public void startElement(
String uri, String localName, String qName, org.xml.sax.Attributes atts)
throws SAXException {
if (DICTIONARY_ELEMENT.equals(localName)) {
mAttributes = new Attributes();
for (int i = 0; i < atts.getLength(); i++) {
mAttributes.setValue(atts.getLocalName(i), atts.getValue(i));
}
/* get the attribute here ... */
if (mAttributes.getValue(ATTRIBUTE_CASE_SENSITIVE) != null) {
mIsCaseSensitiveDictionary =
Boolean.valueOf(mAttributes.getValue(ATTRIBUTE_CASE_SENSITIVE));
}
mAttributes = null;
} else if (ENTRY_ELEMENT.equals(localName)) {
mAttributes = new Attributes();
for (int i = 0; i < atts.getLength(); i++) {
mAttributes.setValue(atts.getLocalName(i), atts.getValue(i));
}
} else if (TOKEN_ELEMENT.equals(localName)) {
mIsInsideTokenElement = true;
}
}
public void init(String name, Attributes atts) {
logger.log(LogService.LOG_DEBUG, "Here is IconHandler:init()"); // $NON-NLS-1$
super.init(name, atts);
String icon_resource_val = atts.getValue(RESOURCE);
if (icon_resource_val == null) {
_isParsedDataValid = false;
logger.log(
LogService.LOG_ERROR,
NLS.bind(
MetaTypeMsg.MISSING_ATTRIBUTE,
new Object[] {
RESOURCE,
name,
atts.getValue(ID),
_dp_url,
_dp_bundle.getBundleId(),
_dp_bundle.getSymbolicName()
}));
return;
}
String icon_size_val = atts.getValue(SIZE);
if (icon_size_val == null) {
// Not a problem, because SIZE is an optional attribute.
icon_size_val = "0"; // $NON-NLS-1$
} else if (icon_size_val.equalsIgnoreCase("")) { // $NON-NLS-1$
icon_size_val = "0"; // $NON-NLS-1$
}
_icon = new Icon(icon_resource_val, Integer.parseInt(icon_size_val), _dp_bundle);
}
public void init(
String name, Attributes atts, Hashtable<String, ObjectClassDefinitionImpl> ocds_hashtable) {
logger.log(LogService.LOG_DEBUG, "Here is OcdHandler():init()"); // $NON-NLS-1$
super.init(name, atts);
_parent_OCDs_hashtable = ocds_hashtable;
collectExtensionAttributes(atts);
String ocd_name_val = atts.getValue(NAME);
if (ocd_name_val == null) {
_isParsedDataValid = false;
logger.log(
LogService.LOG_ERROR,
NLS.bind(
MetaTypeMsg.MISSING_ATTRIBUTE,
new Object[] {
NAME,
name,
atts.getValue(ID),
_dp_url,
_dp_bundle.getBundleId(),
_dp_bundle.getSymbolicName()
}));
return;
}
String ocd_description_val = atts.getValue(DESCRIPTION);
if (ocd_description_val == null) {
// Not a problem, because DESCRIPTION is an optional attribute.
}
_refID = atts.getValue(ID);
if (_refID == null) {
_isParsedDataValid = false;
logger.log(
LogService.LOG_ERROR,
NLS.bind(
MetaTypeMsg.MISSING_ATTRIBUTE,
new Object[] {
ID,
name,
atts.getValue(ID),
_dp_url,
_dp_bundle.getBundleId(),
_dp_bundle.getSymbolicName()
}));
return;
}
_ocd =
new ObjectClassDefinitionImpl(
ocd_name_val, ocd_description_val, _refID, _dp_localization, extensionAttributes);
}
public void startElement(String uri, String sName, String qName, Attributes attrs) {
if (qName.equals("PROPSTABLE")) {
// LogUtil.fine(attrs.getValue("DESC"));
propsAl = new ArrayList();
} else if (qName.equals("PROPSROW")) {
curPROPSROW_DESC = attrs.getValue("DESC");
curProps = new Properties();
} else {
// LogUtil.fine(qName);
curKEY_DESC = attrs.getValue("DESC");
curKey = qName;
textFlag = true;
}
}
public void startElement(String uri, String localName, String qName, Attributes atts) {
logger.log(
LogService.LOG_DEBUG,
"Here is ObjectHandler:startElement():" //$NON-NLS-1$
+ qName);
if (!_isParsedDataValid) return;
String name = getName(localName, qName);
if (name.equalsIgnoreCase(ATTRIBUTE)) {
AttributeHandler attributeHandler = new AttributeHandler(this);
attributeHandler.init(name, atts);
// The ATTRIBUTE element is only used by RFC94, do nothing for it here.
