* @author $author$
* @version $Revision: 1.155 $
*/
-public class Desktop extends jalview.jbgui.GDesktop implements
- DropTargetListener, ClipboardOwner, IProgressIndicator,
+public class Desktop extends jalview.jbgui.GDesktop
+ implements DropTargetListener, ClipboardOwner, IProgressIndicator,
jalview.api.StructureSelectionManagerProvider
{
private static int DEFAULT_MIN_WIDTH = 300;
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
false);
- boolean showjconsole = jalview.bin.Cache.getDefault(
- "SHOW_JAVA_CONSOLE", false);
+ boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE",
+ false);
desktop = new MyDesktopPane(selmemusage);
if (Platform.isAMac())
{
// This line prevents Windows Look&Feel resizing all new windows to maximum
// if previous window was maximised
- desktop.setDesktopManager(new MyDesktopManager(
- new DefaultDesktopManager()));
+ desktop.setDesktopManager(
+ new MyDesktopManager(new DefaultDesktopManager()));
Rectangle dims = getLastKnownDimensions("");
if (dims != null)
else
{
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
- setBounds((screenSize.width - 900) / 2,
- (screenSize.height - 650) / 2, 900, 650);
+ setBounds((screenSize.width - 900) / 2, (screenSize.height - 650) / 2,
+ 900, 650);
}
jconsole = new Console(this, showjconsole);
// add essential build information
- jconsole.setHeader("Jalview Version: "
- + jalview.bin.Cache.getProperty("VERSION") + "\n"
- + "Jalview Installation: "
- + jalview.bin.Cache.getDefault("INSTALLATION", "unknown")
- + "\n" + "Build Date: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n"
- + "Java version: " + System.getProperty("java.version") + "\n"
- + System.getProperty("os.arch") + " "
- + System.getProperty("os.name") + " "
- + System.getProperty("os.version"));
+ jconsole.setHeader(
+ "Jalview Version: " + jalview.bin.Cache.getProperty("VERSION")
+ + "\n" + "Jalview Installation: "
+ + jalview.bin.Cache.getDefault("INSTALLATION",
+ "unknown")
+ + "\n" + "Build Date: "
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+ + "\n" + "Java version: "
+ + System.getProperty("java.version") + "\n"
+ + System.getProperty("os.arch") + " "
+ + System.getProperty("os.name") + " "
+ + System.getProperty("os.version"));
showConsole(showjconsole);
showNews.setVisible(false);
-
+
experimentalFeatures.setSelected(showExperimental());
getIdentifiersOrgData();
.getStructureSelectionManager(this);
if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
{
- ssm.setAddTempFacAnnot(jalview.bin.Cache.getDefault(
- Preferences.ADD_TEMPFACT_ANN, true));
- ssm.setProcessSecondaryStructure(jalview.bin.Cache.getDefault(
- Preferences.STRUCT_FROM_PDB, true));
- ssm.setSecStructServices(jalview.bin.Cache.getDefault(
- Preferences.USE_RNAVIEW, true));
+ ssm.setAddTempFacAnnot(jalview.bin.Cache
+ .getDefault(Preferences.ADD_TEMPFACT_ANN, true));
+ ssm.setProcessSecondaryStructure(jalview.bin.Cache
+ .getDefault(Preferences.STRUCT_FROM_PDB, true));
+ ssm.setSecStructServices(
+ jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW, true));
}
else
{
{
long now = System.currentTimeMillis();
Desktop.instance.setProgressBar(
- MessageManager.getString("status.refreshing_news"), now);
+ MessageManager.getString("status.refreshing_news"),
+ now);
jvnews.refreshNews();
Desktop.instance.setProgressBar(null, now);
jvnews.showNews();
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
String x = jalview.bin.Cache.getProperty(windowName + "SCREEN_X");
String y = jalview.bin.Cache.getProperty(windowName + "SCREEN_Y");
- String width = jalview.bin.Cache.getProperty(windowName
- + "SCREEN_WIDTH");
- String height = jalview.bin.Cache.getProperty(windowName
- + "SCREEN_HEIGHT");
+ String width = jalview.bin.Cache
+ .getProperty(windowName + "SCREEN_WIDTH");
+ String height = jalview.bin.Cache
+ .getProperty(windowName + "SCREEN_HEIGHT");
if ((x != null) && (y != null) && (width != null) && (height != null))
{
- int ix = Integer.parseInt(x), iy = Integer.parseInt(y), iw = Integer
- .parseInt(width), ih = Integer.parseInt(height);
+ int ix = Integer.parseInt(x), iy = Integer.parseInt(y),
+ iw = Integer.parseInt(width), ih = Integer.parseInt(height);
if (jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
{
// attempt #1 - try to cope with change in screen geometry - this
// version doesn't preserve original jv aspect ratio.
