public void marshall(
Class parentType,
QName elementType,
ExtensibilityElement extension,
PrintWriter pw,
Definition def,
ExtensionRegistry extReg)
throws WSDLException {
MIMEContent mimeContent = (MIMEContent) extension;
if (mimeContent != null) {
String tagName = DOMUtils.getQualifiedValue(MIMEConstants.NS_URI_MIME, "content", def);
if (parentType != null && MIMEPart.class.isAssignableFrom(parentType)) {
pw.print(" ");
}
pw.print(" <" + tagName);
DOMUtils.printAttribute(MIMEConstants.ATTR_PART, mimeContent.getPart(), pw);
DOMUtils.printAttribute(Constants.ATTR_TYPE, mimeContent.getType(), pw);
Boolean required = mimeContent.getRequired();
if (required != null) {
DOMUtils.printQualifiedAttribute(Constants.Q_ATTR_REQUIRED, required.toString(), def, pw);
}
pw.println("/>");
}
}
private static Object[] parseArguments(String args[])
throws Exception
{
File f;
File f1;
Socket s;
Boolean server = null;
f = new File(args[0]);
f1 = new File(args[1]);
s = null;
if(args.length == 4)
{
int port = Integer.parseInt(args[2]);
server = new Boolean(args[3].trim().equalsIgnoreCase("true"));
if(server.booleanValue())
s = (new ServerSocket(port)).accept();
else
s = new Socket("localhost", port);
}
return (new Object[] {
f, f1, s
});
Exception ex;
ex;
printUsage();
throw ex;
}
public Property get(String category, String key, boolean defaultValue) {
Property prop = get(category, key, Boolean.toString(defaultValue), BOOLEAN);
if (!prop.isBooleanValue()) {
prop.value = Boolean.toString(defaultValue);
}
return prop;
}
private static GeometricObject recreateObject(String data) {
GeometricObject result = null;
String[] token = data.split(",");
if (token[0].equals("Circle")) { // find what constructor to use
String color = token[1];
boolean filled = Boolean.valueOf(token[2]); // find data in the line
double radius = Double.valueOf(token[3]);
try {
return new Circle(color, filled, radius); // attempt to make a circle
} catch (Exception e) {
e.printStackTrace();
}
}
if (token[0].equals("Rectangle")) {
String color = token[1];
boolean filled = Boolean.valueOf(token[2]); // find data
double height = Double.valueOf(token[3]);
double width = Double.valueOf(token[4]);
try {
return new Rectangle(color, filled, height, width); // attempt to make a rectangle
} catch (Exception e) {
e.printStackTrace();
}
}
return result; // default return null GeometricObject
} // end method
/** INTERNAL: Return if the expression is for a direct mapped attribute. */
public boolean isAttribute() {
if (isAttributeExpression == null) {
if (getSession() == null) {
// We can't tell, so say no.
return false;
}
QueryKey queryKey = getQueryKeyOrNull();
if (queryKey != null) {
isAttributeExpression = Boolean.valueOf(queryKey.isDirectQueryKey());
} else {
DatabaseMapping mapping = getMapping();
if (mapping != null) {
if (mapping.isVariableOneToOneMapping()) {
throw QueryException.cannotQueryAcrossAVariableOneToOneMapping(
mapping, mapping.getDescriptor());
} else {
isAttributeExpression = Boolean.valueOf(mapping.isDirectToFieldMapping());
}
} else {
isAttributeExpression = Boolean.FALSE;
}
}
}
return isAttributeExpression.booleanValue();
}
void LoadConfig() {
String id = Long.toString(robot_uid);
limit_top = Double.valueOf(prefs.get(id + "_limit_top", "0"));
limit_bottom = Double.valueOf(prefs.get(id + "_limit_bottom", "0"));
limit_left = Double.valueOf(prefs.get(id + "_limit_left", "0"));
limit_right = Double.valueOf(prefs.get(id + "_limit_right", "0"));
m1invert = Boolean.parseBoolean(prefs.get(id + "_m1invert", "false"));
m2invert = Boolean.parseBoolean(prefs.get(id + "_m2invert", "false"));
}
void SaveConfig() {
String id = Long.toString(robot_uid);
prefs.put(id + "_limit_top", Double.toString(limit_top));
prefs.put(id + "_limit_bottom", Double.toString(limit_bottom));
prefs.put(id + "_limit_right", Double.toString(limit_right));