} 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()
}));
}
}
public void startElement(String uri, String localName, String qName, Attributes atts) {
logger.log(
LogService.LOG_DEBUG,
"Here is MetaDataHandler:startElement():" //$NON-NLS-1$
+ qName);
String name = getName(localName, qName);
if (name.equalsIgnoreCase(DESIGNATE)) {
DesignateHandler designateHandler = new DesignateHandler(this);
designateHandler.init(name, atts);
if (designateHandler._isParsedDataValid) {
_dp_designateHandlers.addElement(designateHandler);
}
} else if (name.equalsIgnoreCase(OCD)) {
OcdHandler ocdHandler = new OcdHandler(this);
ocdHandler.init(name, atts, _dp_OCDs);
} 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()
}));
}
}
public static String saxElementToDebugString(String uri, String qName, Attributes attributes) {
// Open start tag
final StringBuilder sb = new StringBuilder("<");
sb.append(qName);
final Set<String> declaredPrefixes = new HashSet<String>();
mapPrefixIfNeeded(declaredPrefixes, uri, qName, sb);
// Attributes if any
for (int i = 0; i < attributes.getLength(); i++) {
mapPrefixIfNeeded(declaredPrefixes, attributes.getURI(i), attributes.getQName(i), sb);
sb.append(' ');
sb.append(attributes.getQName(i));
sb.append("=\"");
sb.append(attributes.getValue(i));
sb.append('\"');
}
// Close start tag
sb.append('>');
// Content
sb.append("[...]");
// Close element with end tag
sb.append("</");
sb.append(qName);
sb.append('>');
return sb.toString();
}
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()
}));
}
}
public void startElement(String uri, String localName, String qName, Attributes atts) {
logger.log(
LogService.LOG_DEBUG,
"Here is AttributeDefinitionHandler:startElement():" //$NON-NLS-1$
+ qName);
if (!_isParsedDataValid) return;
String name = getName(localName, qName);
if (name.equalsIgnoreCase(OPTION)) {
OptionHandler optionHandler = new OptionHandler(this);
optionHandler.init(name, atts);
if (optionHandler._isParsedDataValid) {
// Only add valid Option
_optionLabel_vector.addElement(optionHandler._label_val);
_optionValue_vector.addElement(optionHandler._value_val);
}
} 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()
}));
}
}
@Override
public void startElement(String namespaceURI, String localName, String raxName, Attributes atts)
throws SAXException {
try {
if (raxName.equals("xmwp:security")) {
message.setKey(atts.getValue("key"));
} else if (raxName.equals("request")) {
request = true;
inform = false;
} else if (raxName.equals("inform")) {
inform = true;
request = false;
} else {
// INFORM elements
if (inform) {
message.addInform(getInformXMWPElement(namespaceURI, localName, raxName, atts));
}
// REQUEST elements
else if (request) {
message.addRequest(getRequestXMWPElement(namespaceURI, localName, raxName, atts));
}
}
} catch (XMWPException e) {
throw new SAXException(e);
}
}
public void startElement(String uri, String localName, String qName, Attributes atts) {
logger.log(
LogService.LOG_DEBUG,
"Here is DesignateHandler:startElement():" //$NON-NLS-1$
+ qName);
if (!_isParsedDataValid) return;
String name = getName(localName, qName);
if (name.equalsIgnoreCase(OBJECT)) {
ObjectHandler objectHandler = new ObjectHandler(this);
objectHandler.init(name, atts);
if (objectHandler._isParsedDataValid) {
_ocdref = objectHandler._ocdref;
}
} 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()
}));
}
}
public void startElement(String nm, String ln, String qn, Attributes as) throws SAXException {
if (level++ == 0)
for (int i = 0; i < as.getLength(); i++)
if (attributename.equals("*") || attributename.equals(as.getQName(i))) {
char[] s = as.getValue(i).toCharArray();
next.characters(s, 0, s.length);
}
}
/**
* Processes xml:language reference is there is one.