// take ratio of current screen size vs original screen size.
- double sw = ((1f * screenSize.width) / (1f * Integer
- .parseInt(jalview.bin.Cache
- .getProperty("SCREENGEOMETRY_WIDTH"))));
- double sh = ((1f * screenSize.height) / (1f * Integer
- .parseInt(jalview.bin.Cache
- .getProperty("SCREENGEOMETRY_HEIGHT"))));
+ double sw = ((1f * screenSize.width) / (1f * Integer.parseInt(
+ jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
+ double sh = ((1f * screenSize.height) / (1f * Integer.parseInt(
+ jalview.bin.Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
// rescale the bounds depending upon the current screen geometry.
ix = (int) (ix * sw);
iw = (int) (iw * sw);
ih = (int) (ih * sh);
while (ix >= screenSize.width)
{
- jalview.bin.Cache.log
- .debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
+ jalview.bin.Cache.log.debug(
+ "Window geometry location recall error: shifting horizontal to within screenbounds.");
ix -= screenSize.width;
}
while (iy >= screenSize.height)
{
- jalview.bin.Cache.log
- .debug("Window geometry location recall error: shifting vertical to within screenbounds.");
+ jalview.bin.Cache.log.debug(
+ "Window geometry location recall error: shifting vertical to within screenbounds.");
iy -= screenSize.height;
}
- jalview.bin.Cache.log.debug("Got last known dimensions for "
- + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
- + " height:" + ih);
+ jalview.bin.Cache.log.debug(
+ "Got last known dimensions for " + windowName + ": x:" + ix
+ + " y:" + iy + " width:" + iw + " height:" + ih);
}
// return dimensions for new instance
return new Rectangle(ix, iy, iw, ih);
}
} catch (Exception ex)
{
- System.out
- .println("Unable to paste alignment from system clipboard:\n"
- + ex);
+ System.out.println(
+ "Unable to paste alignment from system clipboard:\n" + ex);
}
}
// A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
// IF JALVIEW IS RUNNING HEADLESS
// ///////////////////////////////////////////////
- if (instance == null
- || (System.getProperty("java.awt.headless") != null && System
- .getProperty("java.awt.headless").equals("true")))
+ if (instance == null || (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true")))
{
return;
}
if (!ignoreMinSize)
{
- frame.setMinimumSize(new Dimension(DEFAULT_MIN_WIDTH,
- DEFAULT_MIN_HEIGHT));
+ frame.setMinimumSize(
+ new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT));
// Set default dimension for Alignment Frame window.