prefs.put(id + "_limit_left", Double.toString(limit_left));
prefs.put(id + "_m1invert", Boolean.toString(m1invert));
prefs.put(id + "_m2invert", Boolean.toString(m2invert));
}
/**
* @attribute syn
* @aspect GenericsSubtype
* @declaredat
* /Users/eric/Documents/workspaces/clara-soot/JastAddJ/Java1.5Frontend/GenericsSubtype.jrag:212
*/
@SuppressWarnings({"unchecked", "cast"})
public boolean sameStructure(TypeDecl t) {
Object _parameters = t;
if (sameStructure_TypeDecl_values == null)
sameStructure_TypeDecl_values = new java.util.HashMap(4);
ASTNode$State.CircularValue _value;
if (sameStructure_TypeDecl_values.containsKey(_parameters)) {
Object _o = sameStructure_TypeDecl_values.get(_parameters);
if (!(_o instanceof ASTNode$State.CircularValue)) {
return ((Boolean) _o).booleanValue();
} else _value = (ASTNode$State.CircularValue) _o;
} else {
_value = new ASTNode$State.CircularValue();
sameStructure_TypeDecl_values.put(_parameters, _value);
_value.value = Boolean.valueOf(true);
}
ASTNode$State state = state();
if (!state.IN_CIRCLE) {
state.IN_CIRCLE = true;
int num = state.boundariesCrossed;
boolean isFinal = this.is$Final();
boolean new_sameStructure_TypeDecl_value;
do {
_value.visited = new Integer(state.CIRCLE_INDEX);
state.CHANGE = false;
new_sameStructure_TypeDecl_value = sameStructure_compute(t);
if (new_sameStructure_TypeDecl_value != ((Boolean) _value.value).booleanValue()) {
state.CHANGE = true;
_value.value = Boolean.valueOf(new_sameStructure_TypeDecl_value);
}
state.CIRCLE_INDEX++;
} while (state.CHANGE);
if (isFinal && num == state().boundariesCrossed) {
sameStructure_TypeDecl_values.put(_parameters, new_sameStructure_TypeDecl_value);
} else {
sameStructure_TypeDecl_values.remove(_parameters);
state.RESET_CYCLE = true;
sameStructure_compute(t);
state.RESET_CYCLE = false;
}
state.IN_CIRCLE = false;
return new_sameStructure_TypeDecl_value;
}
if (!new Integer(state.CIRCLE_INDEX).equals(_value.visited)) {
_value.visited = new Integer(state.CIRCLE_INDEX);
boolean new_sameStructure_TypeDecl_value = sameStructure_compute(t);
if (state.RESET_CYCLE) {
sameStructure_TypeDecl_values.remove(_parameters);
} else if (new_sameStructure_TypeDecl_value != ((Boolean) _value.value).booleanValue()) {
state.CHANGE = true;
_value.value = new_sameStructure_TypeDecl_value;
}
return new_sameStructure_TypeDecl_value;
}
return ((Boolean) _value.value).booleanValue();
}
/** Synchronizes the state of the actions to the current state of this host. */
private void updateActions() {
final DeviceController currentDeviceController = getDeviceController();
final boolean deviceControllerSet = currentDeviceController != null;
final boolean deviceCapturing = deviceControllerSet && currentDeviceController.isCapturing();
final boolean deviceSetup =
deviceControllerSet && !deviceCapturing && currentDeviceController.isSetup();
getAction(CaptureAction.ID).setEnabled(deviceControllerSet);
getAction(CancelCaptureAction.ID).setEnabled(deviceCapturing);
getAction(RepeatCaptureAction.ID).setEnabled(deviceSetup);
final boolean projectChanged = this.projectManager.getCurrentProject().isChanged();
final boolean projectSavedBefore =
this.projectManager.getCurrentProject().getFilename() != null;
final boolean dataAvailable = this.dataContainer.hasCapturedData();
getAction(SaveProjectAction.ID).setEnabled(projectChanged);
getAction(SaveProjectAsAction.ID).setEnabled(projectSavedBefore && projectChanged);
getAction(SaveDataFileAction.ID).setEnabled(dataAvailable);
getAction(ZoomInAction.ID).setEnabled(dataAvailable);
getAction(ZoomOutAction.ID).setEnabled(dataAvailable);
getAction(ZoomDefaultAction.ID).setEnabled(dataAvailable);
getAction(ZoomFitAction.ID).setEnabled(dataAvailable);
final boolean triggerEnable = dataAvailable && this.dataContainer.hasTriggerData();
getAction(GotoTriggerAction.ID).setEnabled(triggerEnable);
// Update the cursor actions accordingly...
