Version "
+ + jalview.bin.Cache.getProperty("VERSION")
+ + "; last updated: "
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+ }
+
+ if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals(
+ "Checking"))
+ {
+ message.append("
...Checking latest version...");
+ }
+ else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
+ .equals(jalview.bin.Cache.getProperty("VERSION")))
+ {
+ boolean red = false;
+ if (jalview.bin.Cache.getProperty("VERSION").toLowerCase()
+ .indexOf("automated build") == -1)
+ {
+ red = true;
+ // Displayed when code version and jnlp version do not match and code
+ // version is not a development build
+ message.append("");
+ }
+
+ message.append("
!! Version "
+ + jalview.bin.Cache.getDefault("LATEST_VERSION",
+ "..Checking..")
+ + " is available for download from "
+ + jalview.bin.Cache.getDefault("www.jalview.org",
+ "http://www.jalview.org") + " !!");
+ if (red)
+ {
+ message.append("
");
+ }
+ }
+ message.append("
Authors: "
+ + jalview.bin.Cache
+ .getDefault("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"
+ + "");
+ return message;
+ }
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void documentationMenuItem_actionPerformed(ActionEvent e)
{
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)
{
}
}
+ @Override
public void closeAll_actionPerformed(ActionEvent e)
{
+ // TODO show a progress bar while closing?
JInternalFrame[] frames = desktop.getAllFrames();
for (int i = 0; i < frames.length; i++)
{
@@ -668,19 +1311,33 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
}
}
+ Jalview.setCurrentAlignFrame(null);
System.out.println("ALL CLOSED");
- if (v_client!=null)
+ if (v_client != null)
{
// TODO clear binding to vamsas document objects on close_all
-
}
+
+ /*
+ * reset state of singleton objects as appropriate (clear down session state
+ * when all windows are closed)
+ */
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(this);
+ if (ssm != null)
+ {
+ ssm.resetAll();
+ }
+ System.gc();
}
+ @Override
public void raiseRelated_actionPerformed(ActionEvent e)
{
reorderAssociatedWindows(false, false);
}
+ @Override
public void minimizeAssociated_actionPerformed(ActionEvent e)
{
reorderAssociatedWindows(true, false);
@@ -694,8 +1351,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
/*
* (non-Javadoc)
*
- * @see jalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.ActionEvent)
+ * @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.
+ * ActionEvent)
*/
+ @Override
protected void garbageCollect_actionPerformed(ActionEvent e)
{
// We simply collect the garbage
@@ -707,13 +1366,45 @@ public class Desktop extends jalview.jbgui.GDesktop implements
/*
* (non-Javadoc)
*
- * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent)
+ * @see
+ * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
+ * )
*/
+ @Override
protected void showMemusage_actionPerformed(ActionEvent e)
{
desktop.showMemoryUsage(showMemusage.isSelected());
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent
+ * )
+ */
+ @Override
+ protected void showConsole_actionPerformed(ActionEvent e)
+ {
+ showConsole(showConsole.isSelected());
+ }
+
+ Console jconsole = null;
+
+ /**
+ * control whether the java console is visible or not
+ *
+ * @param selected
+ */
+ void showConsole(boolean selected)
+ {
+ showConsole.setSelected(selected);
+ // TODO: decide if we should update properties file
+ Cache.setProperty("SHOW_JAVA_CONSOLE", Boolean.valueOf(selected)
+ .toString());
+ jconsole.setVisible(selected);
+ }
+
void reorderAssociatedWindows(boolean minimize, boolean close)
{
JInternalFrame[] frames = desktop.getAllFrames();
@@ -722,7 +1413,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
return;
}
- AlignViewport source = null, target = null;
+ AlignmentViewport source = null, target = null;
if (frames[0] instanceof AlignFrame)
{
source = ((AlignFrame) frames[0]).getCurrentView();
@@ -795,8 +1486,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
protected void preferences_actionPerformed(ActionEvent e)
{
new Preferences();
@@ -806,54 +1498,132 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void saveState_actionPerformed(ActionEvent e)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"), new String[]
- { "jar" }, new String[]
- { "Jalview Project" }, "Jalview Project");
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "jvp" }, new String[] { "Jalview Project" },
+ "Jalview Project");
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save State");
+ chooser.setDialogTitle(MessageManager.getString("label.save_state"));
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- java.io.File choice = chooser.getSelectedFile();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- new Jalview2XML().SaveState(choice);
+ final Desktop me = this;
+ final java.io.File choice = chooser.getSelectedFile();
+ setProjectFile(choice);
+
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ // TODO: refactor to Jalview desktop session controller action.
