public void mouseReleased(MouseEvent evt) {
Graphics g = canvas.getGraphics();
g.setColor(color);
g.setPaintMode();
end = evt.getPoint();
if (type == 0) {
g.drawRect(start.x, start.y, end.x - start.x, end.y - start.y);
if (filled.getState() == true) g.fillRect(start.x, start.y, end.x - start.x, end.y - start.y);
status.setText("2. Ecke des Rechtecks festgelegt");
} else if (type == 1) {
int radius;
radius = (int) Math.sqrt(Math.pow(end.x - start.x, 2) + Math.pow(end.y - start.y, 2));
g.drawOval(start.x - radius, start.y - radius, 2 * radius, 2 * radius);
if (filled.getState() == true)
g.fillOval(start.x - radius, start.y - radius, 2 * radius, 2 * radius);
status.setText("Radius des Kreises festgelegt");
} else if (type == 2) {
g.drawOval(start.x, start.y, end.x - start.x, end.y - start.y);
if (filled.getState() == true) g.fillOval(start.x, start.y, end.x - start.x, end.y - start.y);
status.setText("Radius der Ellipse festgelegt");
}
}
public void itemStateChanged(ItemEvent evt) {
if (evt.getSource() == farbe) {
status.setText("Farbe " + farben[farbe.getSelectedIndex()] + " ausgewaehlt");
switch (farbe.getSelectedIndex()) {
case 0:
color = Color.blue;
break;
case 1:
color = Color.yellow;
break;
case 2:
color = Color.green;
break;
case 3:
color = Color.red;
break;
case 4:
color = Color.black;
break;
case 5:
color = Color.white;
}
} else if (evt.getSource() == filled) {
if (filled.getState() == true) status.setText("Ausgefuellt zeichnen");
else status.setText("Rahmen zeichnen");
}
}
public void launch() {
setLocation(350, 200);
setLayout(new GridLayout(5, 1));
ItemMonitor im = new ItemMonitor();
// checkbox
checkbox.setLabel("test");
checkbox.addItemListener(im);
add(checkbox);
for (int i = 0; i < 3; i++) {
cb[i] = new Checkbox("item " + i);
cb[i].addItemListener(im);
add(cb[i]);
if (checkbox.getState() == true) {
cb[i].setEnabled(true);
} else {
cb[i].setEnabled(false);
}
if (i == 2) {
cb[i].setState(true);
}
}
// label
lb = new Label();
add(lb);
pack();
setVisible(true);
}
public void itemStateChanged(ItemEvent E) {
// The 'log chat' checkbox
if (E.getSource() == logChat) {
server.logChats = logChat.getState();
// Loop through all of the chat rooms, and set the logging
// state to be the same as the value of the checkbox
for (int count = 0; count < server.chatRooms.size(); count++) {
babylonChatRoom tmp = (babylonChatRoom) server.chatRooms.elementAt(count);
try {
tmp.setLogging(server.logChats);
} catch (IOException e) {
server.serverOutput(
server.strings.get(thisClass, "togglelogerror") + " " + tmp.name + "\n");
}
}
}
// The user list
if (E.getSource() == userList) {
// If anything is selected, enable the 'disconnect user'
// button, otherwise disable it
synchronized (userList) {
disconnect.setEnabled(userList.getSelectedItem() != null);
}
}
}
public static void maybeDrawGraph(GrandFinale.Graph nodeGraph, IRobot r) {
if (!enable.getState()) {
return;
}
if (c++ % 20 == 0) { // Because it's expensive to do this every tick
drawGraph(nodeGraph, r);
}
}
private void recordCheckboxOption(Checkbox cb) {
String label = (String) labels.get((Object) cb);
if (label != null) {
if (cb.getState()) // checked
Recorder.recordOption(label);
else if (Recorder.getCommandOptions() == null) Recorder.recordOption(" ");
}
}
private void loop() {
while (true) {
try {
Thread.sleep(delay);
} catch (InterruptedException e) {
}
if (mode.getState()) {
lookup();
}
}
}
public void itemStateChanged(ItemEvent e) {
Checkbox currentCheckbox = shapeActions.getSelectedCheckbox();
boolean CheckboxState = currentCheckbox.getState();
String currentAction = currentCheckbox.getLabel();
if (CheckboxState) {
myAction = currentAction;
} else {
myAction = "DRAW";
}
applet.repaint();
}
/** Returns the state of the next checkbox. */
public boolean getNextBoolean() {
if (checkbox == null) return false;
Checkbox cb = (Checkbox) (checkbox.elementAt(cbIndex));
if (recorderOn) recordCheckboxOption(cb);
boolean state = cb.getState();
if (macro) {
String label = (String) labels.get((Object) cb);
String key = Macro.trimKey(label);
state = isMatch(macroOptions, key + " ");
}
cbIndex++;
return state;
}
/** Récupère les preférences manquants et ferme la fenêtre */
public void fermer() {
// noms des joueurs
String nom = txt_joueur0.getText();
if (nom.compareTo("") == 0) noms[0] = "J1";
else noms[0] = nom;
nom = txt_joueur1.getText();
if (nom.compareTo("") == 0) noms[1] = "J2";
else noms[1] = nom;
// nombre de vies
nb_vies = new Integer(cbg_vies.getSelectedCheckbox().getLabel()).intValue();