final boolean enableCursors = dataAvailable && this.dataContainer.isCursorsEnabled();
for (int c = 0; c < CapturedData.MAX_CURSORS; c++) {
final boolean enabled = enableCursors && this.dataContainer.isCursorPositionSet(c);
getAction(GotoNthCursorAction.getID(c)).setEnabled(enabled);
}
getAction(GotoFirstCursorAction.ID).setEnabled(enableCursors);
getAction(GotoLastCursorAction.ID).setEnabled(enableCursors);
getAction(SetCursorModeAction.ID).setEnabled(dataAvailable);
getAction(SetCursorModeAction.ID)
.putValue(Action.SELECTED_KEY, Boolean.valueOf(this.dataContainer.isCursorsEnabled()));
boolean anyCursorSet = false;
for (int c = 0; c < CapturedData.MAX_CURSORS; c++) {
final boolean cursorPositionSet = this.dataContainer.isCursorPositionSet(c);
anyCursorSet |= cursorPositionSet;
final Action action = getAction(SetCursorAction.getCursorId(c));
action.setEnabled(dataAvailable);
action.putValue(Action.SELECTED_KEY, Boolean.valueOf(cursorPositionSet));
}
getAction(ClearCursors.ID).setEnabled(enableCursors && anyCursorSet);
}
public void propertyChange(PropertyChangeEvent e) {
String propertyName = e.getPropertyName();
if (e.getPropertyName().equals(Action.NAME)) {
String text = (String) e.getNewValue();
menuItem.setText(text);
} else if (propertyName.equals("enabled")) {
Boolean enabledState = (Boolean) e.getNewValue();
menuItem.setEnabled(enabledState.booleanValue());
}
}
private static void toXml(XmlWriter w, Requirement requirement) throws IOException {
w.element(RepositoryParser.REQUIRE)
.attribute(RepositoryParser.NAME, requirement.getName())
.attribute(RepositoryParser.FILTER, requirement.getFilter())
.attribute(RepositoryParser.EXTEND, Boolean.toString(requirement.isExtend()))
.attribute(RepositoryParser.MULTIPLE, Boolean.toString(requirement.isMultiple()))
.attribute(RepositoryParser.OPTIONAL, Boolean.toString(requirement.isOptional()))
.text(requirement.getComment().trim())
.end();
}
public RegionFile(File file) {
lastModified = 0L;
fileName = file;
debugln((new StringBuilder()).append("REGION LOAD ").append(fileName).toString());
sizeDelta = 0;
try {
if (file.exists()) {
lastModified = file.lastModified();
}
dataFile = new RandomAccessFile(file, "rw");
if (dataFile.length() < 4096L) {
for (int i = 0; i < 1024; i++) {
dataFile.writeInt(0);
}
for (int j = 0; j < 1024; j++) {
dataFile.writeInt(0);
}
sizeDelta += 8192;
}
if ((dataFile.length() & 4095L) != 0L) {
for (int k = 0; (long) k < (dataFile.length() & 4095L); k++) {
dataFile.write(0);
}
}
int l = (int) dataFile.length() / 4096;
sectorFree = new ArrayList(l);
for (int i1 = 0; i1 < l; i1++) {
sectorFree.add(Boolean.valueOf(true));
}
sectorFree.set(0, Boolean.valueOf(false));
sectorFree.set(1, Boolean.valueOf(false));
dataFile.seek(0L);
for (int j1 = 0; j1 < 1024; j1++) {
int l1 = dataFile.readInt();
offsets[j1] = l1;
if (l1 == 0 || (l1 >> 8) + (l1 & 0xff) > sectorFree.size()) {
continue;
}
for (int j2 = 0; j2 < (l1 & 0xff); j2++) {
sectorFree.set((l1 >> 8) + j2, Boolean.valueOf(false));
}
}
for (int k1 = 0; k1 < 1024; k1++) {
int i2 = dataFile.readInt();
chunkTimestamps[k1] = i2;
}
} catch (IOException ioexception) {
ioexception.printStackTrace();
}
}
public void propertyChange(PropertyChangeEvent e) {
String propertyName = e.getPropertyName();
if (e.getPropertyName().equals(Action.NAME)) {
