/*.................................................................................................................*/
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 processCompletedOutputFiles(String[] outputFilePaths) {
if (outputFilePaths.length > 1 && !StringUtil.blank(outputFilePaths[1])) {
ZephyrUtil.copyLogFile(this, "TNT", outputFilePaths[1]);
}
if (outputFilePaths.length > 2 && !StringUtil.blank(outputFilePaths[2])) {
ZephyrUtil.copyOutputText(this, outputFilePaths[2], commands);
}
}
private static void appendHTML(JEditorPane editor, String html) {
try {
html = StringUtil.replaceAll(html, "\t", " ");
html = StringUtil.replaceAll(html, "\r\n", "\n");
html = StringUtil.replaceAll(html, "\r", "");
Vector vt = StringUtil.toStringVector(html, "\n");
HTMLEditorKit kit = (HTMLEditorKit) editor.getEditorKit();
HTMLDocument doc = (HTMLDocument) editor.getDocument();
for (int iIndex = 0; iIndex < vt.size(); iIndex++)
kit.insertHTML(doc, doc.getLength(), (String) vt.elementAt(iIndex), 0, 0, null);
} catch (Exception e) {
e.printStackTrace();
}
}
public boolean isVerified() {
boolean enable = !StringUtil.isEmpty(getProjectName());
try {
enable = (new Float(getProjectVersion()) > 0);
} catch (NumberFormatException e) {
enable = false;
} // end of try-catch
return enable;
}
/*.................................................................................................................*/
public String preparePreferencesForXML() {
StringBuffer buffer = new StringBuffer(200);
StringUtil.appendXMLTag(buffer, 2, "mxram", mxram);
StringUtil.appendXMLTag(buffer, 2, "bootStrapReps", bootstrapreps);
StringUtil.appendXMLTag(buffer, 2, "convertGapsToMissing", convertGapsToMissing);
StringUtil.appendXMLTag(buffer, 2, "resamplingAllConsensusTrees", resamplingAllConsensusTrees);
StringUtil.appendXMLTag(buffer, 2, "harvestOnlyStrictConsensus", harvestOnlyStrictConsensus);
StringUtil.appendXMLTag(buffer, 2, "searchArguments", searchArguments);
StringUtil.appendXMLTag(buffer, 2, "bootstrapSearchArguments", bootstrapSearchArguments);
StringUtil.appendXMLTag(buffer, 2, "searchStyle", searchStyle);
StringUtil.appendXMLTag(buffer, 2, "otherOptions", otherOptions);
preferencesSet = true;
return buffer.toString();
}
/*.................................................................................................................*/
public void processSingleXMLPreference(String tag, String content) {
if ("bootStrapReps".equalsIgnoreCase(tag)) bootstrapreps = MesquiteInteger.fromString(content);
if ("mxram".equalsIgnoreCase(tag)) mxram = MesquiteInteger.fromString(content);
if ("convertGapsToMissing".equalsIgnoreCase(tag))
convertGapsToMissing = MesquiteBoolean.fromTrueFalseString(content);
if ("resamplingAllConsensusTrees".equalsIgnoreCase(tag))
resamplingAllConsensusTrees = MesquiteBoolean.fromTrueFalseString(content);
if ("harvestOnlyStrictConsensus".equalsIgnoreCase(tag))
harvestOnlyStrictConsensus = MesquiteBoolean.fromTrueFalseString(content);
if ("searchStyle".equalsIgnoreCase(tag)) searchStyle = MesquiteInteger.fromString(content);
if ("searchArguments".equalsIgnoreCase(tag))
searchArguments = StringUtil.cleanXMLEscapeCharacters(content);
if ("bootstrapSearchArguments".equalsIgnoreCase(tag))
bootstrapSearchArguments = StringUtil.cleanXMLEscapeCharacters(content);
if ("otherOptions".equalsIgnoreCase(tag))
otherOptions = StringUtil.cleanXMLEscapeCharacters(content);
// parallel, etc.
preferencesSet = true;
}
/**
* A request for the MesquiteModule to perform a command. It is passed two strings, the name of
* the command and the arguments. This should be overridden by any module that wants to respond to
* a command.
