/**
* Adds a popup menu.
*
* @param label the label
* @param items the menu items
* @param defaultItem the menu item initially selected
*/
public void addChoice(String label, String[] items, String defaultItem) {
String label2 = label;
if (label2.indexOf('_') != -1) label2 = label2.replace('_', ' ');
Label theLabel = makeLabel(label2);
c.gridx = 0;
c.gridy = y;
c.anchor = GridBagConstraints.EAST;
c.gridwidth = 1;
if (choice == null) {
choice = new Vector(4);
c.insets = getInsets(5, 0, 5, 0);
} else c.insets = getInsets(0, 0, 5, 0);
grid.setConstraints(theLabel, c);
add(theLabel);
Choice thisChoice = new Choice();
thisChoice.addKeyListener(this);
thisChoice.addItemListener(this);
for (int i = 0; i < items.length; i++) thisChoice.addItem(items[i]);
thisChoice.select(defaultItem);
c.gridx = 1;
c.gridy = y;
c.anchor = GridBagConstraints.WEST;
grid.setConstraints(thisChoice, c);
add(thisChoice);
choice.addElement(thisChoice);
if (Recorder.record || macro) saveLabel(thisChoice, label);
y++;
}
public void itemStateChanged(ItemEvent e) {
System.out.println("itemStateChanged");
if (e.getSource() == ColChoice) // 预选颜色
{
String name = ColChoice.getSelectedItem();
if (name == "black") {
c = new Color(0, 0, 0);
} else if (name == "red") {
c = new Color(255, 0, 0);
} else if (name == "green") {
c = new Color(0, 255, 0);
} else if (name == "blue") {
c = new Color(0, 0, 255);
}
} else if (e.getSource() == SizeChoice) // 画笔大小
{
String selected = SizeChoice.getSelectedItem();
if (selected == "1") {
con = 1;
size = new BasicStroke(con, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL);
} else if (selected == "3") {
con = 3;
size = new BasicStroke(con, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL);
} else if (selected == "5") {
con = 5;
size = new BasicStroke(con, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL);
} else if (selected == "7") {
con = 7;
size = new BasicStroke(con, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL);
} else if (selected == "9") {
con = 9;
size = new BasicStroke(con, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL);
}
} else if (e.getSource() == EraserChoice) // 橡皮大小
{
String Esize = EraserChoice.getSelectedItem();
if (Esize == "5") {
Econ = 5 * 2;
} else if (Esize == "9") {
Econ = 9 * 2;
} else if (Esize == "13") {
Econ = 13 * 2;
} else if (Esize == "17") {
Econ = 17 * 3;
}
}
}
/** Returns the index of the selected item in the next popup menu. */
public int getNextChoiceIndex() {
if (choice == null) return -1;
Choice thisChoice = (Choice) (choice.elementAt(choiceIndex));
int index = thisChoice.getSelectedIndex();
if (macro) {
String label = (String) labels.get((Object) thisChoice);
String oldItem = thisChoice.getSelectedItem();
int oldIndex = thisChoice.getSelectedIndex();
String item = Macro.getValue(macroOptions, label, oldItem);
if (item != null && item.startsWith("&")) // value is macro variable
item = getChoiceVariable(item);
thisChoice.select(item);
index = thisChoice.getSelectedIndex();
if (index == oldIndex && !item.equals(oldItem)) {
// is value a macro variable?
