* This will output a list of JDOM nodes as a fragment of an XML document, firing off the SAX
* events that have been registered.
*
* <p><strong>Warning</strong>: This method does not call the {@link
* ContentHandler#setDocumentLocator}, {@link ContentHandler#startDocument} and {@link
* ContentHandler#endDocument} callbacks on the {@link #setContentHandler ContentHandler}. The
* user shall invoke these methods directly prior/after outputting the document fragments.
*
* @param nodes <code>List</code> of JDOM nodes to output.
* @throws JDOMException if any error occurred.
* @see #outputFragment(org.jdom2.Content)
*/
public void outputFragment(List<? extends Content> nodes) throws JDOMException {
if ((nodes == null) || (nodes.size() == 0)) {
return;
}
// Output node list as a document fragment.
elementContent(nodes, new NamespaceStack());
}
boolean load(Object[] props, int offset) {
if (_values.size() > 0) {
int p = _values.size() - 1;
while (_index[p] > _values.get(p).size() - 1 && p > 0) {
_index[p] = 0;
--p;
++_index[p];
}
if (_index[p] > _values.get(p).size() - 1) {
return false;
}
// System.err.print("\t TypedValueGroup.load{");
for (int i = 0; i < _values.size(); ++i) {
props[i + offset] = _values.get(i).get(_index[i]).data;
// System.err.print("[" + _index[i] + "](" + props[i+offset].getClass().getSimpleName() +
// ')');
}
// System.err.println("}");
++_index[_values.size() - 1];
return true;
} else {
return false;
}
}
public StepDescriptor getStep(int id) {
for (Iterator iterator = steps.iterator(); iterator.hasNext(); ) {
StepDescriptor step = (StepDescriptor) iterator.next();
if (step.getId() == id) {
return step;
}
}
return null;
}
public SplitDescriptor getSplit(int id) {
for (Iterator iterator = splits.iterator(); iterator.hasNext(); ) {
SplitDescriptor splitDescriptor = (SplitDescriptor) iterator.next();
if (splitDescriptor.getId() == id) {
return splitDescriptor;
}
}
return null;
}
public JoinDescriptor getJoin(int id) {
for (Iterator iterator = joins.iterator(); iterator.hasNext(); ) {
JoinDescriptor joinDescriptor = (JoinDescriptor) iterator.next();
if (joinDescriptor.getId() == id) {
return joinDescriptor;
}
}
return null;
}
public ActionDescriptor getInitialAction(int id) {
for (Iterator iterator = initialActions.iterator(); iterator.hasNext(); ) {
ActionDescriptor actionDescriptor = (ActionDescriptor) iterator.next();
if (actionDescriptor.getId() == id) {
return actionDescriptor;
}
}
return null;
}
/**
* This will invoke the <code>ContentHandler.startPrefixMapping</code> callback when a new
* namespace is encountered in the <code>Document</code>.
*
* @param element <code>Element</code> used in callbacks.
* @param namespaces <code>List</code> stack of Namespaces in scope.
* @return <code>Attributes</code> declaring the namespaces local to <code>element</code> or
* <code>null</code>.
*/
private Attributes startPrefixMapping(Element element, NamespaceStack namespaces)
throws JDOMException {
AttributesImpl nsAtts = null; // The namespaces as xmlns attributes
Namespace ns = element.getNamespace();
if (ns != Namespace.XML_NAMESPACE) {
String prefix = ns.getPrefix();
String uri = namespaces.getURI(prefix);
if (!ns.getURI().equals(uri)) {
namespaces.push(ns);
nsAtts = this.addNsAttribute(nsAtts, ns);
try {
contentHandler.startPrefixMapping(prefix, ns.getURI());
} catch (SAXException se) {
throw new JDOMException("Exception in startPrefixMapping", se);
}
}
}
// Fire additional namespace declarations
List additionalNamespaces = element.getAdditionalNamespaces();
if (additionalNamespaces != null) {
Iterator itr = additionalNamespaces.iterator();
while (itr.hasNext()) {
ns = (Namespace) itr.next();
String prefix = ns.getPrefix();
String uri = namespaces.getURI(prefix);
if (!ns.getURI().equals(uri)) {
namespaces.push(ns);
nsAtts = this.addNsAttribute(nsAtts, ns);
try {
contentHandler.startPrefixMapping(prefix, ns.getURI());
} catch (SAXException se) {
throw new JDOMException("Exception in startPrefixMapping", se);
}
}
}
}
return nsAtts;
}
/**
* This will invoke the callbacks for the content of an element.