*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(MesquiteModule.class, null, null, commandName, "paint")) {
MesquiteInteger io = new MesquiteInteger(0);
int column = MesquiteInteger.fromString(arguments, io);
int row = MesquiteInteger.fromString(arguments, io);
if (MesquiteInteger.isCombinable(row)) {
if (!MesquiteLong.isCombinable(currentColor)) removeColor(row, true);
else setColor(row, (int) currentColor);
}
} else if (checker.compare(
this.getClass(),
"Sets the color to be used to paint cells",
"[name of color]",
commandName,
"setColor")) {
int bc = ColorDistribution.standardColorNames.indexOf(parser.getFirstToken(arguments));
if (bc >= 0 && MesquiteLong.isCombinable(bc)) {
removeColor.setValue(false);
currentColor = bc;
savedColor = bc;
colorString = "Color " + ColorDistribution.standardColorNames.getValue(bc);
}
} else if (checker.compare(
this.getClass(),
"Sets the color of selected taxa",
"[name of color]",
commandName,
"setColorSelected")) {
int bc = ColorDistribution.standardColorNames.indexOf(parser.getFirstToken(arguments));
if (bc >= 0 && MesquiteLong.isCombinable(bc)) {
for (int it = 0; it < taxa.getNumTaxa(); it++) if (taxa.getSelected(it)) setColor(it, bc);
}
} else if (checker.compare(
this.getClass(), "Removes color from all the cells", null, commandName, "removeAllColor")) {
removeAllColor(true);
} else if (checker.compare(
this.getClass(),
"Sets the paint brush so that it removes colors from any cells touched",
null,
commandName,
"removeColor")) {
if (StringUtil.blank(arguments)) removeColor.setValue(!removeColor.getValue());
else removeColor.toggleValue(parser.getFirstToken(arguments));
if (removeColor.getValue()) {
colorString = "Remove color";
currentColor = MesquiteLong.unassigned;
} else {
colorString = "Color " + ColorDistribution.standardColorNames.getValue((int) currentColor);
currentColor = savedColor;
}
} else return super.doCommand(commandName, arguments, checker);
return null;
}
public void setNoteName(String noteName) {
int idx = 0;
int i = 0;
for (int c = _lstFile.getElementCount() - 1; i < c; i++) {
ListElement le = (ListElement) _lstFile.getElement(i);
if (StringUtil.equalsIgnoreCase(le.getName(), noteName)) idx = i;
}
_lstFile.setSelectedIndex(idx);
super.btnOk.setEnabled(idx != -1);
}
void fetchUserDetails() {
try {
UserDetails d = plugin.getUserDetails(getMyLoginId(), contactListEntry.getText());
String s =
getMyLoginId()
+ " reports: user details for "
+ contactListEntry.getText()
+ " are:\r\n nick="
+ StringUtil.toPrintableString(d.getNick())
+ ",\r\n real name="
+ StringUtil.toPrintableString(d.getRealName())
+ ",\r\n email="
+ StringUtil.toPrintableString(d.getEmail())
+ ".";
CAT.info(s);
log(s);
} catch (Exception ex) {
printException(ex);
}
}
public final String readCommand(byte[] b)
throws IOException, InterruptedException, MessagingNetworkException {
InputStream is = getInputStream();
synchronized (is) {
long abortTime =
System.currentTimeMillis() + 1000 * MSNMessagingNetwork.REQPARAM_SOCKET_TIMEOUT_SECONDS;
int ofs = 0;
boolean d = false;
for (; ; ) {
if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
int by = is.read();
if (by == -1) throw new IOException("unexpected EOF");
if (by == 10 && d) break;
d = (by == 13);
if (ofs < b.length) {
b[ofs++] = (byte) by;
}
if (System.currentTimeMillis() > abortTime) throw new IOException("connection timed out");
/*
if (len >= buffer.length)
{
...
return ...;
}
int pos = findCRLF();
if (pos != -1) break;
fill(is, abortTime);
*/
}
if (b[ofs - 1] == 13) --ofs;
String line = new String(b, 0, ofs, "ASCII");
if (StringUtil.startsWith(line, "MSG")) {
StringTokenizer st = new StringTokenizer(line);
String len_s = null;
while (st.hasMoreTokens()) {
len_s = st.nextToken();
}
if (len_s == null) throw new AssertException("len_s is null");
int len;
try {
len = Integer.parseInt(len_s);
} catch (NumberFormatException ex) {
ServerConnection.throwProtocolViolated("MSG length must be int");
len = 0;
}
String msg = readMSG(len);
line = line + "\r\n" + msg;
}
if (Defines.DEBUG && CAT.isDebugEnabled()) CAT.debug("S: " + line);
return line;
}
}
/*.................................................................................................................*/
public void appendAdditionalSearchDetails() {
appendToSearchDetails("CIPRes Analysis, " + StringUtil.getDateTime() + "\n");
appendToSearchDetails("Search details: \n");
if (bootstrapOrJackknife()) {
appendToSearchDetails(" Bootstrap analysis\n");
appendToSearchDetails(" " + bootstrapreps + " bootstrap replicates");
} else {
appendToSearchDetails(" Search for maximum-likelihood tree\n");
appendToSearchDetails(" " + numRuns + " search replicate");
if (numRuns > 1) appendToSearchDetails("s");
}
}
/*.................................................................................................................*/