String text = (String) e.getNewValue();
menuItem.setText(text);
} else if (propertyName.equals("enabled")) {
// System.out.println("Debug:TextViewer: ActionChangedListener enabled");
Boolean enabledState = (Boolean) e.getNewValue();
menuItem.setEnabled(enabledState.booleanValue());
}
}
@Override
public SCM newInstance(StaplerRequest req, JSONObject formData) throws FormException {
String path = req.getParameter("fs_scm.path");
String[] filters = req.getParameterValues("fs_scm.filters");
Boolean filterEnabled =
Boolean.valueOf("on".equalsIgnoreCase(req.getParameter("fs_scm.filterEnabled")));
Boolean includeFilter = Boolean.valueOf(req.getParameter("fs_scm.includeFilter"));
Boolean clearWorkspace =
Boolean.valueOf("on".equalsIgnoreCase(req.getParameter("fs_scm.clearWorkspace")));
return new FSSCM(path, clearWorkspace, filterEnabled, includeFilter, filters);
}
private static Map<String, String> nodeAllocationToMap(AssociationEntry entry) {
final HashMap<String, String> map = new HashMap(8);
map.put(FIELD_HOSTNAME, entry.getHostname());
map.put(FIELD_IP, entry.getIpAddress());
map.put(FIELD_MAC, entry.getMac());
map.put(FIELD_BROADCAST, entry.getBroadcast());
map.put(FIELD_SUBNET_MASK, entry.getSubnetMask());
map.put(FIELD_GATEWAY, entry.getGateway());
map.put(FIELD_IN_USE, Boolean.toString(entry.isInUse()));
map.put(FIELD_EXPLICIT_MAC, Boolean.toString(entry.isExplicitMac()));
return map;
}
public static String[] exec(String command, String interpret) {
log.info("RListener - calling DirectJNI.getInstance().exec(" + command + ")");
String[] result =
DirectJNI.getInstance()
.exec(command, Boolean.parseBoolean(interpret), !Boolean.parseBoolean(interpret));
log.info("RListener - DirectJNI returned");
return result;
}
@SuppressWarnings({"unchecked", "cast"})
public boolean subtype(TypeDecl type) {
Object _parameters = type;
if (subtype_TypeDecl_visited == null) subtype_TypeDecl_visited = new java.util.HashMap(4);
if (subtype_TypeDecl_values == null) subtype_TypeDecl_values = new java.util.HashMap(4);
if (subtype_TypeDecl_computed.contains(_parameters))
return ((Boolean) subtype_TypeDecl_values.get(_parameters)).booleanValue();
if (!subtype_TypeDecl_initialized.contains(_parameters)) {
subtype_TypeDecl_initialized.add(_parameters);
subtype_TypeDecl_values.put(_parameters, Boolean.valueOf(true));
}
if (!IN_CIRCLE) {
IN_CIRCLE = true;
int num = boundariesCrossed;
boolean isFinal = this.is$Final();
CIRCLE_INDEX = 1;
boolean new_subtype_TypeDecl_value;
do {
subtype_TypeDecl_visited.put(_parameters, new Integer(CIRCLE_INDEX));
CHANGE = false;
new_subtype_TypeDecl_value = subtype_compute(type);
if (new_subtype_TypeDecl_value
!= ((Boolean) subtype_TypeDecl_values.get(_parameters)).booleanValue()) CHANGE = true;
subtype_TypeDecl_values.put(_parameters, Boolean.valueOf(new_subtype_TypeDecl_value));
CIRCLE_INDEX++;
} while (CHANGE);
if (isFinal && num == boundariesCrossed) {
subtype_TypeDecl_computed.add(_parameters);
} else {
RESET_CYCLE = true;
subtype_compute(type);
RESET_CYCLE = false;
subtype_TypeDecl_computed.remove(_parameters);
subtype_TypeDecl_initialized.remove(_parameters);
}
IN_CIRCLE = false;
return new_subtype_TypeDecl_value;
}
if (!new Integer(CIRCLE_INDEX).equals(subtype_TypeDecl_visited.get(_parameters))) {
subtype_TypeDecl_visited.put(_parameters, new Integer(CIRCLE_INDEX));