aleatoire = cb_aleatoire.getState();
setVisible(false);
} // fermer()
private void clickOpciones() {
JPanel myPanel = new JPanel();
// myPanel.setFont(new Font("Serif",Font.PLAIN,20));
Checkbox cbMovimientosPosibles = new Checkbox("Mostrar movimientos posibles", false);
cbMovimientosPosibles.setFont(new Font("Serif", Font.PLAIN, 20));
myPanel.add(cbMovimientosPosibles);
UIManager.put("OptionPane.buttonFont", new FontUIResource(new Font("Serif", Font.PLAIN, 20)));
int result =
JOptionPane.showConfirmDialog(null, myPanel, "Opciones", JOptionPane.OK_CANCEL_OPTION);
if (result == JOptionPane.OK_OPTION) {
mostrarPosibles = cbMovimientosPosibles.getState();
}
}
public void updateRec() {
try {
setFields();
db.update();
boolean b = delCB.getState();
if (db.deleted() && !b) {
db.undelete();
} else if (!db.deleted() && b) {
db.delete();
}
} // try
catch (Exception e1) {
System.out.println(e1);
System.exit(1);
}
}
void displayWifiPassword() {
Config config = Config.instance();
config.setEmail(emailField.getText());
config.setRememberPassword(rememberPasswordCheckbox.getState());
config.setPassword(passField.getText());
config.updateConfig();
if (Config.instance().getQRImage() == null || Config.instance().getWifiPassword().isEmpty()) {
if (Config.instance().getWifiPassword().isEmpty()) {
wifiPasswordField.setText("");
}
hintLabel.setText("QRCode has not been generated");
qrCodeLabel.setIcon(idleIcon);
return;
}
try {
wifiPasswordField.setText(Config.instance().getWifiPassword());
BufferedImage qrImage = Config.instance().getQRImage();
int width = qrCodeLabel.getWidth();
int height = qrCodeLabel.getHeight();
// make a square image
int length = width < height ? width : height;
ImageIcon imgIcon = new ImageIcon();
imgIcon.setImage(qrImage.getScaledInstance(length, length, Image.SCALE_AREA_AVERAGING));
hintLabel.setText("Scan QRCode with mobile client to login clear-guest!");
wifiPasswordField.setText(Config.instance().getWifiPassword());
qrCodeLabel.setIcon(imgIcon);
} catch (Exception e) {
JOptionPane.showMessageDialog(
mainPanel,
"Failed to generate QR Image, please try again",
"QRCode Generation Failed",
JOptionPane.ERROR_MESSAGE);
e.printStackTrace();
}
}
public static void printRoute(List<GrandFinale.Node> route) {
if (!enable.getState()) {
return;
}
MazeGridPanel panel = getPanel();
Graphics g = panel.getGraphics();
Font fOld = g.getFont();
g.setFont(new Font("Arial", Font.BOLD, fOld.getSize()));
for (int i = 0; i < route.size(); i++) {
Point p = route.get(i).getPoint();
try {
mFill.invoke(panel, p.x, p.y, g, Color.red);
} catch (Exception e) {
}
p = offset(panel, p, 3, 1);
g.setColor(Color.black);
g.drawString(String.valueOf(i), p.x, p.y);
}
}
/**
* Diff�rentes actions men�es suivant le choix de l'utilisateur
*
* @param e evenement d�clench� par le clic sur ok ou annuler
*/
public void actionPerformed(ActionEvent e) {
Object source = e.getSource();
if (source == ok) {
if (plus.getState() == true) {
sign = 1;
} else {
sign = 0;
}
threshold = tf.getText();
try {
thresholdVal = Integer.parseInt(threshold);
if (thresholdVal < 0) {
JOptionPane.showMessageDialog(
this.mf,
"Threshold must be a positive integer",
"Error",
JOptionPane.WARNING_MESSAGE);
this.setVisible(true);
} else {
gz.draw();
gz.creatTrans(thresholdVal, sign);
auto.modif(true);
this.dispose();
}
} catch (NumberFormatException ex) {
JOptionPane.showMessageDialog(
this.mf, "Threshold must be a positive integer.", "Error", JOptionPane.WARNING_MESSAGE);
this.setVisible(true);
}
} else if (source == cancel) {
gz.draw();
bar.displayInfo(mf.frameName);
bar.can = true;
this.dispose();
}
gz.menu.majMenus();
}
public void setFields() {
Field f;
LogicalField lf;
Checkbox c;
TextField t;
int i;
try {
for (i = 1; i <= db.getFieldCount(); i++) {
f = db.getField(i);
if (f.isMemoField() || f.isPictureField()) {
} else if (f.isLogicalField()) {
lf = (LogicalField) f;
c = (Checkbox) fldObjects.elementAt(i - 1);
lf.put(c.getState());
} else {
t = (TextField) fldObjects.elementAt(i - 1);
f.put(t.getText());
}
}
} catch (Exception e1) {
System.out.println(e1);
}
}
boolean showOptions() {
MesquiteInteger buttonPressed = new MesquiteInteger(1);
ExtensibleDialog queryDialog =
new ExtensibleDialog(containerOfModule(), "Reinterpret Node Labels", buttonPressed);
queryDialog.addLargeOrSmallTextLabel(
"Some programs write information as node labels; e.g. MrBayes writes posterior probabilities as if they were the names of clades (= node labels)."