Interpreter interp = Interpreter.getInstance();
String s = interp != null ? interp.getStringVariable(item) : null;
if (s == null)
IJ.error(getTitle(), "\"" + item + "\" is not a valid choice for \"" + label + "\"");
else item = s;
}
}
if (recorderOn) {
int defaultIndex = ((Integer) (defaultChoiceIndexes.elementAt(choiceIndex))).intValue();
if (!(smartRecording && index == defaultIndex)) {
String item = thisChoice.getSelectedItem();
if (!(item.equals("*None*") && getTitle().equals("Merge Channels")))
recordOption(thisChoice, thisChoice.getSelectedItem());
}
}
choiceIndex++;
return index;
}
/** Returns the selected item in the next popup menu. */
public String getNextChoice() {
if (choice == null) return "";
Choice thisChoice = (Choice) (choice.elementAt(choiceIndex));
String item = thisChoice.getSelectedItem();
if (macro) {
String label = (String) labels.get((Object) thisChoice);
item = Macro.getValue(macroOptions, label, item);
if (item != null && item.startsWith("&")) // value is macro variable
item = getChoiceVariable(item);
}
if (recorderOn) recordOption(thisChoice, item);
choiceIndex++;
return item;
}
{
clientStatus.add("Online");
clientStatus.add("Offline");
clientStatus.add("Busy");
clientStatus.select("Offline");
clientStatus.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent e) {
new Thread("icqtest/chooser control handler") {
public void run() {
try {
if (clientStatus.getSelectedItem().equals("Online")) {
if (plugin.getClientStatus(getMyLoginId())
== org.jcq2k.MessagingNetwork.STATUS_OFFLINE) login();
plugin.setClientStatus(
getMyLoginId(), org.jcq2k.MessagingNetwork.STATUS_ONLINE);
} else if (clientStatus.getSelectedItem().equals("Busy")) {
if (plugin.getClientStatus(getMyLoginId())
== org.jcq2k.MessagingNetwork.STATUS_OFFLINE) login();
plugin.setClientStatus(getMyLoginId(), org.jcq2k.MessagingNetwork.STATUS_BUSY);
} else if (clientStatus.getSelectedItem().equals("Offline")) {
if (plugin.getClientStatus(getMyLoginId())
!= org.jcq2k.MessagingNetwork.STATUS_OFFLINE)
plugin.setClientStatus(
getMyLoginId(), org.jcq2k.MessagingNetwork.STATUS_OFFLINE);
} else {
org.jcq2k.util.joe.Lang.ASSERT_FALSE("invalid clientStatus.getSelectedItem()");
}
} catch (Throwable tr) {
printException(tr);
}
}
}.start();
}
});
}
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);
}
paintboard1(String s) {
super(s);
addMouseMotionListener(this);
addMouseListener(this);
paintInfo = new Vector();
/* 各工具按钮及选择项 */
// 颜色选择
ColChoice = new Choice();
ColChoice.add("black");
ColChoice.add("red");
ColChoice.add("blue");
ColChoice.add("green");
ColChoice.addItemListener(this);
// 画笔大小选择
SizeChoice = new Choice();
SizeChoice.add("1");
SizeChoice.add("3");
SizeChoice.add("5");
SizeChoice.add("7");
SizeChoice.add("9");
SizeChoice.addItemListener(this);
// 橡皮大小选择
EraserChoice = new Choice();
EraserChoice.add("5");
EraserChoice.add("9");
EraserChoice.add("13");
EraserChoice.add("17");
EraserChoice.addItemListener(this);
// //////////////////////////////////////////////////
toolPanel = new Panel();
clear = new Button("清除");
eraser = new Button("橡皮");
pen = new Button("画笔");
drLine = new Button("画直线");
drCircle = new Button("画圆形");
drRect = new Button("画矩形");
openPic = new Button("打开图画");
savePic = new Button("保存图画");
colchooser = new Button("显示调色板");
// 各组件事件监听
clear.addActionListener(this);
eraser.addActionListener(this);
pen.addActionListener(this);
drLine.addActionListener(this);
drCircle.addActionListener(this);
drRect.addActionListener(this);
openPic.addActionListener(this);
savePic.addActionListener(this);
colchooser.addActionListener(this);
颜色 = new Label("画笔颜色", Label.CENTER);
大小B = new Label("画笔大小", Label.CENTER);
大小E = new Label("橡皮大小", Label.CENTER);
// 面板添加组件
toolPanel.add(openPic);
toolPanel.add(savePic);
toolPanel.add(pen);
toolPanel.add(drLine);
toolPanel.add(drCircle);
toolPanel.add(drRect);
toolPanel.add(颜色);
toolPanel.add(ColChoice);
toolPanel.add(大小B);
toolPanel.add(SizeChoice);
toolPanel.add(colchooser);
toolPanel.add(eraser);
toolPanel.add(大小E);
toolPanel.add(EraserChoice);
toolPanel.add(clear);
// 工具面板到APPLET面板
add(toolPanel, BorderLayout.NORTH);
setBounds(230, 50, 900, 650);
setVisible(true);
validate();
// dialog for save and load
openPicture = new FileDialog(this, "打开图画", FileDialog.LOAD);
openPicture.setVisible(false);
savePicture = new FileDialog(this, "保存图画", FileDialog.SAVE);
savePicture.setVisible(false);
openPicture.addWindowListener(
new WindowAdapter() {
public void windowClosing(WindowEvent e) {
openPicture.setVisible(false);
}
});
savePicture.addWindowListener(
new WindowAdapter() {
public void windowClosing(WindowEvent e) {
savePicture.setVisible(false);
}
});
addWindowListener(
new WindowAdapter() {
public void windowClosing(WindowEvent e) {
System.exit(0);
}
});
}