// The Alignment Frame window could be added from a number of places,
}
}
-
frame.setVisible(makeVisible);
frame.setClosable(true);
frame.setResizable(resizable);
}
if (frame.getX() < 1 && frame.getY() < 1)
{
- frame.setLocation(xOffset * openFrameCount, yOffset
- * ((openFrameCount - 1) % 10) + yOffset);
+ frame.setLocation(xOffset * openFrameCount,
+ yOffset * ((openFrameCount - 1) % 10) + yOffset);
}
/*
{
} catch (java.lang.ClassCastException cex)
{
- Cache.log
- .warn("Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
- cex);
+ Cache.log.warn(
+ "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
+ cex);
}
}
for (int i = 0; i < files.size(); i++)
{
String file = files.get(i).toString();
- DataSourceType protocol = (protocols == null) ? DataSourceType.FILE
+ DataSourceType protocol = (protocols == null)
+ ? DataSourceType.FILE
: protocols.get(i);
FileFormatI format = null;
public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- JalviewFileChooser chooser = JalviewFileChooser.forRead(
- Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+ JalviewFileChooser chooser = JalviewFileChooser
+ .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.open_local_file"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.open_local_file"));
chooser.setToolTipText(MessageManager.getString("action.open"));
int value = chooser.showOpenDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
+ Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
FileFormatI format = chooser.getSelectedFormat();
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.couldnt_locate",
- new Object[] { url }), MessageManager
- .getString("label.url_not_found"),
+ new Object[]
+ { url }),
+ MessageManager.getString("label.url_not_found"),
JvOptionPane.WARNING_MESSAGE);
return;
if (viewport != null)
{
- new FileLoader()
- .LoadFile(viewport, url, DataSourceType.URL, format);
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+ format);
}
else
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(viewPanel);
Desktop.addInternalFrame(cap,
- MessageManager.getString("label.cut_paste_alignmen_file"),
- true, 600, 500);
+ MessageManager.getString("label.cut_paste_alignmen_file"), true,
+ 600, 500);
}
/*
public void quit()
{
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
- jalview.bin.Cache
- .setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
- jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height
- + "");
- storeLastKnownDimensions("", new Rectangle(getBounds().x,
- getBounds().y, getWidth(), getHeight()));
+ jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH",
+ screen.width + "");
+ jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT",
+ screen.height + "");
+ storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
+ getWidth(), getHeight()));
if (jconsole != null)
{
if (shortv)
{
message.append("<h1><strong>Version: "
- + jalview.bin.Cache.getProperty("VERSION") + "</strong></h1>");
+ + jalview.bin.Cache.getProperty("VERSION")
+ + "</strong></h1>");
message.append("<strong>Last Updated: <em>"
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+ "</em></strong>");
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
}
- if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals(
- "Checking"))
+ if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
+ .equals("Checking"))
{
message.append("<br>...Checking latest version...</br>");
}
"..Checking..")
+ " is available for download from "
+ jalview.bin.Cache.getDefault("www.jalview.org",
- "http://www.jalview.org") + " !!");
+ "http://www.jalview.org")
+ + " !!");
if (red)
{
message.append("</div>");
}
}
- message.append("<br>Authors: "
- + jalview.bin.Cache
- .getDefault("AUTHORFNAMES",
- "The Jalview Authors (See AUTHORS file for current list)")
+ message.append("<br>Authors: " + jalview.bin.Cache.getDefault(
+ "AUTHORFNAMES",
+ "The Jalview Authors (See AUTHORS file for current list)")
+ "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
+ "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
+ "<br><br>If you use Jalview, please cite:"
{
showConsole.setSelected(selected);
// TODO: decide if we should update properties file
- Cache.setProperty("SHOW_JAVA_CONSOLE", Boolean.valueOf(selected)
- .toString());
+ Cache.setProperty("SHOW_JAVA_CONSOLE",
+ Boolean.valueOf(selected).toString());
jconsole.setVisible(selected);
}
{
// TODO: refactor to Jalview desktop session controller action.
setProgressBar(MessageManager.formatMessage(
- "label.saving_jalview_project",
- new Object[] { choice.getName() }), choice.hashCode());
+ "label.saving_jalview_project", new Object[]
+ { choice.getName() }), choice.hashCode());
jalview.bin.Cache.setProperty("LAST_DIRECTORY",
choice.getParent());
// TODO catch and handle errors for savestate
new Jalview2XML().saveState(choice);
} catch (OutOfMemoryError oom)
{
- new OOMWarning("Whilst saving current state to "
- + choice.getName(), oom);
+ new OOMWarning(
+ "Whilst saving current state to " + choice.getName(),
+ oom);
} catch (Exception ex)
{
Cache.log.error(
"Problems whilst trying to save to " + choice.getName(),
ex);
- JvOptionPane.showMessageDialog(me, MessageManager.formatMessage(
- "label.error_whilst_saving_current_state_to",
- new Object[] { choice.getName() }), MessageManager
- .getString("label.couldnt_save_project"),
+ JvOptionPane.showMessageDialog(me,
+ MessageManager.formatMessage(
