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;
}
}
}
{
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 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);
}
}
void init(String[] names1, float[][][] pch1, int psfflag1) {
setLayout(null);
names = names1;
pch = pch1;
psfflag = psfflag1;
ncurves = pch.length;
nparams = 11;
xpts = pch[0].length;
ypts = pch[0][0].length;
checkarray = new Checkbox[ncurves];
include = new boolean[ncurves];
namearray = new TextField[ncurves + 1];
int1array = new TextField[ncurves + 1];
intensity1 = new double[ncurves + 1];
e1array = new TextField[ncurves + 1];
n1array = new TextField[ncurves + 1];
bright1 = new double[ncurves + 1];
number1 = new double[ncurves + 1];
int2array = new TextField[ncurves + 1];
intensity2 = new double[ncurves + 1];
e2array = new TextField[ncurves + 1];
n2array = new TextField[ncurves + 1];
bright2 = new double[ncurves + 1];
number2 = new double[ncurves + 1];
eccarray = new TextField[ncurves + 1];
brightcc = new double[ncurves + 1];
eminccarray = new TextField[ncurves + 1];
brightmincc = new double[ncurves + 1];
c2array = new TextField[ncurves + 1];
c2 = new double[ncurves + 1];
nmeas = new int[ncurves + 1];
avg = new float[xpts][ypts];
indices = new int[ncurves];
beta = 0.05;
getintbright();
for (int i = 0; i < ncurves; i++) {
include[i] = true;
indices[i] = i;
}
updateavg();
int starty = 60;
int startx = 10;
int yinc = 25;
for (int i = 0; i <= ncurves; i++) {
if (i != ncurves) {
checkarray[i] = new Checkbox("", include[i]);
checkarray[i].setBounds(startx, starty + i * yinc, 20, 20);
checkarray[i].addItemListener(this);
add(checkarray[i]);
}
namearray[i] = new TextField(names[i]);
namearray[i].setBounds(startx + 30, starty + i * yinc, 200, 20);
add(namearray[i]);
int1array[i] = new TextField("" + (float) intensity1[i]);
int1array[i].setBounds(startx + 30 + 210, starty + i * yinc, 40, 20);
add(int1array[i]);
e1array[i] = new TextField("" + (float) bright1[i]);
e1array[i].setBounds(startx + 30 + 210 + 50, starty + i * yinc, 40, 20);
add(e1array[i]);
n1array[i] = new TextField("" + (float) number1[i]);
n1array[i].setBounds(startx + 30 + 210 + 50 + 50, starty + i * yinc, 40, 20);
add(n1array[i]);
int2array[i] = new TextField("" + (float) intensity2[i]);
int2array[i].setBounds(startx + 30 + 210 + 50 + 50 + 50, starty + i * yinc, 40, 20);
add(int2array[i]);
e2array[i] = new TextField("" + (float) bright2[i]);
e2array[i].setBounds(startx + 30 + 210 + 50 + 50 + 50 + 50, starty + i * yinc, 40, 20);
add(e2array[i]);
n2array[i] = new TextField("" + (float) number2[i]);
n2array[i].setBounds(startx + 30 + 210 + 50 + 50 + 50 + 50 + 50, starty + i * yinc, 40, 20);
add(n2array[i]);
eccarray[i] = new TextField("" + (float) brightcc[i]);
eccarray[i].setBounds(
startx + 30 + 210 + 50 + 50 + 50 + 50 + 50 + 50, starty + i * yinc, 40, 20);
add(eccarray[i]);
eminccarray[i] = new TextField("" + (float) brightmincc[i]);
eminccarray[i].setBounds(
startx + 30 + 210 + 50 + 50 + 50 + 50 + 50 + 50 + 50, starty + i * yinc, 40, 20);
add(eminccarray[i]);
c2[i] = 0.0;
c2array[i] = new TextField("" + (float) c2[i]);
c2array[i].setBounds(
startx + 30 + 210 + 50 + 50 + 50 + 50 + 50 + 50 + 50 + 50, starty + i * yinc, 80, 20);
add(c2array[i]);
}
namelabel = new Label("Filename");
namelabel.setBounds(startx + 30, starty - 25, 100, 20);
add(namelabel);
intlabel = new Label("<Ig>");
intlabel.setBounds(startx + 30 + 210, starty - 25, 40, 20);
add(intlabel);
brightlabel = new Label("<eg>");
brightlabel.setBounds(startx + 30 + 210 + 50, starty - 25, 40, 20);
add(brightlabel);
nlabel = new Label("<Ng>");
nlabel.setBounds(startx + 30 + 210 + 50 + 50, starty - 25, 40, 20);
add(nlabel);
int2label = new Label("<Ir>");
int2label.setBounds(startx + 30 + 210 + 50 + 50 + 50, starty - 25, 40, 20);
add(int2label);
bright2label = new Label("<er>");
bright2label.setBounds(startx + 30 + 210 + 50 + 50 + 50 + 50, starty - 25, 40, 20);
add(bright2label);