*
* @param atts the attributes potentially containing xml:language declaration
*/
private void processXMLLanguage(@Nonnull Attributes atts) {
checkNotNull(atts, "atts cannot be null");
languages.add(0, language);
String value = atts.getValue(XMLLANG);
if (value != null) {
language = value;
}
}
public void startElement(String uri, String localName, String qname, Attributes atts) {
super.startElement(uri, localName, qname, atts);
if (localName.equals(DataExport.FIELD_EXPORT)) {
String type = atts.getValue(DataExport.EXPORT_TYPE);
textImport = (type != null && type.equals(DataExport.EXPORT_TYPE_TEXT));
} else if (localName.equals(DataRecord.ENCODING_RECORD)) {
// begin of record
record = dataAccess.getPersistence().createNewRecord();
fieldsInImport = new ArrayList<String>();
return;
} else {
if (atts.getValue("key") != null && atts.getValue("key").equalsIgnoreCase("true")) {
overrideKeyField = localName;
}
}
}
public void startElement(
String namespaceURI,
String lName, // local name
String qName, // qualified name
Attributes attrs)
throws SAXException {
element = qName;
if (element.compareToIgnoreCase("presence") == 0) {
presenceTag = new PresenceTag();
String entity = attrs.getValue("entity").trim();
presenceTag.setEntity(entity);
}
if (element.compareToIgnoreCase("presentity") == 0) {
presentityTag = new PresentityTag();
String id = attrs.getValue("id").trim();
presentityTag.setId(id);
}
if (element.compareToIgnoreCase("tuple") == 0) {
tupleTag = new TupleTag();
String id = attrs.getValue("id").trim();
tupleTag.setId(id);
}
if (element.compareToIgnoreCase("status") == 0) {
statusTag = new StatusTag();
}
if (element.compareToIgnoreCase("basic") == 0) {
basicTag = new BasicTag();
}
if (element.compareToIgnoreCase("contact") == 0) {
contactTag = new ContactTag();
String priority = attrs.getValue("priority").trim();
if (priority != null) {
try {
contactTag.setPriority(Float.parseFloat(priority));
} catch (Exception e) {
e.printStackTrace();
}
}
}
if (element.compareToIgnoreCase("note") == 0) {
noteTag = new NoteTag();
}
}
public void init(String name, Attributes attributes) {
logger.log(LogService.LOG_DEBUG, "Here is MetaDataHandler():init()"); // $NON-NLS-1$
super.init(name, attributes);
_dp_localization = attributes.getValue(LOCALIZATION);
if (_dp_localization == null) {
// Not a problem, because LOCALIZATION is an optional attribute.
}
// The global variable "_dp_localization" will be used within
// OcdHandler and AttributeDefinitionHandler later.