+ setProgressBar(MessageManager.formatMessage(
+ "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
+ // TODO prevent user from messing with the Desktop whilst we're saving
+ try
+ {
+ new Jalview2XML().saveState(choice);
+ } catch (OutOfMemoryError 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);
+ JOptionPane.showMessageDialog(me, MessageManager.formatMessage(
+ "label.error_whilst_saving_current_state_to",
+ new Object[] { choice.getName() }), MessageManager
+ .getString("label.couldnt_save_project"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ setProgressBar(null, choice.hashCode());
+ }
+ }).start();
}
}
+ private void setProjectFile(File choice)
+ {
+ this.projectFile = choice;
+ }
+
+ public File getProjectFile()
+ {
+ return this.projectFile;
+ }
+
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void loadState_actionPerformed(ActionEvent e)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"), new String[]
- { "jar" }, new String[]
- { "Jalview Project" }, "Jalview Project");
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
+ "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)
{
- String choice = chooser.getSelectedFile().getAbsolutePath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
- new Jalview2XML().LoadJalviewAlign(choice);
+ final File selectedFile = chooser.getSelectedFile();
+ setProjectFile(selectedFile);
+ final String choice = selectedFile.getAbsolutePath();
+ jalview.bin.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());
+ try
+ {
+ new Jalview2XML().loadJalviewAlign(choice);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Whilst loading project from " + choice, oom);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Problems whilst loading project from "
+ + choice, ex);
+ JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage(
+ "label.error_whilst_loading_project_from",
+ new Object[] { choice }), MessageManager
+ .getString("label.couldnt_load_project"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ setProgressBar(null, choice.hashCode());
+ }
+ }).start();
}
}
+ @Override
public void inputSequence_actionPerformed(ActionEvent e)
{
new SequenceFetcher(this);
@@ -861,47 +1631,57 @@ public class Desktop extends jalview.jbgui.GDesktop implements
JPanel progressPanel;
+ ArrayList fileLoadingPanels = new ArrayList();
+
public void startLoading(final String fileName)
{
if (fileLoadingCount == 0)
{
- addProgressPanel("Loading File: " + fileName + " ");
-
+ fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage(
+ "label.loading_file", new Object[] { fileName })));
}
fileLoadingCount++;
}
- private JProgressBar addProgressPanel(String string)
+ private JPanel addProgressPanel(String string)
{
if (progressPanel == null)
{
- progressPanel = new JPanel(new BorderLayout());
+ progressPanel = new JPanel(new GridLayout(1, 1));
totalProgressCount = 0;
+ instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
}
+ JPanel thisprogress = new JPanel(new BorderLayout(10, 5));
JProgressBar progressBar = new JProgressBar();
progressBar.setIndeterminate(true);
- progressPanel.add(new JLabel(string), BorderLayout.WEST);
+ thisprogress.add(new JLabel(string), BorderLayout.WEST);
- progressPanel.add(progressBar, BorderLayout.CENTER);
-
- instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
- totalProgressCount++;
- validate();
- return progressBar;
+ thisprogress.add(progressBar, BorderLayout.CENTER);
+ progressPanel.add(thisprogress);
+ ((GridLayout) progressPanel.getLayout())
+ .setRows(((GridLayout) progressPanel.getLayout()).getRows() + 1);
+ ++totalProgressCount;
+ instance.validate();
+ return thisprogress;
}
int totalProgressCount = 0;
- private void removeProgressPanel(JProgressBar progbar)
+ private void removeProgressPanel(JPanel progbar)
{
if (progressPanel != null)
{
- progressPanel.remove(progbar);
- 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();
@@ -912,106 +1692,113 @@ public class Desktop extends jalview.jbgui.GDesktop implements
