/** 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;
}
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");
}
}
GChoicePeer(GToolkit toolkit, Choice target) {
super(toolkit, target);
int itemCount = target.getItemCount();
for (int i = 0; i < itemCount; i++) add(target.getItem(i), i);
int selectedIndex = target.getSelectedIndex();
if (selectedIndex >= 0 && itemCount > 0) select(selectedIndex);
}
/**
* 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);
defaultChoiceIndexes = 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]);
if (defaultItem != null) thisChoice.select(defaultItem);
else thisChoice.select(0);
c.gridx = 1;
c.gridy = y;
c.anchor = GridBagConstraints.WEST;
grid.setConstraints(thisChoice, c);
add(thisChoice);
choice.addElement(thisChoice);
int index = thisChoice.getSelectedIndex();
defaultChoiceIndexes.addElement(new Integer(index));
if (Recorder.record || macro) saveLabel(thisChoice, label);
y++;
}
public void itemStateChanged(ItemEvent e) {
beta = Double.parseDouble(betaval.getText());
updatebeta();
boolean avgchanged = false;
for (int i = 0; i < ncurves; i++) {
if (checkarray[i].getState() != include[i]) {
avgchanged = true;
if (include[i]) {
include[i] = false;
} else {
include[i] = true;
}
}
}
if (avgchanged) {
updateavg();
updatebeta();
int1array[ncurves].setText("" + (float) intensity1[ncurves]);
e1array[ncurves].setText("" + (float) bright1[ncurves]);
n1array[ncurves].setText("" + (float) number1[ncurves]);
int2array[ncurves].setText("" + (float) intensity2[ncurves]);
e2array[ncurves].setText("" + (float) bright2[ncurves]);
n2array[ncurves].setText("" + (float) number2[ncurves]);
eccarray[ncurves].setText("" + (float) brightcc[ncurves]);
pwavg.updateSeries(avg, 0, true);
float[] temp = pwavg.getLimits();
temp[4] = 1.0f;
pwavg.setLimits(temp);
}
if (e.getSource() == dispcurvechoice) {
dispcurve = dispcurvechoice.getSelectedIndex();
pwfit.updateSeries(pch[dispcurve], 0, true);
pwfit.updateSeries(fit[dispcurve], 1, true);
float[] temp = pwfit.getLimits();
temp[4] = 1.0f;
pwfit.setLimits(temp);
}
}
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);
}