X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=3f3950c20ed9b5b49ad710aa580c493418f7e20a;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=f05ef17ae8029183ab8d7a182ad8ce8cf0498321;hpb=1b9fc500a75a38d7c4408d4b209384d5236911cc;p=jalview.git
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index f05ef17..3f3950c 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
@@ -24,6 +26,9 @@ import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+import jalview.jbgui.GStructureViewer;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.ws.params.ParamManager;
@@ -86,9 +91,9 @@ import javax.swing.JPopupMenu;
import javax.swing.JProgressBar;
import javax.swing.SwingUtilities;
import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkEvent.EventType;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
-import javax.swing.event.HyperlinkEvent.EventType;
/**
* Jalview Desktop
@@ -109,6 +114,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
*/
private BlogReader jvnews = null;
+ private File projectFile;
+
/**
* @param listener
* @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
@@ -283,7 +290,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
instance = this;
doVamsasClientCheck();
doGroovyCheck();
-
+ doConfigureStructurePrefs();
setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
@@ -314,13 +321,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
else
{
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
- setBounds((int) (screenSize.width - 900) / 2,
- (int) (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 Desktop "
+ 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"
@@ -413,6 +423,27 @@ public class Desktop extends jalview.jbgui.GDesktop implements
});
}
+ public void doConfigureStructurePrefs()
+ {
+ // configure services
+ StructureSelectionManager ssm = StructureSelectionManager
+ .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));
+ }
+ else
+ {
+ ssm.setAddTempFacAnnot(false);
+ ssm.setProcessSecondaryStructure(false);
+ ssm.setSecStructServices(false);
+ }
+ }
+
public void checkForNews()
{
final Desktop me = this;
@@ -449,7 +480,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
public void run()
{
long instance = System.currentTimeMillis();
- Desktop.instance.setProgressBar("Refreshing news", instance);
+ Desktop.instance.setProgressBar(MessageManager.getString("status.refreshing_news"), instance);
jvnews.refreshNews();
Desktop.instance.setProgressBar(null, instance);
jvnews.showNews();
@@ -559,7 +590,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
void showPasteMenu(int x, int y)
{
JPopupMenu popup = new JPopupMenu();
- JMenuItem item = new JMenuItem(MessageManager.getString("label.paste_new_window"));
+ JMenuItem item = new JMenuItem(
+ MessageManager.getString("label.paste_new_window"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
@@ -602,38 +634,85 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* Adds and opens the given frame to the desktop
*
* @param frame
- * DOCUMENT ME!
+ * Frame to show
* @param title
- * DOCUMENT ME!
+ * Visible Title
* @param w
- * DOCUMENT ME!
+ * width
* @param h
- * DOCUMENT ME!
+ * height
*/
public static synchronized void addInternalFrame(
final JInternalFrame frame, String title, int w, int h)
{
- addInternalFrame(frame, title, w, h, true);
+ addInternalFrame(frame, title, true, w, h, true);
}
+
/**
- * DOCUMENT ME!
+ * Add an internal frame to the Jalview desktop
*
* @param frame
- * DOCUMENT ME!
+ * Frame to show
* @param title
- * DOCUMENT ME!
+ * Visible Title
+ * @param makeVisible
+ * When true, display frame immediately, otherwise, caller must call
+ * setVisible themselves.
* @param w
- * DOCUMENT ME!
+ * width
* @param h
- * DOCUMENT ME!
+ * height
+ */
+ public static synchronized void addInternalFrame(
+ final JInternalFrame frame, String title, boolean makeVisible,
+ int w, int h)
+ {
+ addInternalFrame(frame, title, makeVisible, w, h, true);
+ }
+
+ /**
+ * Add an internal frame to the Jalview desktop and make it visible
+ *
+ * @param frame
+ * Frame to show
+ * @param title
+ * Visible Title
+ * @param w
+ * width
+ * @param h
+ * height
* @param resizable
- * DOCUMENT ME!
+ * Allow resize
*/
public static synchronized void addInternalFrame(
final JInternalFrame frame, String title, int w, int h,
boolean resizable)
{
+ addInternalFrame(frame, title, true, w, h, resizable);
+ }
+
+ /**
+ * Add an internal frame to the Jalview desktop
+ *
+ * @param frame
+ * Frame to show
+ * @param title
+ * Visible Title
+ * @param makeVisible
+ * When true, display frame immediately, otherwise, caller must call
+ * setVisible themselves.