+ "label.error_whilst_saving_current_state_to",
+ new Object[]
+ { choice.getName() }),
+ MessageManager.getString("label.couldnt_save_project"),
JvOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
public void loadState_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), new String[] {
- "jvp", "jar" }, new String[] { "Jalview Project",
- "Jalview Project (old)" }, "Jalview Project");
+ Cache.getProperty("LAST_DIRECTORY"), new String[]
+ { "jvp", "jar" },
+ new String[]
+ { "Jalview Project", "Jalview Project (old)" },
+ "Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
final File selectedFile = chooser.getSelectedFile();
setProjectFile(selectedFile);
final String choice = selectedFile.getAbsolutePath();
- Cache.setProperty("LAST_DIRECTORY",
- selectedFile.getParent());
+ Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
new Thread(new Runnable()
{
@Override
public void run()
{
- setProgressBar(
- MessageManager.formatMessage(
- "label.loading_jalview_project",
- new Object[] { choice }), choice.hashCode());
+ setProgressBar(MessageManager.formatMessage(
+ "label.loading_jalview_project", new Object[]
+ { choice }), choice.hashCode());
try
{
new Jalview2XML().loadJalviewAlign(choice);
new OOMWarning("Whilst loading project from " + choice, oom);
} catch (Exception ex)
{
- Cache.log.error("Problems whilst loading project from "
- + choice, ex);
- JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
- .formatMessage(
+ Cache.log.error(
+ "Problems whilst loading project from " + choice, ex);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
"label.error_whilst_loading_project_from",
- new Object[] { choice }), MessageManager
- .getString("label.couldnt_load_project"),
+ new Object[]
+ { choice }),
+ MessageManager.getString("label.couldnt_load_project"),
JvOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
{
if (fileLoadingCount == 0)
{
- fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage(
- "label.loading_file", new Object[] { fileName })));
+ fileLoadingPanels.add(addProgressPanel(MessageManager
+ .formatMessage("label.loading_file", new Object[]
+ { fileName })));
}
fileLoadingCount++;
}
thisprogress.add(progressBar, BorderLayout.CENTER);
progressPanel.add(thisprogress);
- ((GridLayout) progressPanel.getLayout())
- .setRows(((GridLayout) progressPanel.getLayout()).getRows() + 1);
+ ((GridLayout) progressPanel.getLayout()).setRows(
+ ((GridLayout) progressPanel.getLayout()).getRows() + 1);
++totalProgressCount;
instance.validate();
return thisprogress;
for (AlignFrame afr : frames)
{
- if (sequenceSetId == null
- || afr.getViewport().getSequenceSetId()
- .equals(sequenceSetId))
+ if (sequenceSetId == null || afr.getViewport().getSequenceSetId()
+ .equals(sequenceSetId))
{
if (afr.alignPanels != null)
{
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.open_saved_vamsas_session"));
- chooser.setToolTipText(MessageManager
- .getString("label.select_vamsas_session_opened_as_new_vamsas_session"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.open_saved_vamsas_session"));
+ chooser.setToolTipText(MessageManager.getString(
+ "label.select_vamsas_session_opened_as_new_vamsas_session"));
int value = chooser.showOpenDialog(this);
String fle = chooser.getSelectedFile().toString();
if (!vamsasImport(chooser.getSelectedFile()))
{
- JvOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager.formatMessage(
- "label.couldnt_import_as_vamsas_session",
- new Object[] { fle }),
- MessageManager
- .getString("label.vamsas_document_import_failed"),
- JvOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.couldnt_import_as_vamsas_session",
+ new Object[]
+ { fle }),
+ MessageManager
+ .getString("label.vamsas_document_import_failed"),
+ JvOptionPane.ERROR_MESSAGE);
}
}
}
else
{
- jalview.bin.Cache.log
- .error("Implementation error - load session from a running session is not supported.");
+ jalview.bin.Cache.log.error(
+ "Implementation error - load session from a running session is not supported.");
}
}
if (v_client != null)
{
- jalview.bin.Cache.log
- .error("Implementation error - load session from a running session is not supported.");
+ jalview.bin.Cache.log.error(
+ "Implementation error - load session from a running session is not supported.");
return false;
}
{
jalview.bin.Cache.log.error(
"Failed to create new vamsas session from contents of URL "
- + url, ex);
+ + url,
+ ex);
return false;
}
setupVamsasConnectedGui();
if (v_client != null)
{
- jalview.bin.Cache.log
- .error("Implementation error - load session from a running session is not supported.");
+ jalview.bin.Cache.log.error(
+ "Implementation error - load session from a running session is not supported.");
return false;
}
setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from",
- new Object[] { file.getName() }), file.hashCode());
+ "status.importing_vamsas_session_from", new Object[]
+ { file.getName() }), file.hashCode());
try
{
v_client = new jalview.gui.VamsasApplication(this, file, null);
} catch (Exception ex)
{
setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from",
- new Object[] { file.getName() }), file.hashCode());
+ "status.importing_vamsas_session_from", new Object[]
+ { file.getName() }), file.hashCode());
jalview.bin.Cache.log.error(
"New vamsas session from existing session file failed:", ex);
return false;
setupVamsasConnectedGui();
v_client.initial_update(); // TODO: thread ?
setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from",
- new Object[] { file.getName() }), file.hashCode());
+ "status.importing_vamsas_session_from", new Object[]
+ { file.getName() }), file.hashCode());
return v_client.inSession();
}
{
if (v_client != null)
{
- throw new Error(
- MessageManager
- .getString("error.try_join_vamsas_session_another"));
+ throw new Error(MessageManager
+ .getString("error.try_join_vamsas_session_another"));
}
if (mysesid == null)
{
vamsasSave.setVisible(false);
vamsasStop.setVisible(false);
vamsasImport.setVisible(true);
- vamsasStart.setText(MessageManager
- .getString("label.new_vamsas_session"));
+ vamsasStart
+ .setText(MessageManager.getString("label.new_vamsas_session"));
}
@Override
sess = VamsasApplication.getSessionList();
} catch (Exception e)
{
- jalview.bin.Cache.log.warn(
- "Problem getting current sessions list.", e);
+ jalview.bin.Cache.log.warn("Problem getting current sessions list.",
+ e);
sess = null;
}
if (sess != null)
{
- jalview.bin.Cache.log.debug("Got current sessions list: "
- + sess.length + " entries.");
+ jalview.bin.Cache.log.debug(
+ "Got current sessions list: " + sess.length + " entries.");
VamsasStMenu.removeAll();
for (int i = 0; i < sess.length; i++)
{
JMenuItem sessit = new JMenuItem();
sessit.setText(sess[i]);
- sessit.setToolTipText(MessageManager.formatMessage(
- "label.connect_to_session", new Object[] { sess[i] }));
+ sessit.setToolTipText(MessageManager
+ .formatMessage("label.connect_to_session", new Object[]
+ { sess[i] }));
final Desktop dsktp = this;
final String mysesid = sess[i];
sessit.addActionListener(new ActionListener()
{
if (v_client != null)
{
- // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+ // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
JalviewFileChooser chooser = new JalviewFileChooser("vdj",
"Vamsas Document");
if (value == JalviewFileChooser.APPROVE_OPTION)
{
java.io.File choice = chooser.getSelectedFile();
- JPanel progpanel = addProgressPanel(MessageManager.formatMessage(
- "label.saving_vamsas_doc",
- new Object[] { choice.getName() }));
+ JPanel progpanel = addProgressPanel(MessageManager
+ .formatMessage("label.saving_vamsas_doc", new Object[]
+ { choice.getName() }));
Cache.setProperty("LAST_DIRECTORY", choice.getParent());
String warnmsg = null;
String warnttl = null;
{
warnttl = "Serious Problem saving Vamsas Document";
warnmsg = ex.toString();
- jalview.bin.Cache.log.error("Error Whilst saving document to "
- + choice, ex);
+ jalview.bin.Cache.log
+ .error("Error Whilst saving document to " + choice, ex);
} catch (Exception ex)
{
warnttl = "Problem saving Vamsas Document.";
warnmsg = ex.toString();
- jalview.bin.Cache.log.warn("Exception Whilst saving document to "
- + choice, ex);
+ jalview.bin.Cache.log.warn(
+ "Exception Whilst saving document to " + choice, ex);
}
removeProgressPanel(progpanel);
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
+ warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
}
}
}
}
if (b)
{
- vamUpdate = this.addProgressPanel(MessageManager
- .getString("label.updating_vamsas_session"));
+ vamUpdate = this.addProgressPanel(
+ MessageManager.getString("label.updating_vamsas_session"));
}
vamsasStart.setVisible(!b);
vamsasStop.setVisible(!b);
{
check = true;
int barPos = link.indexOf("|");
- String urlMsg = barPos == -1 ? link : link.substring(0,
- barPos) + ": " + link.substring(barPos + 1);
+ String urlMsg = barPos == -1 ? link
+ : link.substring(0, barPos) + ": "
+ + link.substring(barPos + 1);
urls.add(new JLabel(urlMsg));
}
}
JPanel msgPanel = new JPanel();
msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS));
msgPanel.add(Box.createVerticalGlue());
- JLabel msg = new JLabel(
- MessageManager
- .getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
- JLabel msg2 = new JLabel(
- MessageManager
- .getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
+ JLabel msg = new JLabel(MessageManager
+ .getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
+ JLabel msg2 = new JLabel(MessageManager
+ .getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
msgPanel.add(msg);
for (JLabel url : urls)
{
}
}
});
- }
+ }
/**
* Proxy class for JDesktopPane which optionally displays the current memory
FontMetrics fm = g.getFontMetrics();
if (fm != null)
{