}
public void startElement(String uri, String name, String tag, Attributes atts) {
out.append("<").append(tag);
if (atts != null)
for (int i = 0; i < atts.getLength(); i++)
out.append(" ")
.append(atts.getQName(i))
.append("=\"")
.append(atts.getValue(i))
.append("\"");
out.append(">");
}
public void startElement(String nm, String ln, String qn, Attributes as) throws SAXException {
children = new Bag();
Bag attributes = new Bag();
for (int i = 0; i < as.getLength(); i++)
attributes.add(new Tuple(new MR_string(as.getQName(i)), new MR_string(as.getValue(i))));
Tuple t = new Tuple(3);
t.set(0, new MR_string(qn));
t.set(1, attributes);
t.set(2, children);
stack.push(new Union((byte) 0, t));
}
@Override
public void handleAttributes(String elx, String localName, String el, Attributes attr)
throws SAXException {
setPeptideId(attr.getValue("peak")); // num="1"
setScore(XTandemSaxUtilities.getRequiredDoubleAttribute("score", attr));
setRawScore(XTandemSaxUtilities.getRequiredDoubleAttribute("raw_score", attr));
setHyperScore(XTandemSaxUtilities.getRequiredDoubleAttribute("hyperscore", attr));
boolean decoy = XTandemSaxUtilities.getBooleanAttribute("decoy", attr, false);
if (decoy) setDecoy(decoy);
return;
}
public void startElement(String uri, String localName, String name, Attributes attributes)
throws SAXException {
if ("row".equals(name)) { // 如果是行开始 清空cell数据 重来
rowNumber = Integer.valueOf(attributes.getValue("r")); // 当前行号
if (rowNumber == 1) {
return;
}
currentCellData.clear();
}
lastContents = "";
}
public void init(String name, Attributes atts) {
logger.log(LogService.LOG_DEBUG, "Here is DesignateHandler():init()"); // $NON-NLS-1$
super.init(name, atts);
_pid_val = atts.getValue(PID);
_factory_val = atts.getValue(FACTORY);
if (_pid_val == null && _factory_val == null) {
_isParsedDataValid = false;
logger.log(
LogService.LOG_ERROR,
NLS.bind(
MetaTypeMsg.MISSING_DESIGNATE_PID_AND_FACTORYPID,
new Object[] {
elementId, _dp_url, _dp_bundle.getBundleId(), _dp_bundle.getSymbolicName()
}));
return;
}
_bundle_val = atts.getValue(BUNDLE);
if (_bundle_val == null) {
// Not a problem because BUNDLE is an optional attribute.
}
String optional_str = atts.getValue(OPTIONAL);
if (optional_str == null) {
// Not a problem, because OPTIONAL is an optional attribute.
// The default value is "false".
_optional_val = false;
} else {
_optional_val = Boolean.valueOf(optional_str).booleanValue();
}
String merge_str = atts.getValue(MERGE);
if (merge_str == null) {
// Not a problem, because MERGE is an optional attribute.
// The default value is "false".
_merge_val = false;
} else {
_merge_val = Boolean.valueOf(merge_str).booleanValue();
}
}
public void init(String name, Attributes atts) {
logger.log(LogService.LOG_DEBUG, "Here is OptionHandler:init()"); // $NON-NLS-1$
super.init(name, atts);
_label_val = atts.getValue(LABEL);
if (_label_val == null) {
_isParsedDataValid = false;
logger.log(
LogService.LOG_ERROR,
NLS.bind(
MetaTypeMsg.MISSING_ATTRIBUTE,
new Object[] {
LABEL,
name,
atts.getValue(ID),
_dp_url,
_dp_bundle.getBundleId(),
_dp_bundle.getSymbolicName()
}));
return;
}
_value_val = atts.getValue(VALUE);
if (_value_val == null) {
_isParsedDataValid = false;
logger.log(
LogService.LOG_ERROR,
NLS.bind(
MetaTypeMsg.MISSING_ATTRIBUTE,
new Object[] {
VALUE,
name,
atts.getValue(ID),
_dp_url,
_dp_bundle.getBundleId(),
_dp_bundle.getSymbolicName()
}));
return;
}
}
public void init(String name, Attributes atts) {
logger.log(LogService.LOG_DEBUG, "Here is AttributeHandler():init()"); // $NON-NLS-1$
super.init(name, atts);
_adref_val = atts.getValue(ADREF);
if (_adref_val == null) {
_isParsedDataValid = false;
logger.log(
LogService.LOG_ERROR,
NLS.bind(
MetaTypeMsg.MISSING_ATTRIBUTE,
new Object[] {
ADREF,
name,
atts.getValue(ID),
_dp_url,
_dp_bundle.getBundleId(),
_dp_bundle.getSymbolicName()
}));
return;
}
_content_val = atts.getValue(CONTENT);
if (_content_val == null) {
_isParsedDataValid = false;
logger.log(
LogService.LOG_ERROR,
NLS.bind(
MetaTypeMsg.MISSING_ATTRIBUTE,
new Object[] {
CONTENT,
name,
atts.getValue(ID),
_dp_url,
_dp_bundle.getBundleId(),
_dp_bundle.getSymbolicName()
}));
return;
}
}
/**
* This method is called when the start of an XML element is encountered. Instantiates new objects
* when necessary and lets the characters method know what kind of action to take.