fileLoadingCount--;
if (fileLoadingCount < 1)
{
- if (progressPanel != null)
+ while (fileLoadingPanels.size() > 0)
{
- this.getContentPane().remove(progressPanel);
- progressPanel = null;
+ removeProgressPanel(fileLoadingPanels.remove(0));
}
+ fileLoadingPanels.clear();
fileLoadingCount = 0;
}
validate();
}
- public static int getViewCount(String viewId)
+ public static int getViewCount(String alignmentId)
{
- AlignViewport[] aps = getViewports(viewId);
- return (aps==null) ? 0 : aps.length;
+ AlignmentViewport[] aps = getViewports(alignmentId);
+ return (aps == null) ? 0 : aps.length;
}
+
/**
*
- * @param viewId
- * @return all AlignmentPanels concerning the viewId sequence set
+ * @param alignmentId
+ * - if null, all sets are returned
+ * @return all AlignmentPanels concerning the alignmentId sequence set
*/
- public static AlignmentPanel[] getAlignmentPanels(String viewId)
+ public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
{
- int count = 0;
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- ArrayList aps = new ArrayList();
- for (int t = 0; t < frames.length; t++)
+ if (Desktop.desktop == null)
+ {
+ // no frames created and in headless mode
+ // TODO: verify that frames are recoverable when in headless mode
+ return null;
+ }
+ List aps = new ArrayList();
+ AlignFrame[] frames = getAlignFrames();
+ if (frames == null)
+ {
+ return null;
+ }
+ for (AlignFrame af : frames)
{
- if (frames[t] instanceof AlignFrame)
+ for (AlignmentPanel ap : af.alignPanels)
{
- AlignFrame af = (AlignFrame) frames[t];
- for (int a = 0; a < af.alignPanels.size(); a++)
+ if (alignmentId == null
+ || alignmentId.equals(ap.av.getSequenceSetId()))
{
- if (viewId
- .equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av
- .getSequenceSetId()))
- {
- aps.add(af.alignPanels.elementAt(a));
- }
+ aps.add(ap);
}
}
}
- if (aps.size()==0)
+ if (aps.size() == 0)
{
return null;
}
- AlignmentPanel[] vap = new AlignmentPanel[aps.size()];
- for (int t=0;t viewp = new ArrayList();
if (desktop != null)
{
- javax.swing.JInternalFrame[] frames = instance.getAllFrames();
-
- for (int t = 0; t < frames.length; t++)
+ AlignFrame[] frames = Desktop.getAlignFrames();
+
+ for (AlignFrame afr : frames)
{
- if (frames[t] instanceof AlignFrame)
+ if (sequenceSetId == null
+ || afr.getViewport().getSequenceSetId()
+ .equals(sequenceSetId))
{
- AlignFrame afr = ((AlignFrame) frames[t]);
- if (afr.getViewport().getSequenceSetId()
- .equals(sequenceSetId))
+ if (afr.alignPanels != null)
{
- if (afr.alignPanels!=null)
+ for (AlignmentPanel ap : afr.alignPanels)
{
- for (int a = 0; a < afr.alignPanels.size(); a++)
+ if (sequenceSetId == null
+ || sequenceSetId.equals(ap.av.getSequenceSetId()))
{
- if (sequenceSetId
- .equals(((AlignmentPanel) afr.alignPanels.elementAt(a)).av
- .getSequenceSetId()))
- {
- viewp.addElement(((AlignmentPanel)afr.alignPanels.elementAt(a)).av);
- }
+ viewp.add(ap.av);
}
- } else {
- viewp.addElement(((AlignFrame) frames[t]).getViewport());
}
}
+ else
+ {
+ viewp.add(afr.getViewport());
+ }
}
}
if (viewp.size() > 0)
{
- AlignViewport[] vp = new AlignViewport[viewp.size()];
- viewp.copyInto(vp);
- return vp;
+ return viewp.toArray(new AlignmentViewport[viewp.size()]);
}
}
return null;
}
- public void explodeViews(AlignFrame af)
+ /**
+ * Explode the views in the given frame into separate AlignFrame
+ *
+ * @param af
+ */
+ public static void explodeViews(AlignFrame af)
{
int size = af.alignPanels.size();
if (size < 2)
@@ -1021,15 +1808,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements
for (int i = 0; i < size; i++)
{
- AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(i);
+ AlignmentPanel ap = af.alignPanels.get(i);
AlignFrame newaf = new AlignFrame(ap);
- if (ap.av.explodedPosition != null
- && !ap.av.explodedPosition.equals(af.getBounds()))
+
+ /*
+ * Restore the view's last exploded frame geometry if known. Multiple
+ * views from one exploded frame share and restore the same (frame)
+ * position and size.