if (RESET_CYCLE) {
subtype_TypeDecl_computed.remove(_parameters);
subtype_TypeDecl_initialized.remove(_parameters);
return ((Boolean) subtype_TypeDecl_values.get(_parameters)).booleanValue();
}
boolean new_subtype_TypeDecl_value = subtype_compute(type);
if (new_subtype_TypeDecl_value
!= ((Boolean) subtype_TypeDecl_values.get(_parameters)).booleanValue()) CHANGE = true;
subtype_TypeDecl_values.put(_parameters, Boolean.valueOf(new_subtype_TypeDecl_value));
return new_subtype_TypeDecl_value;
}
return ((Boolean) subtype_TypeDecl_values.get(_parameters)).booleanValue();
}
protected boolean queryBoolean(String query) throws IOException {
if (USECACHE) {
if (cache == null) cache = new Hashtable();
Object r = cache.get(query);
if (r != null) return ((Boolean) r).booleanValue();
Boolean r1 = queryBoolean1(query);
cache.put(query, r1);
return r1.booleanValue();
} else {
return queryBoolean1(query).booleanValue();
}
}
public static boolean isScratchImageValid(Image img) {
try {
Boolean lost = (Boolean) tryMethod(img, "contentsLost", new Object[] {});
if (lost == null) return true; // method does not exist->not volatile
// System.out.println("volatile");
return !lost.booleanValue();
} catch (java.security.AccessControlException e) {
// we're not allowed to do this (we're probably an applet)
// we assume we created a nonvolatile image
return true;
}
}
public static String PrintState(ArrayList state) {
StringBuffer sb = new StringBuffer();
Iterator i = state.iterator();
while (i.hasNext()) {
Object o = i.next();
if (o instanceof Boolean) {
Boolean val = (Boolean) o;
sb.append((val.booleanValue() ? "." : "X"));
}
}
return sb.toString();
}
/** Add entries to the Map for node filter parameters from the nodeset */
public static void addAPINodeSetParams(
final HashMap<String, String> params, final NodeSet nodeSet, final Boolean isKeepgoing) {
if (null == nodeSet) {
return;
}
if (nodeSet.getThreadCount() > 0) {
params.put("nodeThreadcount", Integer.toString(nodeSet.getThreadCount()));
}
if (null != isKeepgoing) {
params.put("nodeKeepgoing", Boolean.toString(isKeepgoing));
}
if (nodeSet.isBlank()) {
return;
}
boolean excludeprecedence = true;
if (null != nodeSet.getExclude() && nodeSet.getExclude().isDominant()) {
excludeprecedence = true;
} else if (null != nodeSet.getInclude() && nodeSet.getInclude().isDominant()) {
excludeprecedence = false;
}
params.put("exclude-precedence", Boolean.toString(excludeprecedence));
final NodeSet.Include include = nodeSet.getInclude();
for (final NodeSet.FILTER_ENUM filter : NodeSet.FILTER_ENUM.values()) {
String value = null;
if (null != include && !include.isBlank()) {
value = filter.value(include);
}
final String key = filter.getName();
if (null != value && !"".equals(value)) {
params.put(key, value);
} else {
params.put(key, "");
}
}
final NodeSet.Exclude exclude = nodeSet.getExclude();
for (final NodeSet.FILTER_ENUM filter : NodeSet.FILTER_ENUM.values()) {
String value = null;
if (null != exclude && !exclude.isBlank()) {
value = filter.value(exclude);
}
final String key = filter.getName();
if (null != value && !"".equals(value)) {
params.put("exclude-" + key, value);
} else {
params.put("exclude-" + key, "");
}
}
}
// get licensing features, with appropriate defaults
@SuppressWarnings("unchecked")