+ * @param w
+ * width
+ * @param h
+ * height
+ * @param resizable
+ * Allow resize
+ */
+ public static synchronized void addInternalFrame(
+ final JInternalFrame frame, String title, boolean makeVisible,
+ int w, int h, boolean resizable)
+ {
// TODO: allow callers to determine X and Y position of frame (eg. via
// bounds object).
@@ -649,15 +728,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
// 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;
}
openFrameCount++;
- frame.setVisible(true);
+ frame.setVisible(makeVisible);
frame.setClosable(true);
frame.setResizable(resizable);
frame.setMaximizable(resizable);
@@ -807,7 +887,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
*/
public void drop(DropTargetDropEvent evt)
{
- boolean success=true;
+ boolean success = true;
Transferable t = evt.getTransferable();
java.util.List files = null;
java.util.List protocols = null;
@@ -856,7 +936,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
} catch (Exception e)
{
- success=false;
+ success = false;
}
if (files != null)
@@ -885,10 +965,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
} catch (Exception ex)
{
- success=false;
+ success = false;
}
}
- evt.dropComplete(success); // need this to ensure input focus is properly transfered to any new windows created
+ evt.dropComplete(success); // need this to ensure input focus is properly
+ // transfered to any new windows created
}
/**
@@ -906,7 +987,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
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);
@@ -918,7 +1000,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
.getSelectedFile().getParent());
String format = null;
- if (chooser.getSelectedFormat()!=null && chooser.getSelectedFormat().equals("Jalview"))
+ if (chooser.getSelectedFormat() != null
+ && chooser.getSelectedFormat().equals("Jalview"))
{
format = "Jalview";
}
@@ -949,7 +1032,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
// This construct allows us to have a wider textfield
// for viewing
- JLabel label = new JLabel(MessageManager.getString("label.input_file_url"));
+ JLabel label = new JLabel(
+ MessageManager.getString("label.input_file_url"));
final JComboBox history = new JComboBox();
JPanel panel = new JPanel(new GridLayout(2, 1));
@@ -974,7 +1058,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
- MessageManager.getString("label.input_alignment_from_url"), JOptionPane.OK_CANCEL_OPTION);
+ MessageManager.getString("label.input_alignment_from_url"),
+ JOptionPane.OK_CANCEL_OPTION);
if (reply != JOptionPane.OK_OPTION)
{
@@ -1002,7 +1087,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
if (format.equals("URL NOT FOUND"))
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't locate " + url, "URL not found",
+ MessageManager.formatMessage("label.couldnt_locate", new String[]{url}), MessageManager.getString("label.url_not_found"),
JOptionPane.WARNING_MESSAGE);
return;
@@ -1029,7 +1114,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(viewport);
- Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.cut_paste_alignmen_file"),
+ true, 600, 500);
}
/*
@@ -1104,7 +1191,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
message.append("Version: "
+ jalview.bin.Cache.getProperty("VERSION")
- + "
");
+ + "");
message.append("Last Updated: "
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+ "");
@@ -1151,11 +1238,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
message.append("
Authors: "
+ jalview.bin.Cache
.getDefault(
- "AUTHORNAMES",
- "Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton")
- + "
Development managed by The Barton Group, University of Dundee, Scotland, UK.
"
- + "
For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list"
- + "
If you use Jalview, please cite:"
+ "AUTHORFNAMES",
+ "The Jalview Authors (See AUTHORS file for current list)")
+ + "
Development managed by The Barton Group, University of Dundee, Scotland, UK.
"
+ + "
For help, see the FAQ at www.jalview.org/faq and/or join the jalview-discuss@jalview.org mailing list"
+ + "
If you use Jalview, please cite:"
+ "
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ "
Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+ "
Bioinformatics doi: 10.1093/bioinformatics/btp033"
@@ -1173,13 +1260,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
try
{
- ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
- java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
- javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
-
- javax.help.HelpBroker hb = hs.createHelpBroker();
- hb.setCurrentID("home");
- hb.setDisplayed(true);
+ Help.showHelpWindow();
} catch (Exception ex)
{
}
@@ -1376,7 +1457,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{ "Jalview Project" }, "Jalview Project");
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save State");
+ chooser.setDialogTitle(MessageManager.getString("label.save_state"));
int value = chooser.showSaveDialog(this);
@@ -1384,12 +1465,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
final Desktop me = this;
final java.io.File choice = chooser.getSelectedFile();
+ setProjectFile(choice);
+
+ // TODO or move inside the new Thread?
