/**
* Creates a new connection to the specified host of specified type. <br>
* <br>
* type: Type of connection to create <br>
* destination: Host to connect to (in "host:port" or "host" syntax)
*/
public Connection(java.net.InetAddress host, int port, PluginContext ctx)
throws MessagingNetworkException, java.io.IOException {
if (TRAKTOR_USED) {
if (traktorConnectionDown) throw new IOException("network is down");
traktor = new Frame("" + host + ":" + port + " - Traktor");
final Checkbox c = new Checkbox("break this & ALL future connections");
c.setState(traktorConnectionDown);
c.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent e) {
traktorConnectionDown = c.getState();
try {
if (traktorConnectionDown) closeSocket();
} catch (Exception ex) {
}
}
});
traktor.add(c);
traktor.setSize(100, 50);
traktor.setLocation(230, 450);
traktor.setVisible(true);
} else {
traktor = null;
}
}
/*.................................................................................................................*/
public void actionPerformed(ActionEvent e) {
if (e.getActionCommand().equalsIgnoreCase("setToDefaults")) {
setDefaultTNTCommandsSearchOptions();
searchField.setText(searchArguments);
bootstrapSearchField.setText(bootstrapSearchArguments);
harvestOnlyStrictConsensusBox.setState(harvestOnlyStrictConsensus);
resamplingAllConsensusTreesBox.setState(!resamplingAllConsensusTrees);
bootStrapRepsField.setValue(bootstrapreps);
} else if (e.getActionCommand().equalsIgnoreCase("setToDefaultsOtherOptions")) {
setDefaultTNTCommandsOtherOptions();
otherOptionsField.setText(otherOptions);
convertGapsBox.setState(convertGapsToMissing);
} else if (e.getActionCommand().equalsIgnoreCase("browseSearchScript")
&& searchScriptPathField != null) {
MesquiteString directoryName = new MesquiteString();
MesquiteString fileName = new MesquiteString();
String path =
MesquiteFile.openFileDialog("Choose Search Script File", directoryName, fileName);
if (StringUtil.notEmpty(path)) searchScriptPathField.setText(path);
} else if (e.getActionCommand().equalsIgnoreCase("browseBootSearchScript")
&& bootSearchScriptPathField != null) {
MesquiteString directoryName = new MesquiteString();
MesquiteString fileName = new MesquiteString();
String path =
MesquiteFile.openFileDialog(
"Choose Resampling Search Script File", directoryName, fileName);
if (StringUtil.notEmpty(path)) bootSearchScriptPathField.setText(path);
}
}
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);
}
}
}
/**
* 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 babylonServerWindow(babylonServer parent, String Name) {
super(Name);
server = parent;
myLayout = new GridBagLayout();
setLayout(myLayout);
p = new Panel();
p.setLayout(myLayout);
listening = new Label(server.strings.get(thisClass, "listenport") + " " + server.port);
p.add(
listening,
new babylonConstraints(
0,
0,
1,
1,
0.0,
0.0,
GridBagConstraints.NORTHWEST,
GridBagConstraints.NONE,
new Insets(0, 0, 0, 0),
0,
0));
logChat = new Checkbox(server.strings.get(thisClass, "logchats"), server.logChats);
logChat.addItemListener(this);
p.add(
logChat,
new babylonConstraints(
1,
0,
1,
1,
1.0,
1.0,
GridBagConstraints.NORTHWEST,
GridBagConstraints.NONE,
new Insets(0, 0, 0, 0),
0,
0));
userList = new List(4, false);
userList.addItemListener(this);
p.add(
userList,
new babylonConstraints(
0,
1,
1,
5,
1.0,
1.0,
GridBagConstraints.NORTHWEST,
GridBagConstraints.BOTH,
new Insets(0, 0, 5, 0),
0,
0));
userAdmin = new Button(server.strings.get(thisClass, "usermanagement"));
userAdmin.addActionListener(this);
p.add(
userAdmin,
new babylonConstraints(
1,
1,
1,
1,
1.0,
1.0,
GridBagConstraints.NORTHWEST,
GridBagConstraints.HORIZONTAL,
new Insets(0, 0, 0, 0),
0,
0));
console = new Button(server.strings.get(thisClass, "adminclient"));
console.addActionListener(this);
p.add(
console,
new babylonConstraints(
1,
2,
1,
1,
1.0,
1.0,
GridBagConstraints.NORTHWEST,
GridBagConstraints.HORIZONTAL,
new Insets(0, 0, 0, 0),