+ "\nHere you can reintepret such information.");
// name for information (e.g., "posteriorProbability", "bootstrapFrequency")
queryDialog.addLabel(
"Name for information? (e.g., \"posteriorProbability\", \"bootstrapFrequency\")",
Label.LEFT);
TextField nameField = queryDialog.addTextField(name, 30);
queryDialog.addHorizontalLine(2);
// where to attach
queryDialog.addLabel("Applies to branch or node?", Label.LEFT);
String[] where =
new String[] {
"Information applies to branch (e.g., posterior probability, bootstrap frequency)",
"Information applies to node (e.g., clade name)"
};
RadioButtons whereButtons = queryDialog.addRadioButtons(where, 0);
queryDialog.addLabel(
"(This determines how the information will behave when the tree is rerooted.)", Label.LEFT);
queryDialog.addHorizontalLine(2);
// how to treat
queryDialog.addLabel("Number or text?", Label.LEFT);
String[] what =
new String[] {
"Treat as number (e.g., posterior probability)", "Treat as text (e.g., clade name)"
};
RadioButtons whatButtons = queryDialog.addRadioButtons(what, 0);
queryDialog.addHorizontalLine(2);
// delete internal node labels after reinterpreting?
Checkbox delete =
queryDialog.addCheckBox("Delete internal node labels after reinterpreting?", deleteAfter);
queryDialog.addHorizontalLine(2);
queryDialog.completeAndShowDialog(true);
boolean ok = (queryDialog.query() == 0);
if (ok) {
if (StringUtil.blank(nameField.getText())) {
ok = false;
alert("A name must be entered for the information");
} else {
name = nameField.getText();
nameRef = NameReference.getNameReference(name);
appliesToBranch = whereButtons.getValue() == 0;
isNumber = whatButtons.getValue() == 0;
deleteAfter = delete.getState();
}
}
queryDialog.dispose();
return ok;
}
public static void drawGraph(GrandFinale.Graph g, IRobot r) {
if (!enable.getState()) {
return;
}
drawChain(g, g.getNodeAt(r.getMaze().getStart()), new ArrayList<>());
}
public boolean shouldScale() {
return scaleCheckbox.getState();
}
public void itemStateChanged(ItemEvent e) {
ImagePlus imp = WindowManager.getCurrentImage();
if (imp == null) return;
if (!imp.isComposite()) {
int channels = imp.getNChannels();
if (channels == 1 && imp.getStackSize() <= 4) channels = imp.getStackSize();
if (imp.getBitDepth() == 24 || (channels > 1 && channels < CompositeImage.MAX_CHANNELS)) {
GenericDialog gd = new GenericDialog(imp.getTitle());
gd.addMessage("Convert to multi-channel composite image?");
gd.showDialog();
if (gd.wasCanceled()) return;
else IJ.doCommand("Make Composite");
} else {
IJ.error(
"Channels",
"A composite image is required (e.g., "
+ moreLabel
+ " Open HeLa Cells),\nor create one using "
+ moreLabel
+ " Make Composite.");
return;
}
}
if (!imp.isComposite()) return;
CompositeImage ci = (CompositeImage) imp;
Object source = e.getSource();
if (source == choice) {
int index = ((Choice) source).getSelectedIndex();
switch (index) {
case 0:
ci.setMode(IJ.COMPOSITE);
break;
case 1:
ci.setMode(IJ.COLOR);
break;
case 2:
ci.setMode(IJ.GRAYSCALE);
break;
}
ci.updateAndDraw();
if (Recorder.record) {
String mode = null;
switch (index) {
case 0:
mode = "composite";
break;
case 1:
mode = "color";
break;
case 2:
mode = "grayscale";
break;
}
Recorder.record("Stack.setDisplayMode", mode);
}
} else if (source instanceof Checkbox) {
for (int i = 0; i < checkbox.length; i++) {
Checkbox cb = (Checkbox) source;
if (cb == checkbox[i]) {
if (ci.getMode() == IJ.COMPOSITE) {
boolean[] active = ci.getActiveChannels();
active[i] = cb.getState();
if (Recorder.record) {
String str = "";
for (int c = 0; c < ci.getNChannels(); c++) str += active[c] ? "1" : "0";
Recorder.record("Stack.setActiveChannels", str);
Recorder.record("//Stack.toggleChannel", imp.getChannel());
}
} else {
imp.setPosition(i + 1, imp.getSlice(), imp.getFrame());
if (Recorder.record) Recorder.record("Stack.setChannel", i + 1);
}
ci.updateAndDraw();
return;
}
}
}
}
/**
* Every time one of the options is changed, this method is called. The parser settings are
* adjusted to the GUI settings, the expression is parsed again, and the results updated.