public void fromString(String description, MesquiteInteger stringPos, int format) {
hasDefaultValues = false;
ParseUtil.getToken(description, stringPos); // RMatrix
ParseUtil.getToken(description, stringPos); // =
ParseUtil.getToken(description, stringPos); // (
for (int i = 0; i < getNumStates(); i++) {
String s = ParseUtil.getToken(description, stringPos);
if (s.equalsIgnoreCase(")") || StringUtil.blank(s)) return;
setStateFreq(i, MesquiteDouble.fromString(s));
}
checkNormality(getStateFrequencies());
}
public String toString() {
if (StringUtil.isEmptyString(alias)) return name;
if (isShowFileName()) {
StringBuffer sb = new StringBuffer();
sb.append(alias);
sb.append("(");
sb.append(name);
sb.append(")");
return sb.toString();
} else {
return alias;
}
}
void insertMatchButton_actionPerformed(ActionEvent e) {
String key = (String) matchComboBox.getSelectedItem();
String format = (String) matchesKeys.get(key);
if (key.equals(STRING_LITERAL)) {
format =
escapeReservedChars(
(String)
JOptionPane.showInputDialog(
this,
"Enter the string you wish to match",
"String Literal Input",
JOptionPane.OK_CANCEL_OPTION));
if (StringUtil.isNullString(format)) {
return;
}
}
if (selectedPane == 0) {
insertText(format, PLAIN_ATTR, editorPane.getSelectionStart());
} else {
// add the combobox data value to the edit box
int pos = formatTextArea.getCaretPosition();
formatTextArea.insert(format, pos);
}
}
private void jbInit() throws Exception {
////////////////////////////////////////////////////////
// Init LAF
////////////////////////////////////////////////////////
ButtonGroup grpLAF = new ButtonGroup();
ActionListener lsnLAF =
new ActionListener() {
public void actionPerformed(ActionEvent evt) {
int iIndex = mvtLAFItem.indexOf(evt.getSource());
if (iIndex >= 0) changeLAF(iIndex);
}
};
////////////////////////////////////////////////////////
UIManager.LookAndFeelInfo laf =
new UIManager.LookAndFeelInfo(
"Kunststoff", "com.incors.plaf.kunststoff.KunststoffLookAndFeel");
marrLaf = UIManager.getInstalledLookAndFeels();
int iIndex = 0;
while (iIndex < marrLaf.length && !marrLaf[iIndex].getName().equals(laf.getName())) iIndex++;
if (iIndex >= marrLaf.length) {
UIManager.installLookAndFeel(laf);
marrLaf = UIManager.getInstalledLookAndFeels();
}
for (iIndex = 0; iIndex < marrLaf.length; iIndex++) {
JMenuItem mnu = new JRadioButtonMenuItem(marrLaf[iIndex].getName());
mnu.addActionListener(lsnLAF);
mvtLAFItem.addElement(mnu);
mnuUI.add(mnu);
grpLAF.add(mnu);
}
mnuUI.addSeparator();
////////////////////////////////////////////////////////
// Init language
////////////////////////////////////////////////////////
ButtonGroup grpLanguage = new ButtonGroup();
ActionListener lsnLanguage =
new ActionListener() {
public void actionPerformed(ActionEvent e) {
int iIndex = mvtLanguageItem.indexOf(e.getSource());
if (iIndex >= 0) changeDictionary((String) mvtLanguage.elementAt(iIndex));
}
};
////////////////////////////////////////////////////////
String[] str = MonitorDictionary.getSupportedLanguage();
for (iIndex = 0; iIndex < str.length; iIndex++) {
JMenuItem mnu =
new JRadioButtonMenuItem(MonitorDictionary.getDictionary(str[iIndex]).getLanguage());
mnu.addActionListener(lsnLanguage);
mvtLanguage.addElement(str[iIndex]);
mvtLanguageItem.addElement(mnu);
mnuUI.add(mnu);
grpLanguage.add(mnu);
}
////////////////////////////////////////////////////////
// Add to main menu
////////////////////////////////////////////////////////
mnuMain.removeAll();
mnuMain.add(mnuSystem);
mnuSystem.add(mnuSystem_Login);
mnuSystem.add(mnuSystem_ChangePassword);
mnuSystem.addSeparator();
mnuSystem.add(mnuSystem_StopServer);
mnuSystem.add(mnuSystem_EnableThreads);
mnuMain.add(mnuUI);
mnuMain.add(mnuHelp);
mnuHelp.add(mnuHelp_About);
////////////////////////////////////////////////////////
mnuMain.add(chkVietnamese);
mnuMain.add(lblStatus);
////////////////////////////////////////////////////////
pnlThread.setTabPlacement(JTabbedPane.LEFT);
pnlThread.setTabLayoutPolicy(JTabbedPane.SCROLL_TAB_LAYOUT);
////////////////////////////////////////////////////////
tblUser.addColumn("", 1, false);
tblUser.addColumn("", 2, false, Global.FORMAT_DATE_TIME);
tblUser.addColumn("", 3, false);
////////////////////////////////////////////////////////
JPanel pnlMessage = new JPanel();
pnlMessage.setLayout(new GridBagLayout());
pnlMessage.add(
new JScrollPane(txtBoard),
new GridBagConstraints(
0,
0,
2,
1,
1.0,
1.0,
GridBagConstraints.CENTER,
GridBagConstraints.BOTH,
new Insets(2, 2, 2, 2),
0,
0));
pnlMessage.add(
txtMessage,
new GridBagConstraints(
0,
1,
1,
1,
1.0,
0.0,
GridBagConstraints.CENTER,
GridBagConstraints.BOTH,
new Insets(2, 2, 2, 2),
0,
0));
pnlMessage.add(
btnSend,
new GridBagConstraints(
1,
1,
1,
1,
0.0,
0.0,
GridBagConstraints.CENTER,
GridBagConstraints.NONE,