+ */
+ Rectangle geometry = ap.av.getExplodedGeometry();
+ if (geometry != null)
{
- newaf.setBounds(ap.av.explodedPosition);
+ newaf.setBounds(geometry);
}
- ap.av.gatherViewsHere = false;
+ ap.av.setGatherViewsHere(false);
addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
@@ -1040,12 +1833,20 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
+ /**
+ * Gather expanded views (separate AlignFrame's) with the same sequence set
+ * identifier back in to this frame as additional views, and close the
+ * expanded views. Note the expanded frames may themselves have multiple
+ * views. We take the lot.
+ *
+ * @param source
+ */
public void gatherViews(AlignFrame source)
{
- source.viewport.gatherViewsHere = true;
- source.viewport.explodedPosition = source.getBounds();
+ source.viewport.setGatherViewsHere(true);
+ source.viewport.setExplodedGeometry(source.getBounds());
JInternalFrame[] frames = desktop.getAllFrames();
- String viewId = source.viewport.sequenceSetID;
+ String viewId = source.viewport.getSequenceSetId();
for (int t = 0; t < frames.length; t++)
{
@@ -1055,12 +1856,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
boolean gatherThis = false;
for (int a = 0; a < af.alignPanels.size(); a++)
{
- AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a);
+ AlignmentPanel ap = af.alignPanels.get(a);
if (viewId.equals(ap.av.getSequenceSetId()))
{
gatherThis = true;
- ap.av.gatherViewsHere = false;
- ap.av.explodedPosition = af.getBounds();
+ ap.av.setGatherViewsHere(false);
+ ap.av.setExplodedGeometry(af.getBounds());
source.addAlignmentPanel(ap, false);
}
}
@@ -1077,36 +1878,38 @@ public class Desktop extends jalview.jbgui.GDesktop implements
jalview.gui.VamsasApplication v_client = null;
+ @Override
public void vamsasImport_actionPerformed(ActionEvent e)
{
if (v_client == null)
{
// Load and try to start a session.
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"));
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Open a saved VAMSAS session");
- chooser
- .setToolTipText("select a vamsas session to be opened as a 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);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- try
- {
- v_client = new jalview.gui.VamsasApplication(this, chooser
- .getSelectedFile());
- } catch (Exception ex)
+ String fle = chooser.getSelectedFile().toString();
+ if (!vamsasImport(chooser.getSelectedFile()))
{
- jalview.bin.Cache.log.error(
- "New vamsas session from existing session file failed:",
- ex);
- return;
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.couldnt_import_as_vamsas_session",
+ new Object[] { fle }),
+ MessageManager
+ .getString("label.vamsas_document_import_failed"),
+ JOptionPane.ERROR_MESSAGE);
}
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
}
}
else
@@ -1116,6 +1919,111 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
+ /**
+ * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
+ *
+ * @param file
+ * @return true if import was a success and a session was started.
+ */
+ public boolean vamsasImport(URL url)
+ {
+ // TODO: create progress bar
+ if (v_client != null)
+ {
+
+ jalview.bin.Cache.log
+ .error("Implementation error - load session from a running session is not supported.");
+ return false;
+ }
+
+ try
+ {
+ // copy the URL content to a temporary local file
+ // TODO: be a bit cleverer here with nio (?!)