n2label = new Label("<Nr>");
n2label.setBounds(startx + 30 + 210 + 50 + 50 + 50 + 50 + 50, starty - 25, 40, 20);
add(n2label);
brightcclabel = new Label("<ecc>");
brightcclabel.setBounds(startx + 30 + 210 + 50 + 50 + 50 + 50 + 50 + 50, starty - 25, 40, 20);
add(brightcclabel);
brightccminlabel = new Label("min");
brightccminlabel.setBounds(
startx + 30 + 210 + 50 + 50 + 50 + 50 + 50 + 50 + 50, starty - 25, 40, 20);
add(brightccminlabel);
c2label = new Label("chi^2");
c2label.setBounds(
startx + 30 + 210 + 50 + 50 + 50 + 50 + 50 + 50 + 50 + 50, starty - 25, 80, 20);
add(c2label);
int buttonsx = startx + 30 + 210 + 50 + 50 + 50 + 50 + 50 + 50 + 50 + 50 + 90;
fitavgbutton = new Button("Fit Avg");
fitavgbutton.setBounds(buttonsx, starty - 25, 100, 40);
fitavgbutton.addActionListener(this);
add(fitavgbutton);
fitglobalbutton = new Button("Fit Global");
fitglobalbutton.setBounds(buttonsx, starty - 25 + 50, 100, 40);
fitglobalbutton.addActionListener(this);
add(fitglobalbutton);
clearparamsbutton = new Button("Reset Fit Params");
clearparamsbutton.setBounds(buttonsx, starty - 25 + 50 + 50, 100, 40);
clearparamsbutton.addActionListener(this);
add(clearparamsbutton);
checkc2 = false;
fitclass = new NLLSfit(this, 0.0001, 50, 0.1);
globalfitclass = new NLLSglobalfit(this, 0.0001, 50, 0.1);
pchfunc = new pch2D((int) ((double) xpts * 1.5), (int) ((double) ypts * 1.5), psfflag);
avgfit = new float[xpts][ypts];
fit = new float[ncurves][xpts][ypts];
xvals = new float[ncurves][xpts][ypts];
for (int i = 0; i < ncurves; i++) {
for (int j = 0; j < xpts; j++) {
for (int k = 0; k < ypts; k++) {
xvals[i][j][k] = (float) k;
fit[i][j][k] = 1.0f;
}
}
}
globalc2label = new Label("Global chi^2 = " + (float) 0.0);
globalc2label.setBounds(buttonsx, starty - 25 + 50 + 50 + 50, 140, 20);
add(globalc2label);
dispcurvelabel = new Label("Display Fit #");
dispcurvelabel.setBounds(buttonsx, starty - 25 + 50 + 50 + 50 + 30, 70, 20);
add(dispcurvelabel);
dispcurvechoice = new Choice();
for (int i = 0; i < ncurves; i++) {
dispcurvechoice.add("" + (i + 1));
}
dispcurve = 0;
dispcurvechoice.select(0);
dispcurvechoice.setBounds(buttonsx + 80, starty - 25 + 50 + 50 + 50 + 30, 40, 20);
dispcurvechoice.addItemListener(this);
add(dispcurvechoice);
betalabel = new Label("Bleedthrough f");
betalabel.setBounds(buttonsx, starty - 25 + 50 + 50 + 50 + 30 + 30, 100, 20);
add(betalabel);
betaval = new TextField("" + (float) beta);
betaval.setBounds(buttonsx + 110, starty - 25 + 50 + 50 + 50 + 30 + 30, 40, 20);
betaval.addActionListener(this);
add(betaval);
beta = Double.parseDouble(betaval.getText());
updatebeta();
undobutton = new Button("Undo Global Fit");
undobutton.setBounds(buttonsx, starty - 25 + 50 + 50 + 50 + 30 + 30 + 50, 100, 40);
undobutton.addActionListener(this);
add(undobutton);
geterrorsbutton = new Button("Get Errors");
geterrorsbutton.setBounds(buttonsx, starty - 25 + 50 + 50 + 50 + 30 + 30 + 50 + 50, 100, 40);
geterrorsbutton.addActionListener(this);
add(geterrorsbutton);
copylabel = new Label("copyright 2009 Jay Unruh ([email protected]) non-profit use only");
copylabel.setBounds(10, 790, 400, 20);
add(copylabel);
n_b_label = new Label("N and B Analysis");
n_b_label.setBounds(250, 10, 100, 20);
add(n_b_label);
pwavg = new PlotWindow3D("Avg", "kg", "kr", "Frequency", avg, 0);
pwavg.setLogAxes(false, false, true);
pwavg.draw();
pwavg.addPoints(avgfit, true, 0);
float[] temp = pwavg.getLimits();
temp[4] = 1.0f;
pwavg.setLimits(temp);
float[][] temppch = new float[xpts][ypts];
for (int i = 0; i < xpts; i++) {
System.arraycopy(pch[dispcurve][i], 0, temppch[i], 0, ypts);
}
pwfit = new PlotWindow3D("Selected Curve", "kg", "kr", "Frequency", temppch, 0);
pwfit.setLogAxes(false, false, true);
pwfit.draw();
pwfit.addPoints(fit[dispcurve], true, 0);
float[] temp2 = pwfit.getLimits();
temp2[4] = 1.0f;
pwfit.setLimits(temp2);
resetparams();
repaint();
}
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);
}
});
}