/**
* Parses a list of tags from the command line, assuming it comes from the GATK Engine tags, and
* returns the corresponding EnumSet.
*
* @param arg the actual engine arg, used for the UserException if there's an error
* @param tags a list of string tags that should be converted to the MissingPedField value
* @return
*/
public static final EnumSet<MissingPedField> parseMissingFieldTags(
final Object arg, final List<String> tags) {
final EnumSet<MissingPedField> missingFields = EnumSet.noneOf(MissingPedField.class);
for (final String tag : tags) {
try {
missingFields.add(MissingPedField.valueOf(tag));
} catch (IllegalArgumentException e) {
throw new UserException.BadArgumentValue(
arg.toString(),
"Unknown tag " + tag + " allowed values are " + MissingPedField.values());
}
}
return missingFields;
}
static EnumSet<FileAttribute> parse(String s) {
if (s == null || s.length() == 0) {
return EnumSet.allOf(FileAttribute.class);
}
EnumSet<FileAttribute> set = EnumSet.noneOf(FileAttribute.class);
FileAttribute[] attributes = values();
for (char c : s.toCharArray()) {
int i = 0;
for (; i < attributes.length && c != attributes[i].symbol; i++) ;
if (i < attributes.length) {
if (!set.contains(attributes[i])) {
set.add(attributes[i]);
} else {
throw new IllegalArgumentException(
"There are more than one '" + attributes[i].symbol + "' in " + s);
}
} else {
throw new IllegalArgumentException("'" + c + "' in " + s + " is undefined.");
}
}
return set;
}
static Arguments valueOf(String[] args, Configuration conf) throws IOException {
List<Path> srcs = new ArrayList<Path>();
Path dst = null;
Path log = null;
EnumSet<Options> flags = EnumSet.noneOf(Options.class);
String presevedAttributes = null;
String mapredSslConf = null;
long filelimit = Long.MAX_VALUE;
long sizelimit = Long.MAX_VALUE;
for (int idx = 0; idx < args.length; idx++) {
Options[] opt = Options.values();
int i = 0;
for (; i < opt.length && !args[idx].startsWith(opt[i].cmd); i++) ;
if (i < opt.length) {
flags.add(opt[i]);
if (opt[i] == Options.PRESERVE_STATUS) {
presevedAttributes = args[idx].substring(2);
FileAttribute.parse(presevedAttributes); // validation
} else if (opt[i] == Options.FILE_LIMIT) {
filelimit = Options.FILE_LIMIT.parseLong(args, ++idx);
} else if (opt[i] == Options.SIZE_LIMIT) {
sizelimit = Options.SIZE_LIMIT.parseLong(args, ++idx);
}
} else if ("-f".equals(args[idx])) {
if (++idx == args.length) {
throw new IllegalArgumentException("urilist_uri not specified in -f");
}
srcs.addAll(fetchFileList(conf, new Path(args[idx])));
} else if ("-log".equals(args[idx])) {
if (++idx == args.length) {
throw new IllegalArgumentException("logdir not specified in -log");
}
log = new Path(args[idx]);
} else if ("-mapredSslConf".equals(args[idx])) {
if (++idx == args.length) {
throw new IllegalArgumentException("ssl conf file not specified in -mapredSslConf");
}
mapredSslConf = args[idx];
} else if ("-m".equals(args[idx])) {
if (++idx == args.length) {
throw new IllegalArgumentException("num_maps not specified in -m");
}
try {
conf.setInt(MAX_MAPS_LABEL, Integer.valueOf(args[idx]));
} catch (NumberFormatException e) {
throw new IllegalArgumentException("Invalid argument to -m: " + args[idx]);
}
} else if ('-' == args[idx].codePointAt(0)) {
throw new IllegalArgumentException("Invalid switch " + args[idx]);