private void loadLicensingFeatures(Element licensingElt) {
List<LicensingFeature> licensingFeats = new ArrayList<LicensingFeature>();
boolean containsLexFeat = false;
if (licensingElt != null) {
for (Iterator<Element> it = licensingElt.getChildren("feat").iterator(); it.hasNext(); ) {
Element featElt = it.next();
String attr = featElt.getAttributeValue("attr");
if (attr.equals("lex")) containsLexFeat = true;
String val = featElt.getAttributeValue("val");
List<String> alsoLicensedBy = null;
String alsoVals = featElt.getAttributeValue("also-licensed-by");
if (alsoVals != null) {
alsoLicensedBy = Arrays.asList(alsoVals.split("\\s+"));
}
boolean licenseEmptyCats = true;
boolean licenseMarkedCats = false;
boolean instantiate = true;
byte loc = LicensingFeature.BOTH;
String lmc = featElt.getAttributeValue("license-marked-cats");
if (lmc != null) {
licenseMarkedCats = Boolean.valueOf(lmc).booleanValue();
// change defaults
licenseEmptyCats = false;
loc = LicensingFeature.TARGET_ONLY;
instantiate = false;
}
String lec = featElt.getAttributeValue("license-empty-cats");
if (lec != null) {
licenseEmptyCats = Boolean.valueOf(lec).booleanValue();
}
String inst = featElt.getAttributeValue("instantiate");
if (inst != null) {
instantiate = Boolean.valueOf(inst).booleanValue();
}
String locStr = featElt.getAttributeValue("location");
if (locStr != null) {
if (locStr.equals("target-only")) loc = LicensingFeature.TARGET_ONLY;
if (locStr.equals("args-only")) loc = LicensingFeature.ARGS_ONLY;
if (locStr.equals("both")) loc = LicensingFeature.BOTH;
}
licensingFeats.add(
new LicensingFeature(
attr, val, alsoLicensedBy, licenseEmptyCats, licenseMarkedCats, instantiate, loc));
}
}
if (!containsLexFeat) {
licensingFeats.add(LicensingFeature.defaultLexFeature);
}
_licensingFeatures = new LicensingFeature[licensingFeats.size()];
licensingFeats.toArray(_licensingFeatures);
}
public static boolean shouldSkipPlugin(final IdeaPluginDescriptor descriptor) {
if (descriptor instanceof IdeaPluginDescriptorImpl) {
IdeaPluginDescriptorImpl descriptorImpl = (IdeaPluginDescriptorImpl) descriptor;
Boolean skipped = descriptorImpl.getSkipped();
if (skipped != null) {
return skipped.booleanValue();
}
boolean result = shouldSkipPlugin(descriptor, ourPlugins);
descriptorImpl.setSkipped(result);
return result;
}
return shouldSkipPlugin(descriptor, ourPlugins);
}
private Element generatePortNode(Document doc, Port port) {
Element portEl = doc.createElement(EL_PORT);
portEl.setAttribute(ATR_NAME, port.getName());
portEl.setAttribute(ATR_TYPE, port.getType());
portEl.setAttribute(ATR_X, Integer.toString(port.getX()));
portEl.setAttribute(ATR_Y, Integer.toString(port.getY()));
portEl.setAttribute(ATR_PORT_CONNECTION, port.isArea() ? "area" : "");
portEl.setAttribute(ATR_STRICT, Boolean.toString(port.isStrict()));
portEl.setAttribute(ATR_MULTI, Boolean.toString(port.isMulti()));
return portEl;
}
public void startElement(String uri, String localName, String qName, Attributes attributes)
throws SAXException {
if ("tag".equals(qName)) {
String name = attributes.getValue("name");
String content = attributes.getValue("content");
String section = attributes.getValue("section");
String deprecated = attributes.getValue("deprecated");
String unique = attributes.getValue("unique");