*/
private void optionsChanged() {
myParser.setImplicitMul(implicitCheckbox.getState());
myParser.setAllowUndeclared(undeclaredCheckbox.getState());
parseExpression();
updateResult();
}
/** Ensures that the options dialog has no mutually exclusive options. */
private void verifyOptions(Object src) {
// record GUI state
boolean autoscaleEnabled = autoscaleBox.isEnabled();
boolean colorModeEnabled = colorModeChoice.isEnabled();
boolean concatenateEnabled = concatenateBox.isEnabled();
boolean cropEnabled = cropBox.isEnabled();
boolean groupFilesEnabled = groupFilesBox.isEnabled();
boolean ungroupFilesEnabled = ungroupFilesBox.isEnabled();
boolean openAllSeriesEnabled = openAllSeriesBox.isEnabled();
// boolean recordEnabled = recordBox.isEnabled();
boolean showMetadataEnabled = showMetadataBox.isEnabled();
boolean showOMEXMLEnabled = showOMEXMLBox.isEnabled();
boolean specifyRangesEnabled = specifyRangesBox.isEnabled();
boolean splitZEnabled = splitZBox.isEnabled();
boolean splitTEnabled = splitTBox.isEnabled();
boolean splitCEnabled = splitCBox.isEnabled();
// boolean stackFormatEnabled = stackFormatChoice.isEnabled();
boolean stackOrderEnabled = stackOrderChoice.isEnabled();
boolean swapDimsEnabled = swapDimsBox.isEnabled();
boolean virtualEnabled = virtualBox.isEnabled();
boolean isAutoscale = autoscaleBox.getState();
String colorModeValue = colorModeChoice.getSelectedItem();
boolean isConcatenate = concatenateBox.getState();
boolean isCrop = cropBox.getState();
boolean isGroupFiles = groupFilesBox.getState();
boolean isUngroupFiles = ungroupFilesBox.getState();
boolean isOpenAllSeries = openAllSeriesBox.getState();
// boolean isRecord = recordBox.getState();
boolean isShowMetadata = showMetadataBox.getState();
boolean isShowOMEXML = showOMEXMLBox.getState();
boolean isSpecifyRanges = specifyRangesBox.getState();
boolean isSplitZ = splitZBox.getState();
boolean isSplitT = splitTBox.getState();
boolean isSplitC = splitCBox.getState();
String stackFormatValue = stackFormatChoice.getSelectedItem();
boolean isStackNone = stackFormatValue.equals(ImporterOptions.VIEW_NONE);
boolean isStackStandard = stackFormatValue.equals(ImporterOptions.VIEW_STANDARD);
boolean isStackHyperstack = stackFormatValue.equals(ImporterOptions.VIEW_HYPERSTACK);
boolean isStackBrowser = stackFormatValue.equals(ImporterOptions.VIEW_BROWSER);
boolean isStackImage5D = stackFormatValue.equals(ImporterOptions.VIEW_IMAGE_5D);
boolean isStackView5D = stackFormatValue.equals(ImporterOptions.VIEW_VIEW_5D);
String stackOrderValue = stackOrderChoice.getSelectedItem();
boolean isSwap = swapDimsBox.getState();
boolean isVirtual = virtualBox.getState();
// toggle availability of each option based on state of earlier options
// NB: The order the options are examined here defines their order of
// precedence. This ordering is necessary because it affects which
// component states are capable of graying out other components.
// For example, we want to disable autoscaleBox when virtualBox is checked,
// so the virtualBox logic must appear before the autoscaleBox logic.
// To make it more intuitive for the user, the order of precedence should
// match the component layout from left to right, top to bottom, according
// to subsection.
// == Stack viewing ==
// stackOrderChoice
stackOrderEnabled = isStackStandard;
if (src == stackFormatChoice) {
if (isStackHyperstack || isStackBrowser || isStackImage5D) {
stackOrderValue = ImporterOptions.ORDER_XYCZT;
} else if (isStackView5D) stackOrderValue = ImporterOptions.ORDER_XYZCT;
else stackOrderValue = ImporterOptions.ORDER_DEFAULT;
}
// == Metadata viewing ==
// showMetadataBox
showMetadataEnabled = !isStackNone;
if (!showMetadataEnabled) isShowMetadata = true;
// showOMEXMLBox
// NB: no other options affect showOMEXMLBox
// == Dataset organization ==
// groupFilesBox
if (src == stackFormatChoice && isStackBrowser) {
isGroupFiles = true;
} else if (!options.isLocal()) {
isGroupFiles = false;
groupFilesEnabled = false;
}
// ungroupFilesBox
if (options.isOMERO()) {
isUngroupFiles = false;
ungroupFilesEnabled = false;
}
// swapDimsBox
// NB: no other options affect swapDimsBox
// openAllSeriesBox
// NB: no other options affect openAllSeriesBox
// concatenateBox
// NB: no other options affect concatenateBox
// == Memory management ==
// virtualBox
virtualEnabled = !isStackNone && !isStackImage5D && !isStackView5D && !isConcatenate;
if (!virtualEnabled) isVirtual = false;
else if (src == stackFormatChoice && isStackBrowser) isVirtual = true;
// recordBox
// recordEnabled = isVirtual;
// if (!recordEnabled) isRecord = false;
// specifyRangesBox
specifyRangesEnabled = !isStackNone && !isVirtual;
if (!specifyRangesEnabled) isSpecifyRanges = false;
// cropBox
cropEnabled = !isStackNone && !isVirtual;
if (!cropEnabled) isCrop = false;
// == Color options ==
// colorModeChoice
colorModeEnabled = !isStackImage5D && !isStackView5D && !isStackStandard;
if (!colorModeEnabled) colorModeValue = ImporterOptions.COLOR_MODE_DEFAULT;
// autoscaleBox
autoscaleEnabled = !isVirtual;
if (!autoscaleEnabled) isAutoscale = false;
// == Split into separate windows ==
boolean splitEnabled = !isStackNone && !isStackBrowser && !isStackImage5D && !isStackView5D;
// TODO: Make splitting work with Data Browser.