} else if (idx == args.length - 1) {
dst = new Path(args[idx]);
} else {
srcs.add(new Path(args[idx]));
}
}
// mandatory command-line parameters
if (srcs.isEmpty() || dst == null) {
throw new IllegalArgumentException("Missing " + (dst == null ? "dst path" : "src"));
}
// incompatible command-line flags
final boolean isOverwrite = flags.contains(Options.OVERWRITE);
final boolean isUpdate = flags.contains(Options.UPDATE);
final boolean isDelete = flags.contains(Options.DELETE);
if (isOverwrite && isUpdate) {
throw new IllegalArgumentException("Conflicting overwrite policies");
}
if (isDelete && !isOverwrite && !isUpdate) {
throw new IllegalArgumentException(
Options.DELETE.cmd
+ " must be specified with "
+ Options.OVERWRITE
+ " or "
+ Options.UPDATE
+ ".");
}
return new Arguments(
srcs, dst, log, flags, presevedAttributes, filelimit, sizelimit, mapredSslConf);
}
protected void paintEvent(WPaintDevice paintDevice) {
if (!(this.chart_ != null) || !this.chart_.cObjCreated_) {
return;
}
if (this.chart_.getSeries(this.seriesColumn_).getType() != SeriesType.LineSeries
&& this.chart_.getSeries(this.seriesColumn_).getType() != SeriesType.CurveSeries) {
if (this.getMethod() == WPaintedWidget.Method.HtmlCanvas) {
StringBuilder ss = new StringBuilder();
ss.append("jQuery.removeData(").append(this.getJsRef()).append(",'sobj');");
ss.append("\nif (")
.append(this.getObjJsRef())
.append(") {")
.append(this.getObjJsRef())
.append(".canvas.style.cursor = 'auto';")
.append("setTimeout(")
.append(this.getObjJsRef())
.append(".repaint,0);}\n");
this.doJavaScript(ss.toString());
}
logger.error(
new StringWriter()
.append("WAxisSliderWidget is not associated with a line or curve series.")
.toString());
return;
}
WPainter painter = new WPainter(paintDevice);
boolean horizontal = this.chart_.getOrientation() == Orientation.Vertical;
double w = horizontal ? this.getWidth().getValue() : this.getHeight().getValue();
double h = horizontal ? this.getHeight().getValue() : this.getWidth().getValue();
boolean autoPadding = this.autoPadding_;
if (autoPadding
&& EnumUtils.mask(paintDevice.getFeatures(), WPaintDevice.FeatureFlag.HasFontMetrics)
.equals(0)
&& this.labelsEnabled_) {
logger.error(
new StringWriter()
.append(
"setAutoLayout(): device does not have font metrics (not even server-side font metrics).")
.toString());
autoPadding = false;
}
if (autoPadding) {
if (horizontal) {
if (this.labelsEnabled_) {
this.setSelectionAreaPadding(0, EnumSet.of(Side.Top));
this.setSelectionAreaPadding(
(int)
(this.chart_
.getAxis(Axis.XAxis)
.calcMaxTickLabelSize(paintDevice, Orientation.Vertical)
+ 10),
EnumSet.of(Side.Bottom));
this.setSelectionAreaPadding(
(int)
Math.max(
this.chart_
.getAxis(Axis.XAxis)
.calcMaxTickLabelSize(paintDevice, Orientation.Horizontal)
/ 2,
10.0),
EnumSet.of(Side.Left, Side.Right));
} else {
this.setSelectionAreaPadding(0, EnumSet.of(Side.Top));
this.setSelectionAreaPadding(5, EnumSet.of(Side.Left, Side.Right, Side.Bottom));
}
} else {
if (this.labelsEnabled_) {
this.setSelectionAreaPadding(0, EnumSet.of(Side.Right));
this.setSelectionAreaPadding(
(int)
Math.max(
this.chart_
.getAxis(Axis.XAxis)
.calcMaxTickLabelSize(paintDevice, Orientation.Vertical)
/ 2,
10.0),
EnumSet.of(Side.Top, Side.Bottom));
this.setSelectionAreaPadding(
(int)
(this.chart_
.getAxis(Axis.XAxis)