String ignorePermitted = attributes.getValue("ignore-permitted");
tagInfo =
new TagInfo(
name,
"all".equals(content)
? TagInfo.CONTENT_ALL
: ("none".equals(content) ? TagInfo.CONTENT_NONE : TagInfo.CONTENT_TEXT),
"all".equals(section)
? TagInfo.HEAD_AND_BODY
: ("head".equals(section) ? TagInfo.HEAD : TagInfo.BODY),
deprecated != null && "true".equals(deprecated),
unique != null && "true".equals(unique),
ignorePermitted != null && "true".equals(ignorePermitted));
if (generateCode) {
String s = "tagInfo = new TagInfo(\"#1\", #2, #3, #4, #5, #6);";
s = s.replaceAll("#1", name);
s =
s.replaceAll(
"#2",
"all".equals(content)
? "TagInfo.CONTENT_ALL"
: ("none".equals(content)
? "TagInfo.CONTENT_NONE"
: " TagInfo.CONTENT_TEXT"));
s =
s.replaceAll(
"#3",
"all".equals(section)
? "TagInfo.HEAD_AND_BODY"
: ("head".equals(section) ? "TagInfo.HEAD" : "TagInfo.BODY"));
s = s.replaceAll("#4", Boolean.toString(deprecated != null && "true".equals(deprecated)));
s = s.replaceAll("#5", Boolean.toString(unique != null && "true".equals(unique)));
s =
s.replaceAll(
"#6",
Boolean.toString(ignorePermitted != null && "true".equals(ignorePermitted)));
System.out.println(s);
}
} else if (!"tags".equals(qName)) {
dependencyName = qName;
}
}
/**
* Parses the arguments table from the GATK Report and creates a RAC object with the proper
* initialization values
*
* @param table the GATKReportTable containing the arguments and its corresponding values
* @return a RAC object properly initialized with all the objects in the table
*/
private RecalibrationArgumentCollection initializeArgumentCollectionTable(GATKReportTable table) {
final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
for (int i = 0; i < table.getNumRows(); i++) {
final String argument = table.get(i, "Argument").toString();
Object value = table.get(i, RecalUtils.ARGUMENT_VALUE_COLUMN_NAME);
if (value.equals("null"))
value =
null; // generic translation of null values that were printed out as strings | todo --
// add this capability to the GATKReport
if (argument.equals("covariate") && value != null)
RAC.COVARIATES = value.toString().split(",");
else if (argument.equals("standard_covs"))
RAC.DO_NOT_USE_STANDARD_COVARIATES = Boolean.parseBoolean((String) value);
else if (argument.equals("solid_recal_mode"))
RAC.SOLID_RECAL_MODE = RecalUtils.SOLID_RECAL_MODE.recalModeFromString((String) value);
else if (argument.equals("solid_nocall_strategy"))
RAC.SOLID_NOCALL_STRATEGY =
RecalUtils.SOLID_NOCALL_STRATEGY.nocallStrategyFromString((String) value);
else if (argument.equals("mismatches_context_size"))
RAC.MISMATCHES_CONTEXT_SIZE = Integer.parseInt((String) value);
else if (argument.equals("indels_context_size"))
RAC.INDELS_CONTEXT_SIZE = Integer.parseInt((String) value);
else if (argument.equals("mismatches_default_quality"))
RAC.MISMATCHES_DEFAULT_QUALITY = Byte.parseByte((String) value);
else if (argument.equals("insertions_default_quality"))
RAC.INSERTIONS_DEFAULT_QUALITY = Byte.parseByte((String) value);
else if (argument.equals("deletions_default_quality"))
RAC.DELETIONS_DEFAULT_QUALITY = Byte.parseByte((String) value);
else if (argument.equals("maximum_cycle_value"))
RAC.MAXIMUM_CYCLE_VALUE = Integer.parseInt((String) value);
else if (argument.equals("low_quality_tail"))
RAC.LOW_QUAL_TAIL = Byte.parseByte((String) value);