// splitCBox
splitCEnabled = splitEnabled;
if (!splitCEnabled) isSplitC = false;
// splitZBox
splitZEnabled = splitEnabled;
if (!splitZEnabled) isSplitZ = false;
// splitTBox
splitTEnabled = splitEnabled;
if (!splitTEnabled) isSplitT = false;
// update state of each option, in case anything changed
autoscaleBox.setEnabled(autoscaleEnabled);
colorModeChoice.setEnabled(colorModeEnabled);
concatenateBox.setEnabled(concatenateEnabled);
cropBox.setEnabled(cropEnabled);
groupFilesBox.setEnabled(groupFilesEnabled);
ungroupFilesBox.setEnabled(ungroupFilesEnabled);
openAllSeriesBox.setEnabled(openAllSeriesEnabled);
// recordBox.setEnabled(recordEnabled);
showMetadataBox.setEnabled(showMetadataEnabled);
showOMEXMLBox.setEnabled(showOMEXMLEnabled);
specifyRangesBox.setEnabled(specifyRangesEnabled);
splitZBox.setEnabled(splitZEnabled);
splitTBox.setEnabled(splitTEnabled);
splitCBox.setEnabled(splitCEnabled);
// stackFormatChoice.setEnabled(stackFormatEnabled);
stackOrderChoice.setEnabled(stackOrderEnabled);
swapDimsBox.setEnabled(swapDimsEnabled);
virtualBox.setEnabled(virtualEnabled);
autoscaleBox.setState(isAutoscale);
colorModeChoice.select(colorModeValue);
concatenateBox.setState(isConcatenate);
cropBox.setState(isCrop);
groupFilesBox.setState(isGroupFiles);
ungroupFilesBox.setState(isUngroupFiles);
openAllSeriesBox.setState(isOpenAllSeries);
// recordBox.setState(isRecord);
showMetadataBox.setState(isShowMetadata);
showOMEXMLBox.setState(isShowOMEXML);
specifyRangesBox.setState(isSpecifyRanges);
splitZBox.setState(isSplitZ);
splitTBox.setState(isSplitT);
splitCBox.setState(isSplitC);
// stackFormatChoice.select(stackFormatValue);
stackOrderChoice.select(stackOrderValue);
swapDimsBox.setState(isSwap);
virtualBox.setState(isVirtual);
if (IS_GLITCHED) {
// HACK - work around a Mac OS X bug where GUI components do not update
// list of affected components
Component[] c = {
autoscaleBox,
colorModeChoice,
concatenateBox,
cropBox,
groupFilesBox,
ungroupFilesBox,
openAllSeriesBox,
// recordBox,
showMetadataBox,
showOMEXMLBox,
specifyRangesBox,
splitZBox,
splitTBox,
splitCBox,
stackFormatChoice,
stackOrderChoice,
swapDimsBox,
virtualBox
};
// identify currently focused component
Component focused = null;
for (int i = 0; i < c.length; i++) {
if (c[i].isFocusOwner()) focused = c[i];
}
// temporarily disable focus events
for (int i = 0; i < c.length; i++) c[i].removeFocusListener(this);
// cycle through focus on all components
for (int i = 0; i < c.length; i++) c[i].requestFocusInWindow();
// clear the focus globally
KeyboardFocusManager kfm = KeyboardFocusManager.getCurrentKeyboardFocusManager();
kfm.clearGlobalFocusOwner();
sleep(100); // doesn't work if this value is too small
// refocus the originally focused component
if (focused != null) focused.requestFocusInWindow();
// reenable focus events
for (int i = 0; i < c.length; i++) c[i].addFocusListener(this);
}
}
/** Returns 'true' if this dialog has a "Preview" checkbox and it is enabled. */
public boolean isPreviewActive() {
return previewCheckbox != null && previewCheckbox.getState();
}
void apply(ImagePlus imp, ImageProcessor ip) {
// this.setCursor(wait);
// IJ.showStatus("Bandpassing slice "+previousSlice);
java.awt.Color col;
if (invert.getState()) col = Toolbar.getForegroundColor();
else col = Toolbar.getBackgroundColor();
ip.setColor(col);
int fill = ip.BLACK;
int keep = 0;
if (bandPassH.getState() && bandPassS.getState() && bandPassB.getState()) { // PPP All pass
for (int j = 0; j < numPixels; j++) {
int hue = hSource[j] & 0xff;
int sat = sSource[j] & 0xff;
int bri = bSource[j] & 0xff;
if (((hue < minHue) || (hue > maxHue))
|| ((sat < minSat) || (sat > maxSat))
|| ((bri < minBri) || (bri > maxBri))) fillMask[j] = fill;
else fillMask[j] = keep;
}
} else if (!bandPassH.getState()
&& !bandPassS.getState()
&& !bandPassB.getState()) { // SSS All stop
for (int j = 0; j < numPixels; j++) {
int hue = hSource[j] & 0xff;
int sat = sSource[j] & 0xff;