.calcMaxTickLabelSize(paintDevice, Orientation.Horizontal)
+ 10),
EnumSet.of(Side.Left));
} else {
this.setSelectionAreaPadding(0, EnumSet.of(Side.Right));
this.setSelectionAreaPadding(5, EnumSet.of(Side.Top, Side.Bottom, Side.Left));
}
}
}
double left =
horizontal
? this.getSelectionAreaPadding(Side.Left)
: this.getSelectionAreaPadding(Side.Top);
double right =
horizontal
? this.getSelectionAreaPadding(Side.Right)
: this.getSelectionAreaPadding(Side.Bottom);
double top =
horizontal
? this.getSelectionAreaPadding(Side.Top)
: this.getSelectionAreaPadding(Side.Right);
double bottom =
horizontal
? this.getSelectionAreaPadding(Side.Bottom)
: this.getSelectionAreaPadding(Side.Left);
double maxW = w - left - right;
WRectF drawArea = new WRectF(left, 0, maxW, h);
List<WAxis.Segment> segmentsBak =
new ArrayList<WAxis.Segment>(this.chart_.getAxis(Axis.XAxis).segments_);
double renderIntervalBak = this.chart_.getAxis(Axis.XAxis).renderInterval_;
this.chart_
.getAxis(Axis.XAxis)
.prepareRender(
horizontal ? Orientation.Horizontal : Orientation.Vertical, drawArea.getWidth());
final WRectF chartArea = this.chart_.chartArea_;
WRectF selectionRect = null;
{
double u =
-this.chart_.xTransformHandle_.getValue().getDx()
/ (chartArea.getWidth() * this.chart_.xTransformHandle_.getValue().getM11());
selectionRect = new WRectF(0, top, maxW, h - (top + bottom));
this.transform_.setValue(
new WTransform(
1 / this.chart_.xTransformHandle_.getValue().getM11(), 0, 0, 1, u * maxW, 0));
}
WRectF seriesArea = new WRectF(left, top + 5, maxW, h - (top + bottom + 5));
WTransform selectionTransform =
this.hv(new WTransform(1, 0, 0, 1, left, 0).multiply(this.transform_.getValue()));
WRectF rect = selectionTransform.map(this.hv(selectionRect));
painter.fillRect(this.hv(new WRectF(left, top, maxW, h - top - bottom)), this.background_);
painter.fillRect(rect, this.selectedAreaBrush_);
final double TICK_LENGTH = 5;
final double ANGLE1 = 15;
final double ANGLE2 = 80;
double tickStart = 0.0;
double tickEnd = 0.0;
double labelPos = 0.0;
AlignmentFlag labelHFlag = AlignmentFlag.AlignCenter;
AlignmentFlag labelVFlag = AlignmentFlag.AlignMiddle;
final WAxis axis = this.chart_.getAxis(Axis.XAxis);
if (horizontal) {
tickStart = 0;
tickEnd = TICK_LENGTH;
labelPos = TICK_LENGTH;
labelVFlag = AlignmentFlag.AlignTop;
} else {
tickStart = -TICK_LENGTH;
tickEnd = 0;
labelPos = -TICK_LENGTH;
labelHFlag = AlignmentFlag.AlignRight;
}
if (horizontal) {
if (axis.getLabelAngle() > ANGLE1) {
labelHFlag = AlignmentFlag.AlignRight;
if (axis.getLabelAngle() > ANGLE2) {
labelVFlag = AlignmentFlag.AlignMiddle;
}
} else {
if (axis.getLabelAngle() < -ANGLE1) {
labelHFlag = AlignmentFlag.AlignLeft;
if (axis.getLabelAngle() < -ANGLE2) {
labelVFlag = AlignmentFlag.AlignMiddle;
}
}
}
} else {
if (axis.getLabelAngle() > ANGLE1) {
labelVFlag = AlignmentFlag.AlignBottom;
if (axis.getLabelAngle() > ANGLE2) {
labelHFlag = AlignmentFlag.AlignCenter;
}
} else {
if (axis.getLabelAngle() < -ANGLE1) {
labelVFlag = AlignmentFlag.AlignTop;
if (axis.getLabelAngle() < -ANGLE2) {
labelHFlag = AlignmentFlag.AlignCenter;
}
}
}
}
EnumSet<AxisProperty> axisProperties = EnumSet.of(AxisProperty.Line);
if (this.labelsEnabled_) {
axisProperties.add(AxisProperty.Labels);
}
if (horizontal) {
axis.render(
painter,
axisProperties,