+ File file = File.createTempFile("vdocfromurl", ".vdj");
+ FileOutputStream fos = new FileOutputStream(file);
+ BufferedInputStream bis = new BufferedInputStream(url.openStream());
+ byte[] buffer = new byte[2048];
+ int ln;
+ while ((ln = bis.read(buffer)) > -1)
+ {
+ fos.write(buffer, 0, ln);
+ }
+ bis.close();
+ fos.close();
+ v_client = new jalview.gui.VamsasApplication(this, file,
+ url.toExternalForm());
+ } catch (Exception ex)
+ {
+ jalview.bin.Cache.log.error(
+ "Failed to create new vamsas session from contents of URL "
+ + url, ex);
+ return false;
+ }
+ setupVamsasConnectedGui();
+ v_client.initial_update(); // TODO: thread ?
+ return v_client.inSession();
+ }
+
+ /**
+ * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
+ *
+ * @param file
+ * @return true if import was a success and a session was started.
+ */
+ public boolean vamsasImport(File file)
+ {
+ if (v_client != null)
+ {
+
+ 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());
+ 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());
+ 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());
+ return v_client.inSession();
+ }
+
+ public boolean joinVamsasSession(String mysesid)
+ {
+ if (v_client != null)
+ {
+ throw new Error(
+ MessageManager
+ .getString("error.try_join_vamsas_session_another"));
+ }
+ if (mysesid == null)
+ {
+ throw new Error(
+ MessageManager.getString("error.invalid_vamsas_session_id"));
+ }
+ v_client = new VamsasApplication(this, mysesid);
+ setupVamsasConnectedGui();
+ v_client.initial_update();
+ return (v_client.inSession());
+ }
+
+ @Override
public void vamsasStart_actionPerformed(ActionEvent e)
{
if (v_client == null)
@@ -1134,7 +2042,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
*
* if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
* jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
- *
*/
v_client = new VamsasApplication(this);
setupVamsasConnectedGui();
@@ -1149,11 +2056,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
protected void setupVamsasConnectedGui()
{
- vamsasStart.setText("Session Update");
+ vamsasStart.setText(MessageManager.getString("label.session_update"));
vamsasSave.setVisible(true);
vamsasStop.setVisible(true);
vamsasImport.setVisible(false); // Document import to existing session is
- // not possible for vamsas-client-1.0.
+ // not possible for vamsas-client-1.0.
}
protected void setupVamsasDisconnectedGui()
@@ -1161,9 +2068,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
vamsasSave.setVisible(false);
vamsasStop.setVisible(false);
vamsasImport.setVisible(true);
- vamsasStart.setText("New Vamsas Session");
+ vamsasStart.setText(MessageManager
+ .getString("label.new_vamsas_session"));
}
+ @Override
public void vamsasStop_actionPerformed(ActionEvent e)
{
if (v_client != null)
@@ -1197,12 +2106,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
JMenuItem sessit = new JMenuItem();
sessit.setText(sess[i]);
- sessit.setToolTipText("Connect to session " + 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()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
if (dsktp.v_client == null)
@@ -1210,6 +2121,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
Thread rthr = new Thread(new Runnable()
{
+ @Override
public void run()
{
dsktp.v_client = new VamsasApplication(dsktp, mysesid);
@@ -1242,24 +2154,28 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
+ @Override
public void vamsasSave_actionPerformed(ActionEvent e)
{
if (v_client != null)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"), new String[]
- { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
- new String[]
- { "Vamsas Document" }, "Vamsas Document");
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+ { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+ new String[] { "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(MessageManager.formatMessage(
+ "label.saving_vamsas_doc",
+ new Object[] { choice.getName() }));
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
String warnmsg = null;
String warnttl = null;
@@ -1281,6 +2197,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
+ choice, ex);
}
+ removeProgressPanel(progpanel);
if (warnmsg != null)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -1291,13 +2208,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
- JProgressBar vamUpdate = null;
+ JPanel vamUpdate = null;
/**
* hide vamsas user gui bits when a vamsas document event is being handled.