*
* @param name Name of the element that is encountered.
* @param atts The attributes encountered.
* @throws SAXException Exception thrown if is wrong type of XML file.
*/
public void startElement(String namespace, String name, String qName, Attributes atts)
throws SAXException {
// Make sure is correct file type
if (count == 0)
if (!name.equals("feature_vector_file") && !qName.equals("feature_vector_file"))
throw new SAXException("\n\nIt is in reality of the type " + name + ".");
count++;
// Identify the type of tag
tag_identifier = 0;
if (name.equals("data_set") || qName.equals("data_set")) {
// Create a new Dataset and add it to root_datasets.
current_root_dataset = new DataSet();
root_datasets.add(current_root_dataset);
} else if (name.equals("section") || qName.equals("section")) {
// Create a new set of sub-sets of a data set if subset_datasets is null
if (subset_datasets == null) subset_datasets = new LinkedList<DataSet>();
// Create a new sub-set DataSet. Place this DataSet in the list of
// sub-set DataSets and gives it a reference to it's parent root
// DataSet.
current_subset_dataset = new DataSet();
current_subset_dataset.parent = current_root_dataset;
subset_datasets.add(current_subset_dataset);
// Extract the name of the DataSet from the id attribute
current_subset_dataset.start = Double.parseDouble(atts.getValue(0));
current_subset_dataset.stop = Double.parseDouble(atts.getValue(1));
} else if (name.equals("feature") || qName.equals("feature")) {
// Prepare the linked lists to store feature values
if (feature_name_list == null) {
feature_name_list = new LinkedList<String>();
feature_values_list = new LinkedList<double[]>();
}
feature_indidual_values_list = new LinkedList<String>();
} else if (name.equals("data_set_id") || qName.equals("data_set_id")) tag_identifier = 1;
else if (name.equals("name") || qName.equals("name")) tag_identifier = 2;
else if (name.equals("v") || qName.equals("v")) tag_identifier = 3;
}
public void startElement(String uri, String localName, String qName, Attributes attributes)
throws SAXException {
throw new SAXException(
NLS.bind(
MetaTypeMsg.UNEXPECTED_ELEMENT,
new Object[] {
qName,
attributes.getValue(ID),
_dp_url,
_dp_bundle.getBundleId(),
_dp_bundle.getSymbolicName()
}));
}
/**
* @param attributes source attributes
* @return new AttributesImpl containing all attributes that were in src attributes and that were
* in the default name space.