new Insets(2, 2, 2, 2),
0,
0));
txtBoard.setEditable(false);
txtBoard.setAutoscrolls(true);
txtBoard.setContentType("text/html");
clearAll(txtBoard);
////////////////////////////////////////////////////////
JPanel pnlUserButton = new JPanel(new GridLayout(1, 2, 4, 4));
pnlUserButton.add(btnKick);
pnlUserButton.add(btnRefresh);
////////////////////////////////////////////////////////
JPanel pnlManager = new JPanel(new GridBagLayout());
pnlManager.add(
new JScrollPane(tblUser),
new GridBagConstraints(
0,
0,
1,
1,
1.0,
1.0,
GridBagConstraints.CENTER,
GridBagConstraints.BOTH,
new Insets(2, 2, 2, 2),
0,
0));
pnlManager.add(
pnlUserButton,
new GridBagConstraints(
0,
1,
1,
1,
0.0,
0.0,
GridBagConstraints.CENTER,
GridBagConstraints.NONE,
new Insets(4, 2, 4, 2),
0,
0));
////////////////////////////////////////////////////////
pnlUser.setDividerLocation(320);
pnlUser.setLeftComponent(pnlManager);
pnlUser.setRightComponent(pnlMessage);
pnlUser.setOneTouchExpandable(true);
////////////////////////////////////////////////////////
setOrientation(JSplitPane.VERTICAL_SPLIT);
setOneTouchExpandable(true);
pnlThread.setVisible(false);
pnlUser.setVisible(false);
setTopComponent(pnlThread);
setBottomComponent(pnlUser);
////////////////////////////////////////////////////////
pmn.add(mnuSelectAll);
pmn.addSeparator();
pmn.add(mnuClearSelected);
pmn.add(mnuClearAll);
////////////////////////////////////////////////////////
setBorder(BorderFactory.createEmptyBorder());
pnlUser.setBorder(BorderFactory.createEmptyBorder());
pnlManager.setBorder(
BorderFactory.createBevelBorder(
javax.swing.border.BevelBorder.RAISED,
Color.white,
UIManager.getColor("Panel.background"),
UIManager.getColor("Panel.background"),
UIManager.getColor("Panel.background")));
pnlMessage.setBorder(
BorderFactory.createBevelBorder(
javax.swing.border.BevelBorder.RAISED,
Color.white,
UIManager.getColor("Panel.background"),
UIManager.getColor("Panel.background"),
UIManager.getColor("Panel.background")));
////////////////////////////////////////////////////////
Skin.applySkin(mnuMain);
Skin.applySkin(tblUser);
Skin.applySkin(pmn);
Skin.applySkin(this);
////////////////////////////////////////////////////////
// Default setting
////////////////////////////////////////////////////////
Hashtable prt = null;
try {
prt = Global.loadHashtable(Global.FILE_CONFIG);
} catch (Exception e) {
prt = new Hashtable();
}
changeLAF(Integer.parseInt(StringUtil.nvl(prt.get("LAF"), "0")));
changeDictionary(StringUtil.nvl(prt.get("Language"), "VN"));
Skin.LANGUAGE_CHANGE_LISTENER = this;
MonitorProcessor.setRootObject(this);
updateKeyboardUI();
////////////////////////////////////////////////////////
// Event handler
////////////////////////////////////////////////////////
tblUser.addMouseListener(
new MouseAdapter() {
public void mouseClicked(MouseEvent e) {
if (e.getClickCount() > 1) btnKick.doClick();
}
});
////////////////////////////////////////////////////////
btnRefresh.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent evt) {
try {
DDTP request = new DDTP();
request.setRequestID(String.valueOf(System.currentTimeMillis()));
DDTP response = channel.sendRequest("ThreadProcessor", "queryUserList", request);
if (response != null) {
tblUser.setData((Vector) response.getReturn());
if (mstrChannel != null) removeUser(mstrChannel);
}
} catch (Exception e) {
e.printStackTrace();
MessageBox.showMessageDialog(pnlThread, e, Global.APP_NAME, MessageBox.ERROR_MESSAGE);
}
}
});
////////////////////////////////////////////////////////
btnKick.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent evt) {
int iSelected = tblUser.getSelectedRow();
if (iSelected < 0) return;
int iResult =
MessageBox.showConfirmDialog(
pnlThread,
mdic.getString("ConfirmKick"),
Global.APP_NAME,
MessageBox.YES_NO_OPTION);
if (iResult == MessageBox.NO_OPTION) return;
try {
String strChannel = (String) tblUser.getRow(iSelected).elementAt(0);
DDTP request = new DDTP();
request.setRequestID(String.valueOf(System.currentTimeMillis()));
request.setString("strChannel", strChannel);
DDTP response = channel.sendRequest("ThreadProcessor", "kickUser", request);
} catch (Exception e) {
e.printStackTrace();
MessageBox.showMessageDialog(pnlThread, e, Global.APP_NAME, MessageBox.ERROR_MESSAGE);
}
}
});
////////////////////////////////////////////////////////
txtMessage.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent evt) {
btnSend.doClick();
}
});
////////////////////////////////////////////////////////
btnSend.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent evt) {
if (txtMessage.getText().length() == 0) return;
try {
DDTP request = new DDTP();
request.setString("strMessage", txtMessage.getText());
channel.sendRequest("ThreadProcessor", "sendMessage", request);
txtMessage.setText("");
} catch (Exception e) {