+ saveChimeraSessions(choice.getAbsolutePath());
+
new Thread(new Runnable()
{
public void run()
{
- setProgressBar("Saving jalview project " + choice.getName(),
+ setProgressBar(MessageManager.formatMessage("label.saving_jalview_project", new String[]{choice.getName()}),
choice.hashCode());
jalview.bin.Cache.setProperty("LAST_DIRECTORY",
choice.getParent());
@@ -1397,7 +1483,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
// TODO prevent user from messing with the Desktop whilst we're saving
try
{
- new Jalview2XML().SaveState(choice);
+ new Jalview2XML().saveState(choice);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Whilst saving current state to "
@@ -1409,8 +1495,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
ex);
JOptionPane.showMessageDialog(
me,
- "Error whilst saving current state to "
- + choice.getName(), "Couldn't save project",
+ MessageManager.formatMessage("label.error_whilst_saving_current_state_to", new String[]{ choice.getName()}),
+ MessageManager.getString("label.couldnt_save_project"),
JOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
@@ -1420,6 +1506,42 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
/**
+ * Request any open, linked Chimera sessions to save their state.
+ *
+ * @param jalviewProjectFilename
+ * the filename of the Jalview project; Chimera session files should
+ * be given distinct, but obviously related, names.
+ */
+ public void saveChimeraSessions(String jalviewProjectFilename)
+ {
+ int i = 0;
+ for (JInternalFrame frame : getAllFrames())
+ {
+ if (frame instanceof ChimeraViewFrame)
+ {
+ /*
+ * Construct a filename for the Chimera session by append _chimera.py
+ * to the Jalview project file name.
+ */
+ String chimeraPath = jalviewProjectFilename + "_chimera_" + i
+ + ".py";
+ ((ChimeraViewFrame) frame).saveSession(chimeraPath);
+ i++;
+ }
+ }
+ }
+
+ private void setProjectFile(File choice)
+ {
+ this.projectFile = choice;
+ }
+
+ public File getProjectFile()
+ {
+ return this.projectFile;
+ }
+
+ /**
* DOCUMENT ME!
*
* @param e
@@ -1429,27 +1551,29 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jvp","jar" }, new String[]
- { "Jalview Project", "Jalview Project (old)" }, "Jalview Project");
+ { "jvp", "jar" }, new String[]
+ { "Jalview Project", "Jalview Project (old)" },
+ "Jalview Project");
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Restore state");
+ chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
int value = chooser.showOpenDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- final String choice = chooser.getSelectedFile().getAbsolutePath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
+ final File selectedFile = chooser.getSelectedFile();
+ setProjectFile(selectedFile);
+ final String choice = selectedFile.getAbsolutePath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
new Thread(new Runnable()
{
public void run()
{
- setProgressBar("loading jalview project " + choice,
+ setProgressBar(MessageManager.formatMessage("label.loading_jalview_project", new String[]{choice}),
choice.hashCode());
try
{
- new Jalview2XML().LoadJalviewAlign(choice);
+ new Jalview2XML().loadJalviewAlign(choice);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Whilst loading project from " + choice, oom);
@@ -1458,8 +1582,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
Cache.log.error("Problems whilst loading project from "
+ choice, ex);
JOptionPane.showMessageDialog(Desktop.desktop,
- "Error whilst loading project from " + choice,
- "Couldn't load project", JOptionPane.WARNING_MESSAGE);
+ MessageManager.formatMessage("label.error_whilst_loading_project_from", new String[]{choice}),
+ MessageManager.getString("label.couldnt_load_project"), JOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
}
@@ -1480,8 +1604,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
if (fileLoadingCount == 0)
{
- fileLoadingPanels.add(addProgressPanel("Loading File: " + fileName
- + " "));
+ fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage("label.loading_file", new String[]{fileName})));
}
fileLoadingCount++;
}
@@ -1515,13 +1638,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
if (progressPanel != null)
{
- progressPanel.remove(progbar);
- GridLayout gl = (GridLayout) progressPanel.getLayout();
- gl.setRows(gl.getRows() - 1);
- if (--totalProgressCount < 1)