int bri = bSource[j] & 0xff;
if (((hue >= minHue) && (hue <= maxHue))
|| ((sat >= minSat) && (sat <= maxSat))
|| ((bri >= minBri) && (bri <= maxBri))) fillMask[j] = fill;
else fillMask[j] = keep;
}
} else if (bandPassH.getState() && bandPassS.getState() && !bandPassB.getState()) { // PPS
for (int j = 0; j < numPixels; j++) {
int hue = hSource[j] & 0xff;
int sat = sSource[j] & 0xff;
int bri = bSource[j] & 0xff;
if (((hue < minHue) || (hue > maxHue))
|| ((sat < minSat) || (sat > maxSat))
|| ((bri >= minBri) && (bri <= maxBri))) fillMask[j] = fill;
else fillMask[j] = keep;
}
} else if (!bandPassH.getState() && !bandPassS.getState() && bandPassB.getState()) { // SSP
for (int j = 0; j < numPixels; j++) {
int hue = hSource[j] & 0xff;
int sat = sSource[j] & 0xff;
int bri = bSource[j] & 0xff;
if (((hue >= minHue) && (hue <= maxHue))
|| ((sat >= minSat) && (sat <= maxSat))
|| ((bri < minBri) || (bri > maxBri))) fillMask[j] = fill;
else fillMask[j] = keep;
}
} else if (bandPassH.getState() && !bandPassS.getState() && !bandPassB.getState()) { // PSS
for (int j = 0; j < numPixels; j++) {
int hue = hSource[j] & 0xff;
int sat = sSource[j] & 0xff;
int bri = bSource[j] & 0xff;
if (((hue < minHue) || (hue > maxHue))
|| ((sat >= minSat) && (sat <= maxSat))
|| ((bri >= minBri) && (bri <= maxBri))) fillMask[j] = fill;
else fillMask[j] = keep;
}
} else if (!bandPassH.getState() && bandPassS.getState() && bandPassB.getState()) { // SPP
for (int j = 0; j < numPixels; j++) {
int hue = hSource[j] & 0xff;
int sat = sSource[j] & 0xff;
int bri = bSource[j] & 0xff;
if (((hue >= minHue) && (hue <= maxHue))
|| ((sat < minSat) || (sat > maxSat))
|| ((bri < minBri) || (bri > maxBri))) fillMask[j] = fill;
else fillMask[j] = keep;
}
} else if (!bandPassH.getState() && bandPassS.getState() && !bandPassB.getState()) { // SPS
for (int j = 0; j < numPixels; j++) {
int hue = hSource[j] & 0xff;
int sat = sSource[j] & 0xff;
int bri = bSource[j] & 0xff;
if (((hue >= minHue) && (hue <= maxHue))
|| ((sat < minSat) || (sat > maxSat))
|| ((bri >= minBri) && (bri <= maxBri))) fillMask[j] = fill;
else fillMask[j] = keep;
}
} else if (bandPassH.getState() && !bandPassS.getState() && bandPassB.getState()) { // PSP
for (int j = 0; j < numPixels; j++) {
int hue = hSource[j] & 0xff;
int sat = sSource[j] & 0xff;
int bri = bSource[j] & 0xff;
if (((hue < minHue) || (hue > maxHue))
|| ((sat >= minSat) && (sat <= maxSat))
|| ((bri < minBri) || (bri > maxBri))) fillMask[j] = fill;
else fillMask[j] = keep;
}
}
ip.fill(fillMask);
if (threshold.getState()) {
ip.invert();
for (int j = 0; j < numPixels; j++) {
if (fillMask[j] == fill) fillMask[j] = keep;
else fillMask[j] = fill;
}
ip.fill(fillMask);
ip.invert();
}
}
public boolean queryOptions() {
if (!okToInteractWithUser(
CAN_PROCEED_ANYWAY,
"Querying Options")) // Debugg.println needs to check that options set well enough to
// proceed anyway
return true;
boolean closeWizard = false;
if ((MesquiteTrunk.isMacOSXBeforeSnowLeopard()) && MesquiteDialog.currentWizard == null) {
CommandRecord cRec = null;
cRec = MesquiteThread.getCurrentCommandRecordDefIfNull(null);
if (cRec != null) {
cRec.requestEstablishWizard(true);
closeWizard = true;
}
}
MesquiteInteger buttonPressed = new MesquiteInteger(1);
queryOptionsDialog =
new ExtensibleDialog(
containerOfModule(),
"TNT Options & Locations",
buttonPressed); // MesquiteTrunk.mesquiteTrunk.containerOfModule()
// queryOptionsDialog.addLabel("TNT - Options and Locations");
String helpString =
"This module will prepare a matrix for TNT, and ask TNT do to an analysis. A command-line version of TNT must be installed. "
+ "You can ask it to do a bootstrap analysis or not. "
+ "Mesquite will read in the trees found by TNT. ";
queryOptionsDialog.appendToHelpString(helpString);
queryOptionsDialog.setHelpURL(zephyrRunnerEmployer.getProgramURL());
MesquiteTabbedPanel tabbedPanel = queryOptionsDialog.addMesquiteTabbedPanel();
tabbedPanel.addPanel("TNT Program Details", true);