else if (argument.equals("default_platform")) RAC.DEFAULT_PLATFORM = (String) value;
else if (argument.equals("force_platform")) RAC.FORCE_PLATFORM = (String) value;
else if (argument.equals("quantizing_levels"))
RAC.QUANTIZING_LEVELS = Integer.parseInt((String) value);
else if (argument.equals("recalibration_report"))
RAC.existingRecalibrationReport = (value == null) ? null : new File((String) value);
else if (argument.equals("binary_tag_name"))
RAC.BINARY_TAG_NAME = (value == null) ? null : (String) value;
else if (argument.equals("sort_by_all_columns"))
RAC.SORT_BY_ALL_COLUMNS = Boolean.parseBoolean((String) value);
}
return RAC;
}
public CreateObjectMonitor(String n, ObjectURL wturl, WithHash w, Boolean r) {
super();
name = n;
with = w;
this.wturl = wturl;
replace = r.booleanValue();
}
public void load(InputStream inputStream) throws Exception {
BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(inputStream));
ArrayList<String> us = new ArrayList<>();
while (bufferedReader.ready()) {
us.add(bufferedReader.readLine());
}
for (int i = 0; i < us.size(); i += 5) {
User user = new User();
user.setFirstName(us.get(i));
user.setLastName(us.get(i + 1));
user.setBirthDate(new Date(Long.parseLong(us.get(i + 2))));
user.setMale(Boolean.valueOf(us.get(i + 3)));
String country = us.get(i + 4);
User.Country country1 = null;
if (country.equals("UKRAINE")) {
country1 = User.Country.UKRAINE;
} else if (country.equals("RUSSIA")) {
country1 = User.Country.RUSSIA;
} else if (country.equals("OTHER")) {
country1 = User.Country.OTHER;
}
user.setCountry(country1);
users.add(user);
}
bufferedReader.close();
}
public void init() throws ServletException {
if (!inited) {
secureDirPath = getServletContext().getRealPath(SECURE_CONTEXT_PATH);
strongProtection = Boolean.valueOf(getInitParameter("strongProtection")).booleanValue();
File secureDir = new File(secureDirPath);
if (secureDirPath != null && secureDir.isDirectory()) {
inited = true;
if (DEBUG)
log(
"Initialization OK (Strong protection "
+ (strongProtection ? "enabled" : "DISABLED (better enable it check web.xml) !!!")
+ "). Setting secureDirPath to "
+ secureDirPath);
} else {
if (DEBUG)
log(
"Initialization problem, please check if "
+ getServletContext().getRealPath(SECURE_CONTEXT_PATH)
+ " exists and if it is directory !!!");
}
}
dateFormat = DateFormat.getDateInstance();
dateFormat.setTimeZone(java.util.TimeZone.getTimeZone("GMT"));
}
public PacksModel(InstallData idata) {
this.installData = idata;
this.rules = idata.getRules();
try {
this.messages = idata.getMessages().newMessages(PackHelper.LANG_FILE_NAME);
} catch (com.izforge.izpack.api.exception.ResourceNotFoundException ex) {
this.messages = idata.getMessages();
}
this.variables = idata.getVariables();
this.packsToInstall = idata.getSelectedPacks();
this.modifyInstallation = Boolean.valueOf(idata.getVariable(InstallData.MODIFY_INSTALLATION));
this.installedPacks = loadInstallationInformation(modifyInstallation);
this.packs = getVisiblePacks();
this.hiddenPacks = getHiddenPacks();
this.allPacks = idata.getAvailablePacks();
this.nameToRow = getNametoRowMapping(packs);
this.nameToPack = getNametoPackMapping(allPacks);
this.packs = setPackProperties(packs, nameToPack);
this.checkValues = initCheckValues(packs, packsToInstall);
updateConditions(true);
updatePacksToInstall();
}