e.printStackTrace();
MessageBox.showMessageDialog(pnlThread, e, Global.APP_NAME, MessageBox.ERROR_MESSAGE);
}
}
});
////////////////////////////////////////////////////////
mnuClearAll.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
clearAll(txtBoard);
}
});
////////////////////////////////////////////////////////
mnuClearSelected.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
txtBoard.setEditable(true);
txtBoard.replaceSelection("");
txtBoard.setEditable(false);
}
});
////////////////////////////////////////////////////////
mnuSelectAll.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
txtBoard.requestFocus();
txtBoard.selectAll();
}
});
////////////////////////////////////////////////////////
txtBoard.addMouseListener(
new MouseAdapter() {
public void mouseClicked(MouseEvent e) {
if (e.getButton() == e.BUTTON3) pmn.show(txtBoard, e.getX(), e.getY());
}
});
////////////////////////////////////////////////////////
mnuSystem_Login.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
login();
}
});
////////////////////////////////////////////////////////
mnuSystem_ChangePassword.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
changePassword();
}
});
////////////////////////////////////////////////////////
mnuSystem_StopServer.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
stopServer();
}
});
////////////////////////////////////////////////////////
mnuSystem_EnableThreads.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
manageThreads();
}
});
////////////////////////////////////////////////////////
mnuHelp_About.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
WindowManager.centeredWindow(new DialogAbout(PanelThreadManager.this));
}
});
////////////////////////////////////////////////////////
chkVietnamese.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
switchKeyboard();
}
});
}
public String getAppVersion() {
return StringUtil.nvl(mstrAppVersion, "Unknown version");
}
public String getAppName() {
return StringUtil.nvl(mstrAppName, "Unknown application");
}
/*.................................................................................................................*/
void getArguments(
MultipartEntityBuilder builder,
StringBuffer sb,
String fileName,
String LOCproteinModel,
String LOCdnaModel,
String LOCotherOptions,
int LOCbootstrapreps,
int LOCbootstrapSeed,
int LOCnumRuns,
String LOCoutgroupTaxSetString,
String LOCMultipleModelFile,
boolean preflight) {
if (builder == null) return;
/*
if (preflight)
arguments += " -n preflight.out ";
else
arguments += " -s " + fileName + " -n file.out ";
*/
if (isProtein) {
if (StringUtil.blank(LOCproteinModel))
addArgument(builder, sb, "vparam.protein_opts_", "PROTGAMMAJTT");
else addArgument(builder, sb, "vparam.protein_opts_", LOCproteinModel);
} else if (StringUtil.blank(LOCdnaModel))
addArgument(builder, sb, "vparam.dna_gtrcat_", "GTRGAMMA");
else addArgument(builder, sb, "vparam.dna_gtrcat_", "GTRGAMMA");
// builder.addTextBody("vparam.dna_gtrcat_",LOCdnaModel);
/*
if (StringUtil.notEmpty(LOCMultipleModelFile))
arguments += " -q " + ShellScriptUtil.protectForShellScript(LOCMultipleModelFile);
if (!StringUtil.blank(LOCotherOptions))
arguments += " " + LOCotherOptions;
*/
addArgument(builder, sb, "vparam.provide_parsimony_seed_", "1");
addArgument(builder, sb, "vparam.parsimony_seed_val_", "" + randomIntSeed);
if (bootstrapOrJackknife()) {
if (LOCbootstrapreps > 0) {
addArgument(builder, sb, "vparam.choose_bootstrap_", "b");
addArgument(builder, sb, "vparam.bootstrap_value_", "" + LOCbootstrapreps);
addArgument(builder, sb, "vparam.seed_value_", "" + LOCbootstrapSeed);
// addArgument(builder, sb, "vparam.bootstrap_",""+LOCbootstrapreps);
// addArgument(builder, sb, "vparam.mulparambootstrap_seed_",""+LOCbootstrapSeed);
} else Debugg.println("TOO FEW BOOTSTRAP REPS");
} else {
addArgument(builder, sb, "vparam.specify_runs_", "1");
addArgument(builder, sb, "vparam.altrun_number_", "" + LOCnumRuns);
// if (RAxML814orLater)
// addArgument(builder, sb, "vparam.mesquite_output_","1");
}
TaxaSelectionSet outgroupSet = null;
if (!StringUtil.blank(LOCoutgroupTaxSetString)) {
outgroupSet =
(TaxaSelectionSet) taxa.getSpecsSet(LOCoutgroupTaxSetString, TaxaSelectionSet.class);
if (outgroupSet != null)
addArgument(builder, sb, "vparam.outgroup_", outgroupSet.getStringList(",", true));
arguments += " -o " + outgroupSet.getStringList(",", true);
}
}
public void login() {
mbAutoLogIn = false;
while (!mbAutoLogIn) {
try {
// Confirm logout
if (isOpen()) {
if (MessageBox.showConfirmDialog(
this,
MonitorDictionary.getString("Confirm.Exit"),
Global.APP_NAME,
MessageBox.YES_NO_OPTION)
== MessageBox.NO_OPTION) return;
// Disconnect from server
disconnect();
}
// Login
DialogLogin dlgLogin = new DialogLogin(this);
WindowManager.centeredWindow(dlgLogin);