*
* @param b
- * true to hide gui, false to reveal gui
+ * true to hide gui, false to reveal gui
*/
public void setVamsasUpdate(boolean b)
{
@@ -1310,7 +2227,8 @@ 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);
@@ -1345,6 +2263,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
public class MyDesktopPane extends JDesktopPane implements Runnable
{
+ private static final float ONE_MB = 1048576f;
+
boolean showMemoryUsage = false;
Runtime runtime;
@@ -1359,10 +2279,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
showMemoryUsage(showMemoryUsage);
}
- public void showMemoryUsage(boolean showMemoryUsage)
+ public void showMemoryUsage(boolean showMemory)
{
- this.showMemoryUsage = showMemoryUsage;
- if (showMemoryUsage)
+ this.showMemoryUsage = showMemory;
+ if (showMemory)
{
Thread worker = new Thread(this);
worker.start();
@@ -1374,6 +2294,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
return showMemoryUsage;
}
+ @Override
public void run()
{
df = java.text.NumberFormat.getNumberInstance();
@@ -1384,10 +2305,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
try
{
- Thread.sleep(3000);
- maxMemory = runtime.maxMemory() / 1048576f;
- allocatedMemory = runtime.totalMemory() / 1048576f;
- freeMemory = runtime.freeMemory() / 1048576f;
+ maxMemory = runtime.maxMemory() / ONE_MB;
+ allocatedMemory = runtime.totalMemory() / ONE_MB;
+ freeMemory = runtime.freeMemory() / ONE_MB;
totalFreeMemory = freeMemory + (maxMemory - allocatedMemory);
percentUsage = (totalFreeMemory / maxMemory) * 100;
@@ -1399,7 +2319,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
// instance.set.setBorder(border1);
}
repaint();
-
+ // sleep after showing usage
+ Thread.sleep(3000);
} catch (Exception ex)
{
ex.printStackTrace();
@@ -1407,46 +2328,96 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
+ @Override
public void paintComponent(Graphics g)
{
- if (showMemoryUsage)
+ if (showMemoryUsage && g != null && df != null)
{
if (percentUsage < 20)
+ {
g.setColor(Color.red);
-
- g.drawString("Total Free Memory: " + df.format(totalFreeMemory)
- + "MB; Max Memory: " + df.format(maxMemory) + "MB; "
- + df.format(percentUsage) + "%", 10, getHeight()
- - g.getFontMetrics().getHeight());
+ }
+ 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());
+ }
}
}
+ }
+
+ /**
+ * fixes stacking order after a modal dialog to ensure windows that should be
+ * on top actually are
+ */
+ public void relayerWindows()
+ {
}
protected JMenuItem groovyShell;
- public void doGroovyCheck()
+ /**
+ * Accessor method to quickly get all the AlignmentFrames loaded.
+ *
+ * @return an array of AlignFrame, or null if none found
+ */
+ public static AlignFrame[] getAlignFrames()
{
- if (jalview.bin.Cache.groovyJarsPresent())
+ if (Jalview.isHeadlessMode())
+ {
+ // Desktop.desktop is null in headless mode
+ return new AlignFrame[] { Jalview.currentAlignFrame };
+ }
+
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+ if (frames == null)
+ {
+ return null;
+ }
+ List avp = new ArrayList();
+ // REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
{
- groovyShell = new JMenuItem();
- groovyShell.setText("Groovy Console...");
- groovyShell.addActionListener(new ActionListener()
+ if (frames[i] instanceof AlignFrame)
{
- public void actionPerformed(ActionEvent e)
+ avp.add((AlignFrame) frames[i]);
+ }
+ else if (frames[i] instanceof SplitFrame)
+ {
+ /*
+ * Also check for a split frame containing an AlignFrame
+ */
+ GSplitFrame sf = (GSplitFrame) frames[i];
+ if (sf.getTopFrame() instanceof AlignFrame)
{
- groovyShell_actionPerformed(e);
+ avp.add((AlignFrame) sf.getTopFrame());
}
- });
- toolsMenu.add(groovyShell);
- groovyShell.setVisible(true);
+ if (sf.getBottomFrame() instanceof AlignFrame)
+ {
+ avp.add((AlignFrame) sf.getBottomFrame());
+ }
+ }
+ }
+ if (avp.size() == 0)
+ {
+ return null;
}
+ AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]);
+ return afs;
}
/**
- * Accessor method to quickly get all the AlignmentFrames loaded.