*
* @param content element content as a <code>List</code> of nodes.
* @param namespaces <code>List</code> stack of Namespaces in scope.
*/
private void elementContent(List content, NamespaceStack namespaces) throws JDOMException {
for (Iterator i = content.iterator(); i.hasNext(); ) {
Object obj = i.next();
if (obj instanceof Content) {
this.elementContent((Content) obj, namespaces);
} else {
// Not a valid element child. This could happen with
// application-provided lists which may contain non
// JDOM objects.
handleError(new JDOMException("Invalid element content: " + obj));
}
}
}
/**
* Returns the content of a JDOM Element detached from it.
*
* @param elt the element to get the content from.
* @return a (possibly empty) list of JDOM nodes, detached from their parent.
*/
private List getDetachedContent(Element elt) {
List content = elt.getContent();
List nodes = new ArrayList(content.size());
while (content.size() != 0) {
Object o = content.remove(0);
nodes.add(o);
}
return (nodes);
}
/**
* This will output a list of JDOM nodes as a document, firing off the SAX events that have been
* registered.
*
* <p><strong>Warning</strong>: This method may output ill-formed XML documents if the list
* contains top-level objects that are not legal at the document level (e.g. Text or CDATA nodes,
* multiple Element nodes, etc.). Thus, it should only be used to output document portions towards
* ContentHandlers capable of accepting such ill-formed documents (such as XSLT processors).
*
* @param nodes <code>List</code> of JDOM nodes to output.
* @throws JDOMException if any error occurred.
* @see #output(org.jdom2.Document)
*/
public void output(List<? extends Content> nodes) throws JDOMException {
if ((nodes == null) || (nodes.size() == 0)) {
return;
}
// contentHandler.setDocumentLocator()
documentLocator(null);
// contentHandler.startDocument()
startDocument();
// Process node list.
elementContent(nodes, new NamespaceStack());
// contentHandler.endDocument()
endDocument();
}
/** finish handling and set up the enclosed object Usually called when the end tag is seen */
@Override
public void finishProcessing() {
IMeasuredSpectrum pMeasured = null;
final double pScore = getScore();
final double pHyperScore = getHyperScore();
final double rawScore = getRawScore();
IonTypeScorer scorer = getIonScore();
IProteinPosition[] containedInProteins = m_Positions.toArray(IProteinPosition.EMPTY_ARRAY);
((Polypeptide) m_Peptide).setContainedInProteins(containedInProteins);
SpectralMatch scan =
new SpectralMatch(m_Peptide, pMeasured, pScore, pHyperScore, rawScore, scorer, null);
if (m_Usage != null) scan.getUsage().addTo(m_Usage);
setElementObject(scan);
}
// returns list of statements
public static void replaceMult(Statement st, NodeFactory f, Map o2n, Collection result)
throws ModelException {
List l1 = new ArrayList();
replaceMultSPO(st, f, o2n, l1, st.subject(), 0);
List l2 = new ArrayList();
for (int i = 0; i < l1.size(); i++)
replaceMultSPO((Statement) l1.get(i), f, o2n, l2, st.predicate(), 1);
for (int i = 0; i < l2.size(); i++)
replaceMultSPO((Statement) l2.get(i), f, o2n, result, st.object(), 2);
}