new WPointF(drawArea.getLeft(), h - bottom),
new WPointF(drawArea.getRight(), h - bottom),
tickStart,
tickEnd,
labelPos,
EnumSet.of(labelHFlag, labelVFlag));
WPainterPath line = new WPainterPath();
line.moveTo(drawArea.getLeft() + 0.5, h - (bottom - 0.5));
line.lineTo(drawArea.getRight(), h - (bottom - 0.5));
painter.strokePath(line, this.chart_.getAxis(Axis.XAxis).getPen());
} else {
axis.render(
painter,
axisProperties,
new WPointF(this.getSelectionAreaPadding(Side.Left) - 1, drawArea.getLeft()),
new WPointF(this.getSelectionAreaPadding(Side.Left) - 1, drawArea.getRight()),
tickStart,
tickEnd,
labelPos,
EnumSet.of(labelHFlag, labelVFlag));
WPainterPath line = new WPainterPath();
line.moveTo(this.getSelectionAreaPadding(Side.Left) - 0.5, drawArea.getLeft() + 0.5);
line.lineTo(this.getSelectionAreaPadding(Side.Left) - 0.5, drawArea.getRight());
painter.strokePath(line, this.chart_.getAxis(Axis.XAxis).getPen());
}
WPainterPath curve = new WPainterPath();
{
WTransform t =
new WTransform(1, 0, 0, 1, seriesArea.getLeft(), seriesArea.getTop())
.multiply(
new WTransform(
seriesArea.getWidth() / chartArea.getWidth(),
0,
0,
seriesArea.getHeight() / chartArea.getHeight(),
0,
0))
.multiply(new WTransform(1, 0, 0, 1, -chartArea.getLeft(), -chartArea.getTop()));
if (!horizontal) {
t.assign(
new WTransform(
0,
1,
1,
0,
this.getSelectionAreaPadding(Side.Left)
- this.getSelectionAreaPadding(Side.Right)
- 5,
0)
.multiply(t)
.multiply(new WTransform(0, 1, 1, 0, 0, 0)));
}
curve.assign(t.map(this.chart_.pathForSeries(this.seriesColumn_)));
}
{
WRectF leftHandle = this.hv(new WRectF(-5, top, 5, h - top - bottom));
WTransform t =
new WTransform(1, 0, 0, 1, left, -top)
.multiply(
new WTransform()
.translate(this.transform_.getValue().map(selectionRect.getTopLeft())));
painter.fillRect(this.hv(t).map(leftHandle), this.handleBrush_);
}
{
WRectF rightHandle = this.hv(new WRectF(0, top, 5, h - top - bottom));
WTransform t =
new WTransform(1, 0, 0, 1, left, -top)
.multiply(
new WTransform()
.translate(this.transform_.getValue().map(selectionRect.getTopRight())));
painter.fillRect(this.hv(t).map(rightHandle), this.handleBrush_);
}
if (this.selectedSeriesPen_ != this.seriesPen_
&& !this.selectedSeriesPen_.equals(this.seriesPen_)) {
WPainterPath clipPath = new WPainterPath();
clipPath.addRect(this.hv(selectionRect));
painter.setClipPath(selectionTransform.map(clipPath));
painter.setClipping(true);
painter.setPen(this.getSelectedSeriesPen());
painter.drawPath(curve);
WPainterPath leftClipPath = new WPainterPath();
leftClipPath.addRect(
this.hv(new WTransform(1, 0, 0, 1, -selectionRect.getWidth(), 0).map(selectionRect)));
painter.setClipPath(
this.hv(
new WTransform(1, 0, 0, 1, left, -top)
.multiply(
new WTransform()
.translate(
this.transform_.getValue().map(selectionRect.getTopLeft()))))
.map(leftClipPath));
painter.setPen(this.getSeriesPen());
painter.drawPath(curve);
WPainterPath rightClipPath = new WPainterPath();
rightClipPath.addRect(
this.hv(new WTransform(1, 0, 0, 1, selectionRect.getWidth(), 0).map(selectionRect)));
painter.setClipPath(
this.hv(
new WTransform(1, 0, 0, 1, left - selectionRect.getRight(), -top)
.multiply(
new WTransform()
.translate(
this.transform_.getValue().map(selectionRect.getTopRight()))))
.map(rightClipPath));
painter.drawPath(curve);
painter.setClipping(false);