0,
0));
disconnect = new Button(server.strings.get(thisClass, "disconnectuser"));
disconnect.setEnabled(false);
disconnect.addActionListener(this);
p.add(
disconnect,
new babylonConstraints(
1,
3,
1,
1,
1.0,
1.0,
GridBagConstraints.NORTHWEST,
GridBagConstraints.HORIZONTAL,
new Insets(0, 0, 0, 0),
0,
0));
disconnectAll = new Button(server.strings.get(thisClass, "disconnectall"));
disconnectAll.setEnabled(false);
disconnectAll.addActionListener(this);
p.add(
disconnectAll,
new babylonConstraints(
1,
4,
1,
1,
1.0,
1.0,
GridBagConstraints.NORTHWEST,
GridBagConstraints.HORIZONTAL,
new Insets(0, 0, 0, 0),
0,
0));
shutdown = new Button(server.strings.get(thisClass, "shutdown"));
shutdown.addActionListener(this);
p.add(
shutdown,
new babylonConstraints(
1,
5,
1,
1,
1.0,
1.0,
GridBagConstraints.NORTHWEST,
GridBagConstraints.HORIZONTAL,
new Insets(0, 0, 0, 0),
0,
0));
stats =
new TextField(
server.strings.get(thisClass, "connectionscurrent")
+ " 0 "
+ server.strings.get(thisClass, "connectionspeak")
+ " 0 "
+ server.strings.get(thisClass, "connectionstotal")
+ " 0",
40);
stats.setEditable(false);
p.add(
stats,
new babylonConstraints(
0,
7,
2,
1,
1.0,
1.0,
GridBagConstraints.NORTHWEST,
GridBagConstraints.BOTH,
new Insets(0, 0, 0, 0),
0,
0));
logWindow =
new TextArea(
server.strings.get(thisClass, "activitylog") + "\n",
10,
40,
TextArea.SCROLLBARS_VERTICAL_ONLY);
logWindow.setEditable(false);
p.add(
logWindow,
new babylonConstraints(
0,
8,
2,
1,
1.0,
1.0,
GridBagConstraints.NORTHWEST,
GridBagConstraints.BOTH,
new Insets(0, 0, 5, 0),
0,
0));
canvas = new babylonPictureCanvas(this);
p.add(
canvas,
new babylonConstraints(
0,
9,
2,
1,
1.0,
1.0,
GridBagConstraints.NORTHWEST,
GridBagConstraints.BOTH,
new Insets(0, 0, 0, 0),
0,
0));
add(
p,
new babylonConstraints(
0,
0,
1,
1,
1.0,
1.0,
GridBagConstraints.NORTHWEST,
GridBagConstraints.BOTH,
new Insets(5, 5, 5, 5),
0,
0));
try {
URL url = new URL("file", "localhost", "babylonPic.jpg");
Image image = getToolkit().getImage(url);
canvas.setimage(image);
} catch (Exception e) {
System.out.println(e);
}
try {
URL iconUrl = new URL("file", "localhost", "babylonIcon.jpg");
ImageIcon icon = new ImageIcon(iconUrl);
this.setIconImage(icon.getImage());
} catch (Exception e) {
/* Not important */
}
addWindowListener(this);
setSize(600, 600);
pack();
}
public void focusLost(FocusEvent e) {
int id = 0;
boolean res = false;
JTextField t = (JTextField) e.getSource();
if (t == tpid) {
try {
id = Integer.parseInt(tpid.getText());
res = patient.psearch(id);
} catch (Exception e1) {
}
if (res) {
int no, ag = 0, fee = 0;
String pfn = "",
bg = "",
pmn = "",
dt1 = "",
pln = "",
add = "",
sym = "",
dn = "",
dig = "",
cn = "",
gender = "",
wgt = "";
try {
dt1 = patient.rs.getString(1);
no = patient.rs.getInt(2);
pfn = patient.rs.getString(3);
pmn = patient.rs.getString(4);
pln = patient.rs.getString(5);
gender = patient.rs.getString(6);
ag = patient.rs.getInt(7);
wgt = patient.rs.getString(8);
add = patient.rs.getString(9);
cn = patient.rs.getString(10);
dn = patient.rs.getString(11);
sym = patient.rs.getString(12);
dig = patient.rs.getString(13);
fee = patient.rs.getInt(14);
bg = patient.rs.getString(15);
dir = patient.rs.getString(17);
s = dir;
repaint();
j13 = new JLabel("OLD IMAGE");
j13.setBounds(840, 5, 300, 300);
JLabel j12 =
new JLabel("OLD PHOTO") {
public void paint(Graphics g) {
ImageIcon ic = new ImageIcon(s);
Image img = ic.getImage();
g.drawImage(img, 0, 0, 150, 150, this);
}
};
// q.flushAll()
/*ImageIcon ic=new ImageIcon(dir);
JLabel j12=new JLabel("",ic,JLabel.CENTER);*/
j12.setBounds(670, 70, 300, 300);
// image.setBounds(700,300,100,100);
q.add(j12);
q.add(j13);
repaint();
System.out.println("8743t32874" + dir);
} catch (Exception e2) {
}
if (gender.equals("Male")) cm.setState(true);
else cf.setState(true);
tdt.setText(dt1);
tpfnm.setText(pfn);
tpmnm.setText(pmn);
tplnm.setText(pln);
tage.setText("" + ag);
tfee.setText("" + fee);