+ synchronized (progressPanel)
{
- this.getContentPane().remove(progressPanel);
- progressPanel = null;
+ progressPanel.remove(progbar);
+ GridLayout gl = (GridLayout) progressPanel.getLayout();
+ gl.setRows(gl.getRows() - 1);
+ if (--totalProgressCount < 1)
+ {
+ this.getContentPane().remove(progressPanel);
+ progressPanel = null;
+ }
}
}
validate();
@@ -1532,9 +1658,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
fileLoadingCount--;
if (fileLoadingCount < 1)
{
- for (JPanel flp : fileLoadingPanels)
+ while (fileLoadingPanels.size() > 0)
{
- removeProgressPanel(flp);
+ removeProgressPanel(fileLoadingPanels.remove(0));
}
fileLoadingPanels.clear();
fileLoadingCount = 0;
@@ -1716,8 +1842,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Open a 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);
@@ -1726,10 +1853,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
String fle = chooser.getSelectedFile().toString();
if (!vamsasImport(chooser.getSelectedFile()))
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.couldnt_import_as_vamsas_session", new String[]{fle}),
- MessageManager.getString("label.vamsas_document_import_failed"),
- JOptionPane.ERROR_MESSAGE);
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.couldnt_import_as_vamsas_session",
+ new String[]
+ { fle }),
+ MessageManager
+ .getString("label.vamsas_document_import_failed"),
+ JOptionPane.ERROR_MESSAGE);
}
}
}
@@ -1802,22 +1935,22 @@ public class Desktop extends jalview.jbgui.GDesktop implements
return false;
}
- setProgressBar("Importing VAMSAS session from " + file.getName(),
+ setProgressBar(MessageManager.formatMessage("status.importing_vamsas_session_from", new String[]{file.getName()}),
file.hashCode());
try
{
v_client = new jalview.gui.VamsasApplication(this, file, null);
} catch (Exception ex)
{
- setProgressBar("Importing VAMSAS session from " + file.getName(),
- file.hashCode());
+ setProgressBar(MessageManager.formatMessage("status.importing_vamsas_session_from", new String[]{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("Importing VAMSAS session from " + file.getName(),
+ setProgressBar(MessageManager.formatMessage("status.importing_vamsas_session_from", new String[]{file.getName()}),
file.hashCode());
return v_client.inSession();
}
@@ -1826,12 +1959,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
if (v_client != null)
{
- throw new Error(
- "Trying to join a vamsas session when another is already connected.");
+ throw new Error(MessageManager.getString("error.try_join_vamsas_session_another"));
}
if (mysesid == null)
{
- throw new Error("Invalid vamsas session id.");
+ throw new Error(MessageManager.getString("error.invalid_vamsas_session_id"));
}
v_client = new VamsasApplication(this, mysesid);
setupVamsasConnectedGui();
@@ -1883,7 +2015,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
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"));
}
public void vamsasStop_actionPerformed(ActionEvent e)
@@ -1919,7 +2052,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
JMenuItem sessit = new JMenuItem();
sessit.setText(sess[i]);
- sessit.setToolTipText(MessageManager.formatMessage("label.connect_to_session", new String[]{sess[i]}));
+ sessit.setToolTipText(MessageManager.formatMessage(
+ "label.connect_to_session", new String[]
+ { sess[i] }));
final Desktop dsktp = this;
final String mysesid = sess[i];
sessit.addActionListener(new ActionListener()
@@ -1975,15 +2110,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{ "Vamsas Document" }, "Vamsas Document");
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save Vamsas Document Archive");
+ chooser.setDialogTitle(MessageManager.getString("label.save_vamsas_document_archive"));
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
java.io.File choice = chooser.getSelectedFile();
- JPanel progpanel = addProgressPanel("Saving VAMSAS Document to "
- + choice.getName());
+ JPanel progpanel = addProgressPanel(MessageManager.formatMessage("label.saving_vamsas_doc", new String[]{choice.getName()}));
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
String warnmsg = null;
String warnttl = null;
@@ -2035,7 +2169,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
if (b)
{
- vamUpdate = this.addProgressPanel("Updating vamsas session");