*/
public static AttributesImpl getAttributesFromDefaultNamespace(final Attributes attributes) {
final AttributesImpl ret = new AttributesImpl();
final int size = attributes.getLength();
for (int i = 0; i < size; i++) {
final String ns = attributes.getURI(i);
if (!"".equals(ns)) continue;
final String lnam = attributes.getLocalName(i);
final String qnam = attributes.getQName(i);
final String typ = attributes.getType(i);
final String val = attributes.getValue(i);
ret.addAttribute(ns, lnam, qnam, typ, val);
}
return ret;
}
public void cacheStartElement(String uri, String name, String tag, Attributes atts) {
cached_events++;
putByte((byte) 0);
putString(uri);
putString(name);
putString(tag);
if (atts != null) {
putShort((short) atts.getLength());
for (int i = 0; i < atts.getLength(); i++) {
putString(atts.getQName(i));
putString(atts.getValue(i));
}
} else putShort((short) 0);
}
@Override
public void startElement(String uri, String localName, String qName, Attributes attributes)
throws SAXException {
curElem = true;
// check for a known tag
if (qName.equals("details")) {
data = new HashMap<String, MissionInfo>();
mLoaded = false;
} else if (qName.equals("mission")) {
curName = attributes.getValue("id");
curMission = new MissionInfo();
curMission.setName(curName);
} else if (qName.equals("reward")) {
int level = Integer.parseInt(attributes.getValue("level"));
int exp = Integer.parseInt(attributes.getValue("exp"));
int gold = Integer.parseInt(attributes.getValue("gold"));
curMission.setExp(level, exp);
curMission.setGold(level, gold);
// Log.v(tag, String.format("Diff: %d, %d, %d", level, exp, gold));
}
}
/**
* This method is called when the start of an XML element is encountered. Instantiates new objects
* when necessary and lets the characters method know what kind of action to take.
*
* @param name Name of the element that is encountered.
* @param atts The attributes encountered.
* @throws SAXException Exception thrown if is wrong type of XML file.
*/
public void startElement(String namespace, String name, String qName, Attributes atts)
throws SAXException {
// Make sure is correct file type
if (count == 0)
if (!name.equals("classifications_file"))
throw new SAXException("\n\nIt is in reality of the type " + name + ".");
count++;
// Identify the type of tag
tag_identifier = 0;
if (name.equals("data_set")) {
// Create a new SegmentedClassification and add it to root_classifications.
current_root_classification = new SegmentedClassification();
root_classifications.add(current_root_classification);
} else if (name.equals("section")) {
// Create a new set of sub-sets of a SegmentedClassificaiton if
// subset_classifications is null
if (subset_classifications == null)
subset_classifications = new LinkedList<SegmentedClassification>();
// Create a new sub-set SegmentedClassificaiton. Place this
// SegmentedClassificaiton in the list of sub-set SegmentedClassificaitons..
current_subset_classification = new SegmentedClassification();
subset_classifications.add(current_subset_classification);
} else if (name.equals("class")) {
// Create a new set of classes if classes is null
if (classes == null) classes = new LinkedList<String>();
// Notify the characters method
tag_identifier = 1;
} else if (name.equals("misc_info")) {
// Create a new set of meta_data_keys and meta_data_info
// if meta_data_keys is null
if (meta_data_keys == null) {
meta_data_keys = new LinkedList<String>();
meta_data_info = new LinkedList<String>();
}
// Extract the name of the meta-data key from the attribute
// and store it
meta_data_keys.add(atts.getValue(0));
// Notify the characters method
tag_identifier = 2;
} else if (name.equals("data_set_id")) tag_identifier = 3;
else if (name.equals("role")) tag_identifier = 4;
else if (name.equals("start")) tag_identifier = 5;
else if (name.equals("stop")) tag_identifier = 6;
}
protected void collectExtensionAttributes(Attributes attributes) {
for (int i = 0; i < attributes.getLength(); i++) {
String key = attributes.getURI(i);
if (key.length() == 0
|| key.startsWith("http://www.osgi.org/xmlns/metatype/v")) // $NON-NLS-1$
continue;
Map<String, String> value = extensionAttributes.get(key);
if (value == null) {
value = new HashMap<String, String>();
extensionAttributes.put(key, value);
}
value.put(
getName(attributes.getLocalName(i), attributes.getQName(i)), attributes.getValue(i));
}
}