if (dlgLogin.miReturn == JOptionPane.OK_OPTION) {
// Update UI
SwingUtilities.updateComponentTreeUI(pnlUser);
SwingUtilities.updateComponentTreeUI(pnlThread);
// Request to connect
Socket sck = new Socket(dlgLogin.mstrHost, Integer.parseInt(dlgLogin.mstrPort));
sck.setSoLinger(true, 0);
// Start up a channel thread that reads messages from the server
channel =
new SocketTransmitter(sck) {
public void close() {
if (msckMain != null) {
super.close();
closeAll();
if (mbAutoLogIn) login();
}
}
};
channel.setUserName(dlgLogin.mstrUserName);
channel.setPackage("com.fss.thread.");
channel.start();
// Request to Server
DDTP request = new DDTP();
request.setRequestID(String.valueOf(System.currentTimeMillis()));
request.setString("UserName", dlgLogin.mstrUserName);
request.setString("Password", dlgLogin.mstrPassword);
// Response from Server
DDTP response = channel.sendRequest("ThreadProcessor", "login", request);
mstrThreadAppName = response.getString("strThreadAppName");
mstrThreadAppVersion = response.getString("strThreadAppVersion");
mstrAppName = response.getString("strAppName");
mstrAppVersion = response.getString("strAppVersion");
if (response != null) {
if (response.getString("PasswordExpired") != null) {
DialogChangePassword frm = new DialogChangePassword(this, channel);
WindowManager.centeredWindow(frm);
if (frm.miReturnValue != JOptionPane.OK_OPTION) throw new AppException("FSS-10003");
}
String strLog = StringUtil.nvl(response.getString("strLog"), "");
showResult(txtBoard, strLog);
Vector vtThread = response.getVector("vtThread");
updateTabBar(vtThread);
mstrChannel = response.getString("strChannel");
if (mstrChannel != null) removeUser(mstrChannel);
}
btnRefresh.doClick();
pnlThread.setVisible(true);
pnlUser.setVisible(true);
setResizeWeight(1);
setDividerLocation((int) (getSize().getHeight() - 160));
}
mbAutoLogIn = true;
updateLanguage();
} catch (Exception e) {
e.printStackTrace();
MessageBox.showMessageDialog(this, e, Global.APP_NAME, MessageBox.ERROR_MESSAGE);
// Disconnect from server
mstrChannel = null;
disconnect();
}
}
}
private boolean recalcPositions(Graphics g) {
Font f = g.getFont();
if (f != oldFont || !(StringUtil.stringsEqual(oldText, text))) {
FontMetrics fm = g.getFontMetrics(f);
sw = MesquiteInteger.maximum(fm.stringWidth("888"), fm.stringWidth(tf.getText()));
sh = fm.getMaxAscent() + fm.getMaxDescent();
}
oldText = text;
oldFont = f;
if (oldTextBoxWidth < sw + MesquiteModule.textEdgeCompensationWidth - 1
|| oldTextBoxHeight < sh + MesquiteModule.textEdgeCompensationHeight - 1) {
textBoxWidth = sw + MesquiteModule.textEdgeCompensationWidth; // 34
textBoxHeight = sh + MesquiteModule.textEdgeCompensationHeight; // 18
oldTextBoxWidth = textBoxWidth;
oldTextBoxHeight = textBoxHeight;
if (horizontal) {
if (stacked) {
totalWidth = textBoxWidth + EnterButton.MIN_DIMENSION + 2;
totalHeight = textBoxHeight + 20;
setSize(totalWidth, totalHeight);
tf.setSize(textBoxWidth, textBoxHeight);
tf.setLocation(0, 0);
decrementButton.setLocation(2, textBoxHeight + 4);
incrementButton.setLocation(totalWidth - 20, textBoxHeight + 4);
} else {
totalWidth = textBoxWidth + 36 + EnterButton.MIN_DIMENSION + 2;
totalHeight = textBoxHeight + 4;
setSize(totalWidth, totalHeight);
tf.setSize(textBoxWidth, textBoxHeight);
decrementButton.setLocation(0, 2);
tf.setLocation(
decrementButton.getBounds().x + decrementButton.getBounds().width + 1,
0); // 1 added to x
incrementButton.setLocation(
tf.getBounds().x + tf.getBounds().width + EnterButton.MIN_DIMENSION + 2,
2); // 1 added to x
}
enterButton.setLocation(tf.getBounds().x + tf.getBounds().width + 1, 2);
} else {
if (stacked) {
totalWidth = textBoxWidth + EnterButton.MIN_DIMENSION + 2;
totalHeight = textBoxHeight + 20;
setSize(totalWidth, totalHeight);
tf.setSize(textBoxWidth, textBoxHeight);
tf.setLocation(0, 0);
decrementButton.setLocation(2, textBoxHeight + 4);
incrementButton.setLocation(totalWidth - 22, textBoxHeight + 4);
enterButton.setLocation(tf.getBounds().x + tf.getBounds().width + 1, 2);
} else {
totalWidth = textBoxWidth; // should be 0
totalHeight = textBoxHeight + 36 + EnterButton.MIN_DIMENSION + 2;
setSize(totalWidth, totalHeight);
tf.setSize(textBoxWidth, textBoxHeight);
incrementButton.setLocation(1, 2);
tf.setLocation(0, incrementButton.getBounds().height + 3);
decrementButton.setLocation(
1, tf.getBounds().y + tf.getBounds().height + EnterButton.MIN_DIMENSION + 2);
enterButton.setLocation(1, tf.getBounds().y + tf.getBounds().height + 1);
}
}
incrementButton.repaint();
decrementButton.repaint();
enterButton.repaint();
repaint();
getParent().repaint();
return true;
}
if (checkBackground()) {
repaint();
return true;
}
/* if (!getBackground().equals(getParent().getBackground())) {
bg =getParent().getBackground();
setBackground(bg);