- g.drawString(MessageManager.formatMessage(
- "label.memory_stats",
- new Object[] { df.format(totalFreeMemory),
- df.format(maxMemory), df.format(percentUsage) }), 10,
- getHeight() - fm.getHeight());
+ g.drawString(MessageManager.formatMessage("label.memory_stats",
+ new Object[]
+ { df.format(totalFreeMemory), df.format(maxMemory),
+ df.format(percentUsage) }),
+ 10, getHeight() - fm.getHeight());
}
}
}
jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.couldnt_create_groovy_shell"),
+ MessageManager.getString("label.couldnt_create_groovy_shell"),
MessageManager.getString("label.groovy_support_failed"),
JvOptionPane.ERROR_MESSAGE);
}
*/
protected void addQuitHandler()
{
- getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
- KeyStroke.getKeyStroke(KeyEvent.VK_Q, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()), "Quit");
+ getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
+ .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()),
+ "Quit");
getRootPane().getActionMap().put("Quit", new AbstractAction()
{
@Override
if (progressBarHandlers == null
|| !progressBars.containsKey(new Long(id)))
{
- throw new Error(
- MessageManager
- .getString("error.call_setprogressbar_before_registering_handler"));
+ throw new Error(MessageManager.getString(
+ "error.call_setprogressbar_before_registering_handler"));
}
progressBarHandlers.put(new Long(id), handler);
final JPanel progressPanel = progressBars.get(new Long(id));
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar(MessageManager.formatMessage(
- "label.cancelled_params",
- new Object[] { ((JLabel) progressPanel.getComponent(0))
- .getText() }), id);
+ us.setProgressBar(MessageManager
+ .formatMessage("label.cancelled_params", new Object[]
+ { ((JLabel) progressPanel.getComponent(0)).getText() }),
+ id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
{
if (desktop != null)
{
- AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId());
+ AlignmentPanel[] aps = getAlignmentPanels(
+ viewport.getSequenceSetId());
for (int panel = 0; aps != null && panel < aps.length; panel++)
{
if (aps[panel] != null && aps[panel].av == viewport)
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(
- changeSupport);
+ t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ .startDiscoverer(changeSupport);
}
Thread t3 = null;
{
} catch (Exception e)
{
}
- alive = (t1 != null && t1.isAlive())
- || (t2 != null && t2.isAlive())
+ alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive())
|| (t3 != null && t3.isAlive())
|| (t0 != null && t0.isAlive());
}
*
* jd.waitForInput();
*/
- JvOptionPane
- .showConfirmDialog(
- Desktop.desktop,
- new JLabel(
- "<html><table width=\"450\"><tr><td>"
- + ermsg
- + "</td></tr></table>"
- + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
- + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
- + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
- + " Tools->Preferences dialog box to change them.</p></html>"),
- "Web Service Configuration Problem",
- JvOptionPane.DEFAULT_OPTION,
- JvOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showConfirmDialog(Desktop.desktop,
+ new JLabel("<html><table width=\"450\"><tr><td>"
+ + ermsg + "</td></tr></table>"
+ + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
+ + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
+ + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
+ + " Tools->Preferences dialog box to change them.</p></html>"),
+ "Web Service Configuration Problem",
+ JvOptionPane.DEFAULT_OPTION,
+ JvOptionPane.ERROR_MESSAGE);
serviceChangedDialog = null;
}
}
else
{
- Cache.log
- .error("Errors reported by JABA discovery service. Check web services preferences.\n"
+ Cache.log.error(
+ "Errors reported by JABA discovery service. Check web services preferences.\n"
+ ermsg);
}
}
{
if (progress != null)
{
- progress.setProgressBar(MessageManager.formatMessage(
- "status.opening_params", new Object[] { url }), this
- .hashCode());
+ progress.setProgressBar(MessageManager
+ .formatMessage("status.opening_params", new Object[]
+ { url }), this.hashCode());
}
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
}
else
{
- System.err.println("Couldn't handle string " + url
- + " as a URL.");
+ System.err.println(
+ "Couldn't handle string " + url + " as a URL.");
}
}
// ignore any exceptions due to dud links.