} else {
painter.setPen(this.getSeriesPen());
painter.drawPath(curve);
}
if (this.getMethod() == WPaintedWidget.Method.HtmlCanvas) {
WApplication app = WApplication.getInstance();
StringBuilder ss = new StringBuilder();
ss.append("new Wt3_3_5.WAxisSliderWidget(")
.append(app.getJavaScriptClass())
.append(",")
.append(this.getJsRef())
.append(",")
.append(this.getObjJsRef())
.append(",")
.append("{chart:")
.append(this.chart_.getCObjJsRef())
.append(",transform:")
.append(this.transform_.getJsRef())
.append(",rect:function(){return ")
.append(rect.getJsRef())
.append("},drawArea:")
.append(drawArea.getJsRef())
.append(",series:")
.append(this.seriesColumn_)
.append("});");
this.doJavaScript(ss.toString());
}
Utils.copyList(segmentsBak, this.chart_.getAxis(Axis.XAxis).segments_);
this.chart_.getAxis(Axis.XAxis).renderInterval_ = renderIntervalBak;
}
/**
* Checks a function for RESTFful annotations.
*
* @return {@code true} if module contains relevant annotations
* @throws QueryException query exception
*/
boolean analyze() throws QueryException {
// parse all annotations
final EnumSet<HTTPMethod> mth = EnumSet.noneOf(HTTPMethod.class);
final boolean[] declared = new boolean[function.args.length];
boolean found = false;
final int as = function.ann.size();
for (int a = 0; a < as; a++) {
final QNm name = function.ann.names[a];
final Value value = function.ann.values[a];
final byte[] local = name.local();
final byte[] uri = name.uri();
final boolean rexq = eq(uri, QueryText.RESTXQURI);
if (rexq) {
if (eq(PATH, local)) {
// annotation "path"
if (path != null) error(ANN_TWICE, "%", name.string());
path = new RestXqPath(toString(value, name));
for (final String s : path) {
if (s.trim().startsWith("{")) checkVariable(s, AtomType.AAT, declared);
}
} else if (eq(CONSUMES, local)) {
// annotation "consumes"
strings(value, name, consumes);
} else if (eq(PRODUCES, local)) {
// annotation "produces"
strings(value, name, produces);
} else if (eq(QUERY_PARAM, local)) {
// annotation "query-param"
queryParams.add(param(value, name, declared));
} else if (eq(FORM_PARAM, local)) {
// annotation "form-param"
formParams.add(param(value, name, declared));
} else if (eq(HEADER_PARAM, local)) {
// annotation "header-param"
headerParams.add(param(value, name, declared));
} else if (eq(COOKIE_PARAM, local)) {
// annotation "cookie-param"
cookieParams.add(param(value, name, declared));
} else {
// method annotations
final HTTPMethod m = HTTPMethod.get(string(local));
if (m == null) error(ANN_UNKNOWN, "%", name.string());
if (!value.isEmpty()) {
// remember post/put variable
if (requestBody != null) error(ANN_TWICE, "%", name.string());
if (m != POST && m != PUT) error(METHOD_VALUE, m);
requestBody = checkVariable(toString(value, name), declared);
}
if (mth.contains(m)) error(ANN_TWICE, "%", name.string());
mth.add(m);
}
} else if (eq(uri, QueryText.OUTPUTURI)) {
// serialization parameters
final String key = string(local);
final String val = toString(value, name);
if (output.get(key) == null) error(UNKNOWN_SER, key);
output.set(key, val);
}
found |= rexq;
}
if (!mth.isEmpty()) methods = mth;
if (found) {
if (path == null) error(ANN_MISSING, PATH);
for (int i = 0; i < declared.length; i++)
if (!declared[i]) error(VAR_UNDEFINED, function.args[i].name.string());
}
return found;
}