//setBackground(Color.green);
tf.setBackground(bg);
decrementButton.setBackground(bg);
incrementButton.setBackground(bg);
enterButton.setBackground(bg);
repaint();
return true;
}*/
return false;
}
void insertButton_actionPerformed(ActionEvent e) {
Object selected = paramComboBox.getSelectedItem();
ConfigParamDescr descr;
String key;
int type = 0;
String format = "";
if (selected instanceof ConfigParamDescr) {
descr = (ConfigParamDescr) selected;
key = descr.getKey();
type = descr.getType();
switch (type) {
case ConfigParamDescr.TYPE_STRING:
case ConfigParamDescr.TYPE_URL:
case ConfigParamDescr.TYPE_BOOLEAN:
format = "%s";
break;
case ConfigParamDescr.TYPE_INT:
case ConfigParamDescr.TYPE_LONG:
case ConfigParamDescr.TYPE_POS_INT:
NumericPaddingDialog dialog = new NumericPaddingDialog();
Point pos = this.getLocationOnScreen();
dialog.setLocation(pos.x, pos.y);
dialog.pack();
dialog.setVisible(true);
StringBuilder fbuf = new StringBuilder("%");
int width = dialog.getPaddingSize();
boolean is_zero = dialog.useZero();
if (width > 0) {
fbuf.append(".");
if (is_zero) {
fbuf.append(0);
}
fbuf.append(width);
}
if (type == ConfigParamDescr.TYPE_LONG) {
fbuf.append("ld");
} else {
fbuf.append("d");
}
format = fbuf.toString();
break;
case ConfigParamDescr.TYPE_YEAR:
if (key.startsWith(DefinableArchivalUnit.PREFIX_AU_SHORT_YEAR)) {
format = "%02d";
} else {
format = "%d";
}
break;
case ConfigParamDescr.TYPE_RANGE:
case ConfigParamDescr.TYPE_NUM_RANGE:
case ConfigParamDescr.TYPE_SET:
format = "%s";
break;
}
if (selectedPane == 0) {
insertParameter(descr, format, editorPane.getSelectionStart());
} else if (selectedPane == 1) {
// add the combobox data value to the edit box
int pos = formatTextArea.getCaretPosition();
formatTextArea.insert(format, pos);
pos = parameterTextArea.getCaretPosition();
parameterTextArea.insert(", " + key, pos);
}
} else {
key = selected.toString();
format =
escapePrintfChars(
(String)
JOptionPane.showInputDialog(
this,
"Enter the string you wish to input",
"String Literal Input",
JOptionPane.OK_CANCEL_OPTION));
if (StringUtil.isNullString(format)) {
return;
}
if (selectedPane == 0) {
insertText(format, PLAIN_ATTR, editorPane.getSelectionStart());
} else if (selectedPane == 1) {
// add the combobox data value to the edit box
formatTextArea.insert(format, formatTextArea.getCaretPosition());
}
}
}
public void runFilesAvailable(int fileNum) {
String[] logFileNames = getLogFileNames();
if ((progIndicator != null && progIndicator.isAborted()) || logFileNames == null) return;
String[] outputFilePaths = new String[logFileNames.length];
outputFilePaths[fileNum] = externalProcRunner.getOutputFilePath(logFileNames[fileNum]);
String filePath = outputFilePaths[fileNum];
if (fileNum == 0
&& outputFilePaths.length > 0
&& !StringUtil.blank(outputFilePaths[0])
&& !bootstrapOrJackknife()) { // tree file
if (ownerModule instanceof NewTreeProcessor) {
String treeFilePath = filePath;
if (taxa != null) {
TaxaSelectionSet outgroupSet =
(TaxaSelectionSet) taxa.getSpecsSet(outgroupTaxSetString, TaxaSelectionSet.class);
((NewTreeProcessor) ownerModule).newTreeAvailable(treeFilePath, outgroupSet);
} else ((NewTreeProcessor) ownerModule).newTreeAvailable(treeFilePath, null);
}
} else if (fileNum == 1
&& outputFilePaths.length > 1
&& !StringUtil.blank(outputFilePaths[1])
&& !bootstrapOrJackknife()) { // log file
if (MesquiteFile.fileExists(filePath)) {
String s = MesquiteFile.getFileLastContents(filePath);
if (!StringUtil.blank(s))
if (progIndicator != null) {
parser.setString(s);
String rep = parser.getFirstToken(); // generation number
logln("");
if (MesquiteInteger.isNumber(rep)) {
int numReps = MesquiteInteger.fromString(rep) + 1;
progIndicator.setText(
"Replicate: " + numReps); // + ", ln L = " + parser.getNextToken());
if (bootstrapOrJackknife()) {
logln("Replicate " + numReps + " of " + bootstrapreps);
}
logln("Replicate " + numReps + " of " + totalNumHits);
progIndicator.spin();
double timePerRep = 0;
if (MesquiteInteger.isCombinable(numReps) && numReps > 0) {
timePerRep = timer.timeSinceVeryStartInSeconds() / numReps; // this is time per rep
}
int timeLeft = 0;
if (bootstrapOrJackknife()) {
timeLeft = (int) ((bootstrapreps - numReps) * timePerRep);
} else {
String token = parser.getNextToken(); // algorithm
token = parser.getNextToken(); // Tree
token = parser.getNextToken(); // Score
String best = parser.getNextToken(); // Best
logln(" Score " + token + "; best found so far " + best);
timeLeft = (int) ((totalNumHits - numReps) * timePerRep);
}
logln(
" Running time so far "
+ StringUtil.secondsToHHMMSS((int) timer.timeSinceVeryStartInSeconds())
+ ", approximate time remaining "
+ StringUtil.secondsToHHMMSS(timeLeft));
}
}
count++;
} else if (MesquiteTrunk.debugMode) logln("*** File does not exist (" + filePath + ") ***");
}
}