{
invalidate();
File of;
- ImageMaker im = new jalview.util.ImageMaker(this, ImageMaker.TYPE.EPS,
- "View of Desktop", getWidth(), getHeight(), of = new File(
- "Jalview_snapshot" + System.currentTimeMillis()
- + ".eps"), "View of desktop", null, 0, false);
+ ImageMaker im = new jalview.util.ImageMaker(
+ this, ImageMaker.TYPE.EPS, "View of Desktop", getWidth(),
+ getHeight(), of = new File("Jalview_snapshot"
+ + System.currentTimeMillis() + ".eps"),
+ "View of desktop", null, 0, false);
try
{
paintAll(im.getGraphics());
AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame();
myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
- myBottomFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
- source.getY(), myBottomFrame.getWidth(), myBottomFrame
- .getHeight()));
+ myBottomFrame.viewport
+ .setExplodedGeometry(new Rectangle(source.getX(), source.getY(),
+ myBottomFrame.getWidth(), myBottomFrame.getHeight()));
myTopFrame.viewport.setGatherViewsHere(true);
myBottomFrame.viewport.setGatherViewsHere(true);
String topViewId = myTopFrame.viewport.getSequenceSetId();
gatherThis = true;
topPanel.av.setGatherViewsHere(false);
bottomPanel.av.setGatherViewsHere(false);
- topPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(),
- topFrame.getSize()));
- bottomPanel.av.setExplodedGeometry(new Rectangle(sf
- .getLocation(), bottomFrame.getSize()));
+ topPanel.av.setExplodedGeometry(
+ new Rectangle(sf.getLocation(), topFrame.getSize()));
+ bottomPanel.av.setExplodedGeometry(
+ new Rectangle(sf.getLocation(), bottomFrame.getSize()));
myTopFrame.addAlignmentPanel(topPanel, false);
myBottomFrame.addAlignmentPanel(bottomPanel, false);
}
public static void transferFromDropTarget(List<String> files,
List<DataSourceType> protocols, DropTargetDropEvent evt,
- Transferable t)
- throws Exception
+ Transferable t) throws Exception
{
DataFlavor uriListFlavor = new DataFlavor(
// fallback to text: workaround - on OSX where there's a JVM bug
Cache.log.debug("standard URIListFlavor failed. Trying text");
// try text fallback
- data = (String) t.getTransferData(new DataFlavor(
- "text/plain;class=java.lang.String"));
+ data = (String) t.getTransferData(
+ new DataFlavor("text/plain;class=java.lang.String"));
if (Cache.log.isDebugEnabled())
{
Cache.log.debug("fallback returned " + data);
{
if (data == null || !added)
{
- Cache.log
- .debug("Couldn't resolve drop data. Here are the supported flavors:");
+ Cache.log.debug(
+ "Couldn't resolve drop data. Here are the supported flavors:");
for (DataFlavor fl : t.getTransferDataFlavors())
{
- Cache.log.debug("Supported transfer dataflavor: "
- + fl.toString());
+ Cache.log.debug(
+ "Supported transfer dataflavor: " + fl.toString());
Object df = t.getTransferData(fl);
if (df != null)
{
git://source.jalview.org / jalview.git / blobdiff