externalProcRunner.addItemsToDialogPanel(queryOptionsDialog);
Checkbox parallelCheckBox =
queryOptionsDialog.addCheckBox("use PVM for parallel processing", parallel);
parallelCheckBox.addItemListener(this);
IntegerField slavesField =
queryOptionsDialog.addIntegerField(
"Number of Slaves", numSlaves, 4, 0, MesquiteInteger.infinite);
IntegerField maxRamField =
queryOptionsDialog.addIntegerField("mxram value", mxram, 4, 0, MesquiteInteger.infinite);
tabbedPanel.addPanel("Search Options", true);
Choice searchStyleChoice = null;
if (bootstrapAllowed)
searchStyleChoice =
queryOptionsDialog.addPopUpMenu(
"Type of search/resampling:",
new String[] {
"Regular Search",
"Bootstrap",
"Jackknife",
"Symmetric Resampled",
"Poisson Bootstrap"
},
searchStyle);
queryOptionsDialog.addLabel("Regular Search Commands");
searchField = queryOptionsDialog.addTextAreaSmallFont(searchArguments, 7, 80);
searchScriptPathField =
queryOptionsDialog.addTextField(
"Path to TNT run file containing search commands", searchScriptPath, 40);
Button browseSearchScriptPathButton =
queryOptionsDialog.addAListenedButton("Browse...", null, this);
browseSearchScriptPathButton.setActionCommand("browseSearchScript");
harvestOnlyStrictConsensusBox =
queryOptionsDialog.addCheckBox("only acquire strict consensus", harvestOnlyStrictConsensus);
queryOptionsDialog.addHorizontalLine(1);
// Checkbox doBootstrapBox = queryOptionsDialog.addCheckBox("do bootstrapping", doBootstrap);
if (bootstrapAllowed) {
bootStrapRepsField =
queryOptionsDialog.addIntegerField(
"Resampling Replicates", bootstrapreps, 8, 0, MesquiteInteger.infinite);
queryOptionsDialog.addLabel("Resampling Search Commands");
bootstrapSearchField =
queryOptionsDialog.addTextAreaSmallFont(bootstrapSearchArguments, 7, 80);
bootSearchScriptPathField =
queryOptionsDialog.addTextField(
"Path to TNT run file containing search commands for resampled",
bootSearchScriptPath,
30);
Button browseBootSearchScriptPathButton =
queryOptionsDialog.addAListenedButton("Browse...", null, this);
browseSearchScriptPathButton.setActionCommand("browseBootSearchScript");
resamplingAllConsensusTreesBox =
queryOptionsDialog.addCheckBox(
"allow TNT to calculate consensus tree", !resamplingAllConsensusTrees);
}
adjustDialogText();
queryOptionsDialog.addHorizontalLine(1);
queryOptionsDialog.addNewDialogPanel();
useDefaultsButton = queryOptionsDialog.addAListenedButton("Set to Defaults", null, this);
useDefaultsButton.setActionCommand("setToDefaults");
tabbedPanel.addPanel("Other Options", true);
convertGapsBox =
queryOptionsDialog.addCheckBox(
"convert gaps to missing (to avoid gap=extra state)", convertGapsToMissing);
queryOptionsDialog.addHorizontalLine(1);
queryOptionsDialog.addLabel("Post-Search TNT Commands");
otherOptionsField = queryOptionsDialog.addTextAreaSmallFont(otherOptions, 7, 80);
queryOptionsDialog.addHorizontalLine(1);
queryOptionsDialog.addNewDialogPanel();
useDefaultsOtherOptionsButton =
queryOptionsDialog.addAListenedButton("Set to Defaults", null, this);
useDefaultsOtherOptionsButton.setActionCommand("setToDefaultsOtherOptions");
tabbedPanel.cleanup();
queryOptionsDialog.nullifyAddPanel();
queryOptionsDialog.completeAndShowDialog("Search", "Cancel", null, null);
if (buttonPressed.getValue() == 0) {
boolean infererOK = (treeInferer == null || treeInferer.optionsChosen());
if (externalProcRunner.optionsChosen() && infererOK) {
if (bootstrapAllowed) {
bootstrapreps = bootStrapRepsField.getValue();
bootstrapSearchArguments = bootstrapSearchField.getText();
bootSearchScriptPath = bootSearchScriptPathField.getText();
harvestOnlyStrictConsensus = harvestOnlyStrictConsensusBox.getState();
resamplingAllConsensusTrees = !resamplingAllConsensusTreesBox.getState();
searchStyle = searchStyleChoice.getSelectedIndex();
}
numSlaves = slavesField.getValue();
otherOptions = otherOptionsField.getText();
convertGapsToMissing = convertGapsBox.getState();
parallel = parallelCheckBox.getState();