/*.................................................................................................................*/
String getComDelim() {
if (externalProcRunner.isWindows()) return ";" + StringUtil.lineEnding();
else return ";" + StringUtil.lineEnding();
}
/*.................................................................................................................*/
public String preparePreferencesForXML() {
StringBuffer buffer = new StringBuffer(200);
StringUtil.appendXMLTag(buffer, 2, "availMemory", availMemory);
buffer.append(super.preparePreferencesForXML());
return buffer.toString();
}
public String getThreadAppName() {
return StringUtil.nvl(mstrThreadAppName, "Unknown platform");
}
/*.................................................................................................................*/
void formCommandFile(String dataFileName, int firstOutgroup) {
if (parallel) {
commands = "";
}
commands += getTNTCommand("mxram " + mxram);
commands += getTNTCommand("report+0/1/0");
commands += getTNTCommand("log " + logFileName);
commands += getTNTCommand("p " + dataFileName);
commands += getTNTCommand("vversion");
if (MesquiteInteger.isCombinable(firstOutgroup) && firstOutgroup >= 0)
commands += getTNTCommand("outgroup " + firstOutgroup);
if (bootstrapOrJackknife()) {
if (parallel) {
commands += indentTNTCommand("ptnt begin parallelRun " + numSlaves + "/ram x 2 = ");
}
if (StringUtil.notEmpty(bootSearchScriptPath)) {
String script = MesquiteFile.getFileContentsAsString(bootSearchScriptPath);
if (StringUtil.notEmpty(script)) commands += script;
} else
commands += StringUtil.lineEnding() + bootstrapSearchArguments + StringUtil.lineEnding();
String saveTreesString = "";
if (resamplingAllConsensusTrees) saveTreesString = " savetrees ";
String bootSearchString = " [xmult; bb]";
bootSearchString = "";
if (parallel) {
int numRepsPerSlave = bootstrapreps / numSlaves;
if (numRepsPerSlave * numSlaves < bootstrapreps) numRepsPerSlave++;
if (searchStyle == BOOTSTRAPSEARCH)
commands +=
getTNTCommand(
"resample boot cut 50 "
+ saveTreesString
+ " replications "
+ numRepsPerSlave
+ " [xmult; bb] savetrees"); // + getComDelim();
else if (searchStyle == JACKKNIFESEARCH)
commands +=
getTNTCommand(
"resample jak cut 50 "
+ saveTreesString
+ " replications "
+ numRepsPerSlave
+ " [xmult; bb] savetrees"); // + getComDelim();
else if (searchStyle == SYMSEARCH)
commands +=
getTNTCommand(
"resample sym cut 50 "
+ saveTreesString
+ " replications "
+ numRepsPerSlave
+ " [xmult; bb] savetrees"); // + getComDelim();
else if (searchStyle == POISSONSEARCH)
commands +=
getTNTCommand(
"resample poisson cut 50 "
+ saveTreesString
+ " replications "
+ numRepsPerSlave
+ " [xmult; bb] savetrees"); // + getComDelim();
commands += getTNTCommand("return");
commands += getTNTCommand("ptnt wait parallelRun");
commands += getTNTCommand("ptnt get parallelRun");
} else {
if (!resamplingAllConsensusTrees) {
commands += getTNTCommand("macro=");
commands += getTNTCommand("ttags =");
}
commands += getTNTCommand("tsave *" + treeFileName);
if (bootstrapAllowed) {
if (searchStyle == BOOTSTRAPSEARCH)
commands +=
getTNTCommand(
"resample boot "
+ saveTreesString
+ " replications "
+ bootstrapreps
+ bootSearchString); // + getComDelim();
else if (searchStyle == JACKKNIFESEARCH)
commands +=
getTNTCommand(
"resample jak cut 50 "
+ saveTreesString
+ " replications "
+ bootstrapreps
+ bootSearchString); // + getComDelim();
else if (searchStyle == SYMSEARCH)
commands +=
getTNTCommand(
"resample sym cut 50 "
+ saveTreesString
+ " replications "
+ bootstrapreps
+ bootSearchString); // + getComDelim();
else if (searchStyle == POISSONSEARCH)
commands +=
getTNTCommand(
"resample poisson cut 50 "
+ saveTreesString
+ " replications "
+ bootstrapreps
+ bootSearchString); // + getComDelim();
}
if (!resamplingAllConsensusTrees) commands += getTNTCommand("save *");
else commands += getTNTCommand("save");
commands += getTNTCommand("tsave/");
if (!resamplingAllConsensusTrees) {
commands += getTNTCommand("ttags -/");
commands += getTNTCommand("macro-");
}
}
// commands += getTNTCommand("proc/") ;
commands += getTNTCommand("log/");
// if (!parallel)
commands += getTNTCommand("quit");
} else {
// commands += getTNTCommand("tsave !5 " + treeFileName) ; // if showing intermediate trees
commands += getTNTCommand("tsave *" + treeFileName);
if (StringUtil.notEmpty(searchScriptPath)) {
String script = MesquiteFile.getFileContentsAsString(searchScriptPath);
if (StringUtil.notEmpty(script)) commands += script;
} else commands += searchArguments;
commands += otherOptions;
if (harvestOnlyStrictConsensus) commands += getTNTCommand("nelsen *");
commands += getTNTCommand("save");
commands += getTNTCommand("log/");
commands += getTNTCommand("tsave/");
commands += getTNTCommand("quit");
}
}