+ * Returns an array of any AppJmol frames in the Desktop (or null if none).
+ *
+ * @return
*/
- public static AlignFrame[] getAlignframes()
+ public GStructureViewer[] getJmols()
{
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
@@ -1454,149 +2425,847 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
return null;
}
- Vector avp = new Vector();
- try
+ List avp = new ArrayList();
+ // REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
{
- // REVERSE ORDER
- for (int i = frames.length - 1; i > -1; i--)
+ if (frames[i] instanceof AppJmol)
{
- if (frames[i] instanceof AlignFrame)
- {
- AlignFrame af = (AlignFrame) frames[i];
- avp.addElement(af);
- }
+ GStructureViewer af = (GStructureViewer) frames[i];
+ avp.add(af);
}
- } catch (Exception ex)
- {
- ex.printStackTrace();
}
if (avp.size() == 0)
{
return null;
}
- AlignFrame afs[] = new AlignFrame[avp.size()];
- for (int i = 0, j = avp.size(); i < j; i++)
- {
- afs[i] = (AlignFrame) avp.elementAt(i);
- }
- avp.clear();
+ GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]);
return afs;
}
/**
* Add Groovy Support to Jalview
*/
- public void groovyShell_actionPerformed(ActionEvent e)
+ public void groovyShell_actionPerformed()
{
- // 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!");
- }
try
{
- Class gcClass = Desktop.class.getClassLoader().loadClass(
- "groovy.ui.Console");
- Constructor gccons = gcClass.getConstructor(null);
- java.lang.reflect.Method setvar = gcClass.getMethod("setVariable",
- new Class[]
- { String.class, Object.class });
- java.lang.reflect.Method run = gcClass.getMethod("run", null);
- Object gc = gccons.newInstance(null);
- setvar.invoke(gc, new Object[]
- { "Jalview", this });
- run.invoke(gc, null);
+ openGroovyConsole();
} catch (Exception ex)
{
jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.",
- "Jalview Groovy Support Failed",
- JOptionPane.ERROR_MESSAGE);
+ MessageManager.getString("label.couldnt_create_groovy_shell"),
+ MessageManager.getString("label.groovy_support_failed"),
+ JOptionPane.ERROR_MESSAGE);
}
}
/**
- * Progress bars managed by the IProgressIndicator method.
- */
- private Hashtable progressBars, progressBarHandlers;
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+ * Open the Groovy console
*/
- public void setProgressBar(String message, long id)
+ void openGroovyConsole()
{
- if (progressBars == null)
+ if (groovyConsole == null)
{
- progressBars = new Hashtable();
- progressBarHandlers = new Hashtable();
- }
+ groovyConsole = new groovy.ui.Console();
+ groovyConsole.setVariable("Jalview", this);
+ groovyConsole.run();
- if (progressBars.get(new Long(id)) != null)
- {
- JProgressBar progressPanel = (JProgressBar) progressBars
- .remove(new Long(id));
- if (progressBarHandlers.contains(new Long(id)))
+ /*
+ * We allow only one console at a time, so that AlignFrame menu option
+ * 'Calculate | Run Groovy script' is unambiguous.