+ vamUpdate = this.addProgressPanel(MessageManager.getString("label.updating_vamsas_session"));
}
vamsasStart.setVisible(!b);
vamsasStop.setVisible(!b);
@@ -2137,12 +2271,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements
if (showMemoryUsage && g != null && df != null)
{
if (percentUsage < 20)
+ {
g.setColor(Color.red);
+ }
FontMetrics fm = g.getFontMetrics();
if (fm != null)
{
- g.drawString(
- MessageManager.formatMessage("label.memory_stats", new String[]{df.format(totalFreeMemory),df.format(maxMemory),df.format(percentUsage)}), 10,
+ g.drawString(MessageManager.formatMessage(
+ "label.memory_stats",
+ new String[]
+ { df.format(totalFreeMemory), df.format(maxMemory),
+ df.format(percentUsage) }), 10,
getHeight() - fm.getHeight());
}
}
@@ -2218,7 +2357,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
return afs;
}
- public AppJmol[] getJmols()
+ public GStructureViewer[] getJmols()
{
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
@@ -2234,7 +2373,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
if (frames[i] instanceof AppJmol)
{
- AppJmol af = (AppJmol) frames[i];
+ GStructureViewer af = (GStructureViewer) frames[i];
avp.addElement(af);
}
}
@@ -2246,10 +2385,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
return null;
}
- AppJmol afs[] = new AppJmol[avp.size()];
+ GStructureViewer afs[] = new GStructureViewer[avp.size()];
for (int i = 0, j = avp.size(); i < j; i++)
{
- afs[i] = (AppJmol) avp.elementAt(i);
+ afs[i] = (GStructureViewer) avp.elementAt(i);
}
avp.clear();
return afs;
@@ -2263,8 +2402,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
// use reflection to avoid creating compilation dependency.
if (!jalview.bin.Cache.groovyJarsPresent())
{
- throw new Error(
- "Implementation Error. Cannot create groovyShell without Groovy on the classpath!");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_create_groovyshell"));
}
try
{
@@ -2286,8 +2424,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
.showInternalMessageDialog(
Desktop.desktop,
- "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.",
- "Jalview Groovy Support Failed",
+ MessageManager.getString("label.couldnt_create_groovy_shell"),
+ MessageManager.getString("label.groovy_support_failed"),
JOptionPane.ERROR_MESSAGE);
}
}
@@ -2338,14 +2476,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
{
- throw new Error(
- "call setProgressBar before registering the progress bar's handler.");
+ throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
}
progressBarHandlers.put(new Long(id), handler);
- final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+ final JPanel progressPanel = progressBars.get(new Long(id));
if (handler.canCancel())
{
- JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+ JButton cancel = new JButton(
+ MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
cancel.addActionListener(new ActionListener()
{
@@ -2353,10 +2491,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar(
- "Cancelled "
- + ((JLabel) progressPanel.getComponent(0))
- .getText(), id);
+ us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
@@ -2443,15 +2578,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements
// JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
if (true)
{
- // todo: changesupport handlers need to be transferred
- if (discoverer == null)
- {
- discoverer = new jalview.ws.jws1.Discoverer();
- // register PCS handler for desktop.
- discoverer.addPropertyChangeListener(changeSupport);
- }
- // JAL-940 - disabled JWS1 service configuration - always start discoverer
- // until we phase out completely
+ // todo: changesupport handlers need to be transferred
+ if (discoverer == null)
+ {
+ discoverer = new jalview.ws.jws1.Discoverer();
+ // register PCS handler for desktop.
+ discoverer.addPropertyChangeListener(changeSupport);
+ }
+ // JAL-940 - disabled JWS1 service configuration - always start discoverer
+ // until we phase out completely
(t0 = new Thread(discoverer)).start();
}
@@ -2564,7 +2699,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
+ ermsg
+ ""
+ "It may be that you have invalid JABA URLs
in your web service preferences,"
- + " or mis-configured HTTP proxy settings.
"
+ + "
or as a command-line argument, or mis-configured HTTP proxy settings."
+ "Check the Connections and Web services tab
of the"
+ " Tools->Preferences dialog box to change them.