// doBootstrap = doBootstrapBox.getState();
searchArguments = searchField.getText();
searchScriptPath = searchScriptPathField.getText();
mxram = maxRamField.getValue();
storeRunnerPreferences();
}
}
queryOptionsDialog.dispose();
if (closeWizard) MesquiteDialog.closeWizard();
return (buttonPressed.getValue() == 0);
}
@SuppressWarnings("unchecked")
@Override
public void actionPerformed(ActionEvent ae) {
String action = ae.getActionCommand();
LinkTriple[] addNodes = null;
if (action.equals("Fetch")) {
addNodes = iSparql.ExploreURI(urlText.getText());
addLinks(addNodes);
// Cytoscape.getCurrentNetwork().addNode( Cytoscape.getCyNode( urlText.getText(), true ) );
}
if (action.equals("Fetch Selected")) {
CyNetwork network = Cytoscape.getCurrentNetwork();
Set nodeset = network.getSelectedNodes();
java.util.List<LinkTriple> nodeList = new LinkedList<LinkTriple>();
for (Object o : nodeset) {
CyNode node = (CyNode) o;
for (LinkTriple newNode : iSparql.ExploreURI(node.getIdentifier())) {
nodeList.add(newNode);
}
}
if (filterCheckbox.getState())
addLinks(iSparql.NodeFilter(null, nodeList.toArray(new LinkTriple[0])));
else addLinks(nodeList.toArray(new LinkTriple[0]));
}
if (action.equals("Find Nodes")) {
CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
CyNetwork network = Cytoscape.getCurrentNetwork();
Set nodeset = network.getSelectedNodes();
java.util.List<Map<String, Object>> nodeList = new LinkedList<Map<String, Object>>();
for (Object o : nodeset) {
CyNode node = (CyNode) o;
Map<String, Object> map = new HashMap<String, Object>();
String id = node.getIdentifier();
map.put("ID", id);
for (String attr : nodeAttr.getAttributeNames()) {
if (nodeAttr.hasAttribute(id, attr)) {
System.out.println(id + " " + attr + " " + nodeAttr.getType(attr));
if (nodeAttr.getType(attr) == CyAttributes.TYPE_STRING) {
Object iAttr = nodeAttr.getAttribute(id, attr);
map.put(attr, iAttr);
}
}
}
nodeList.add(map);
}
LinkTriple[] links = iSparql.NodeSearch(null, nodeList, "ID");
addLinks(links);
}
if (action.equals("Edit Namespaces")) {
Map<String, String> nameMap = prefs.getNameSpaces();
Map<String, String> newMap = NameSpaceEditor.EditDialog(nameMap);
for (String key : nameMap.keySet()) {
prefs.removeNameSpace(key);
}
for (String key : newMap.keySet()) {
prefs.addNameSpace(key, newMap.get(key));
}
}
}
public void keyPressed(KeyEvent e) {
if (e.getSource() == hard & e.getKeyCode() != e.VK_ENTER)
if (hard.getText().length() > 0) hard.setText("");
if (start) {
if (e.getKeyCode() == e.VK_ENTER) {
if (end.getState()) {
norm = false;
start2 = true;
hard.show();
hard.setText("");
all.clearRect(0, 0, dimX, dimY);
}
if (reg.getState()) norm = true;
start = false;
}
repaint();
} else {
if (dir == -1) {
if (e.getKeyCode() == e.VK_LEFT) dir = 0;
if (e.getKeyCode() == e.VK_UP) dir = 1;
if (e.getKeyCode() == e.VK_RIGHT) dir = 2;
if (e.getKeyCode() == e.VK_DOWN) dir = 3;
}
if (dir == 0) {
if (e.getKeyCode() == e.VK_UP) dir2 = 1;
if (e.getKeyCode() == e.VK_RIGHT) dir2 = 2;
if (e.getKeyCode() == e.VK_DOWN) dir2 = 3;
} else if (dir == 1) {
if (e.getKeyCode() == e.VK_LEFT) dir2 = 0;
if (e.getKeyCode() == e.VK_RIGHT) dir2 = 2;
if (e.getKeyCode() == e.VK_DOWN) dir2 = 3;
} else if (dir == 2) {
if (e.getKeyCode() == e.VK_LEFT) dir2 = 0;
if (e.getKeyCode() == e.VK_UP) dir2 = 1;
if (e.getKeyCode() == e.VK_DOWN) dir2 = 3;
} else if (dir == 3) {
if (e.getKeyCode() == e.VK_LEFT) dir2 = 0;
if (e.getKeyCode() == e.VK_UP) dir2 = 1;
if (e.getKeyCode() == e.VK_RIGHT) dir2 = 2;
}
repaint();
if (e.getKeyCode() == e.VK_SPACE & !fire) {
fire = true;
fireX = youX + 5;
fireY = youY - 5;
}
if (e.getKeyCode() == e.VK_P) {
if (move) move = false;
else move = true;
}
if (e.getKeyCode() == e.VK_N) {
lose = false;
flea = false;
score = 0;
level = 1;
lives = 3;
setup();
}
if (e.getKeyCode() == e.VK_T) {
buf.clearRect(0, 0, dimX, dimY);
all.drawImage(img, 0, 0, this);
start = true;
lose = false;
score = 0;
level = 1;
lives = 3;
reg.show();
end.show();
setup();
repaint();
}
}
}