+ * Disable 'Groovy Console', and enable 'Run script', when the console is
+ * opened, and the reverse when it is closed
+ */
+ Window window = (Window) groovyConsole.getFrame();
+ window.addWindowListener(new WindowAdapter()
{
- progressBarHandlers.remove(new Long(id));
- }
- removeProgressPanel(progressPanel);
- }
- else
- {
- progressBars.put(new Long(id), addProgressPanel(message));
+ @Override
+ public void windowClosed(WindowEvent e)
+ {
+ /*
+ * rebind CMD-Q from Groovy Console to Jalview Quit
+ */
+ addQuitHandler();
+ enableExecuteGroovy(false);
+ }
+ });
}
- }
- /* (non-Javadoc)
- * @see jalview.gui.IProgressIndicator#registerHandler(long, jalview.gui.IProgressIndicatorHandler)
- */
- public void registerHandler(final long id, final IProgressIndicatorHandler handler)
- {
- if (progressBarHandlers==null || !progressBars.contains(new Long(id)))
+
+ /*
+ * show Groovy console window (after close and reopen)
+ */
+ ((Window) groovyConsole.getFrame()).setVisible(true);
+
+ /*
+ * if we got this far, enable 'Run Groovy' in AlignFrame menus
+ * and disable opening a second console
+ */
+ enableExecuteGroovy(true);
+ }
+
+ /**
+ * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this
+ * binding when opened
+ */
+ protected void addQuitHandler()
+ {
+ getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
+ KeyStroke.getKeyStroke(KeyEvent.VK_Q, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()),
+ "Quit");
+ getRootPane().getActionMap().put("Quit", new AbstractAction()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ quit();
+ }
+ });
+ }
+
+ /**
+ * Enable or disable 'Run Groovy script' in AlignFrame calculate menus
+ *
+ * @param enabled
+ * true if Groovy console is open
+ */
+ public void enableExecuteGroovy(boolean enabled)
+ {
+ /*
+ * disable opening a second Groovy console
+ * (or re-enable when the console is closed)
+ */
+ groovyShell.setEnabled(!enabled);
+
+ AlignFrame[] alignFrames = getAlignFrames();
+ if (alignFrames != null)
+ {
+ for (AlignFrame af : alignFrames)
+ {
+ af.setGroovyEnabled(enabled);
+ }
+ }
+ }
+
+ /**
+ * Progress bars managed by the IProgressIndicator method.
+ */
+ private Hashtable progressBars;
+
+ private Hashtable progressBarHandlers;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+ */
+ @Override
+ public void setProgressBar(String message, long id)
+ {
+ if (progressBars == null)
+ {
+ progressBars = new Hashtable();
+ progressBarHandlers = new Hashtable();
+ }
+
+ if (progressBars.get(new Long(id)) != null)
+ {
+ JPanel panel = progressBars.remove(new Long(id));
+ if (progressBarHandlers.contains(new Long(id)))
+ {
+ progressBarHandlers.remove(new Long(id));
+ }
+ removeProgressPanel(panel);
+ }
+ else
+ {
+ progressBars.put(new Long(id), addProgressPanel(message));
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.gui.IProgressIndicator#registerHandler(long,
+ * jalview.gui.IProgressIndicatorHandler)
+ */
+ @Override
+ public void registerHandler(final long id,
+ final IProgressIndicatorHandler handler)
+ {
+ if (progressBarHandlers == null
+ || !progressBars.containsKey(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("Cancel");
- final IProgressIndicator us=this;
- cancel.addActionListener(new ActionListener() {
+ JButton cancel = new JButton(
+ MessageManager.getString("action.cancel"));
+ final IProgressIndicator us = this;
+ cancel.addActionListener(new ActionListener()
+ {
+ @Override
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 Object[] { ((JLabel) progressPanel.getComponent(0))
+ .getText() }), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
}
}
+
/**
- * This will return the first AlignFrame viewing AlignViewport av. It will
- * break if there are more than one AlignFrames viewing a particular av. This
*
- * @param av
- * @return alignFrame for av
+ * @return true if any progress bars are still active
*/
- public static AlignFrame getAlignFrameFor(AlignViewport av)
+ @Override
+ public boolean operationInProgress()
+ {
+ if (progressBars != null && progressBars.size() > 0)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * This will return the first AlignFrame holding the given viewport instance.
+ * It will break if there are more than one AlignFrames viewing a particular
+ * av.
+ *
+ * @param viewport
+ * @return alignFrame for viewport
+ */
+ public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
{
if (desktop != null)
{
- AlignmentPanel[] aps = getAlignmentPanels(av.getSequenceSetId());
- for (int panel=0;aps!=null && panel" + ermsg +
+ * " It may be that you have invalid JABA URLs in your web service preferences,"
+ * + " or mis-configured HTTP proxy settings. " +
+ * "Check the Connections and Web services tab of the"
+ * +
+ * " Tools->Preferences dialog box to change them. |