tadd.setText(add);
tdig.setText(dig);
tdnm.setText(dn);
tsym.setText(sym);
tcno.setText(cn);
twt.setText(wgt);
tbg.setText(bg);
// cm.setState(set1State());
// cf.setSelectedCheckbox(gender);
ba.setEnabled(false);
bm.setEnabled(true);
bd.setEnabled(true);
} else {
if (id == 0) {
bl.setEnabled(true);
ba.setEnabled(false);
} else ba.setEnabled(true);
bm.setEnabled(false);
bd.setEnabled(false);
}
}
}
public patientAdd(String s) {
super(s);
image =
new JLabel() {
public void paint(Graphics g) {
ImageIcon ic = new ImageIcon(str);
Image img = ic.getImage();
g.drawImage(img, 0, 0, 150, 150, this);
}
};
image.setBounds(670, 270, 300, 300);
bu = new JButton("UPLOAD");
bu.setBounds(700, 230, 100, 20);
bu.addActionListener(this);
// q.add(bu);
ldt = new JLabel("Date");
lpid = new JLabel("Patient ID");
lpnm = new JLabel("Patient Name");
lgen = new JLabel("Gender");
lbg = new JLabel("Blood Group");
lage = new JLabel("Age");
lwt = new JLabel("Weight Kg");
ladd = new JLabel("Address");
lcno = new JLabel("Cont. no.");
ldnm = new JLabel("Doctor Name Dr.");
lsym = new JLabel("Symptoms");
ldig = new JLabel("Diagnosis");
lfee = new JLabel("Fee Rs.");
cbg = new CheckboxGroup();
cm = new Checkbox("Male", cbg, false);
cm.addItemListener(this);
cf = new Checkbox("Female", cbg, false);
cf.setState(true);
cf.addItemListener(this);
tdt = new JTextField(15);
tpid = new JTextField(6);
tpid.addFocusListener(this);
tpfnm = new JTextField("first");
tpmnm = new JTextField("middle");
tplnm = new JTextField("last");
tage = new JTextField(4);
tage.addFocusListener(this);
tbg = new JTextField(6);
twt = new JTextField(5);
tadd = new TextArea(patient.addr);
tcno = new JTextField(20);
tdnm = new JTextField(20);
tsym = new TextArea();
tdig = new JTextField(20);
tfee = new JTextField(6);
tfee.addFocusListener(this);
ba = new JButton("ADD");
ba.addActionListener(this);
bm = new JButton("CANCEL");
bm.addActionListener(this);
bd = new JButton("DELETE");
bd.addActionListener(this);
bl = new JButton("DISPLAY");
bl.addActionListener(this);
bs = new JButton("SEARCH");
bs.addActionListener(this);
JPanel p = new JPanel();
p.add(ba);
p.add(bm);
// p.add(bd);
// p.add(bl);
// p.add(bs);
add(p, BorderLayout.SOUTH);
q = new JPanel();
q.setLayout(null);
ldt.setBounds(1015, 20, 60, 20);
q.add(ldt);
tdt.setBounds(1060, 20, 170, 20);
q.add(tdt);
lpid.setBounds(70, 60, 80, 20);
q.add(lpid);
tpid.setBounds(200, 60, 60, 20);
q.add(tpid);
lpnm.setBounds(70, 100, 80, 20);
q.add(lpnm);
tpfnm.setBounds(200, 100, 100, 20);
q.add(tpfnm);
tpmnm.setBounds(320, 100, 100, 20);
q.add(tpmnm);
tplnm.setBounds(440, 100, 100, 20);
q.add(tplnm);
lgen.setBounds(70, 140, 60, 20);
q.add(lgen);
lbg.setBounds(370, 140, 80, 20);
q.add(lbg);
tbg.setBounds(470, 140, 60, 20);
q.add(tbg);
cm.setBounds(200, 140, 60, 20);
cf.setBounds(280, 140, 60, 20);
lage.setBounds(70, 180, 40, 20);
q.add(lage);
tage.setBounds(200, 180, 50, 20);
q.add(tage);
lwt.setBounds(370, 180, 200, 20);
q.add(lwt);
twt.setBounds(470, 180, 60, 20);
q.add(twt);
ladd.setBounds(70, 220, 60, 20);
q.add(ladd);
tadd.setBounds(200, 220, 350, 50);
q.add(tadd);
lcno.setBounds(70, 310, 60, 20);
q.add(lcno);
tcno.setBounds(200, 310, 120, 20);
q.add(tcno);
ldnm.setBounds(70, 350, 200, 20);
q.add(ldnm);
tdnm.setBounds(200, 350, 150, 20);
q.add(tdnm);
lsym.setBounds(70, 390, 100, 20);
q.add(lsym);
tsym.setBounds(200, 390, 300, 70);
q.add(tsym);
ldig.setBounds(70, 480, 60, 20);
q.add(ldig);
tdig.setBounds(200, 480, 100, 20);
q.add(tdig);
lfee.setBounds(70, 520, 200, 20);
q.add(lfee);
tfee.setBounds(200, 520, 40, 20);
q.add(tfee);
q.add(cm);
q.add(cf);
q.add(image);
q.add(bu);
add(q, BorderLayout.CENTER);
addWindowListener(
new WindowAdapter() {
public void windowClosing(WindowEvent e) {
try {
patient.con.close();
System.exit(0);
} catch (Exception e8) {
}
}
});
System.out.println(tadd.getText());
setSize(1330, 740);
setVisible(true);
}
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);
}
