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...");
}
- // TODO: update this text for each release or centrally store it for lite
- // and application
- message
- .append("\nAuthors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,\n David Martin & Geoff Barton."
- + "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n"
- + "\nFor help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\n"
- + "\nIf you use Jalview, please cite:"
- + "\nWaterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
- + "\nJalview Version 2 - a multiple sequence alignment editor and analysis workbench"
- + "\nBioinformatics doi: 10.1093/bioinformatics/btp033");
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ 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.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
+ 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;
}
/**
@@ -963,24 +1347,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* @param e
* 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++)
{
@@ -991,19 +1372,33 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
}
}
+ Jalview.setCurrentAlignFrame(null);
System.out.println("ALL CLOSED");
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);
@@ -1020,6 +1415,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.
* ActionEvent)
*/
+ @Override
protected void garbageCollect_actionPerformed(ActionEvent e)
{
// We simply collect the garbage
@@ -1035,6 +1431,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
* )
*/
+ @Override
protected void showMemusage_actionPerformed(ActionEvent e)
{
desktop.showMemoryUsage(showMemusage.isSelected());
@@ -1047,6 +1444,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent
* )
*/
+ @Override
protected void showConsole_actionPerformed(ActionEvent e)
{
showConsole(showConsole.isSelected());
@@ -1063,8 +1461,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
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);
}
@@ -1076,7 +1474,7 @@ 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();
@@ -1151,6 +1549,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void preferences_actionPerformed(ActionEvent e)
{
new Preferences();
@@ -1162,108 +1561,191 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* @param e
* 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("jvp",
+ "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();
- JProgressBar progpanel = addProgressPanel("Saving jalview project "
- + choice.getName());
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- // TODO catch and handle errors for savestate
- new Jalview2XML().SaveState(choice);
- removeProgressPanel(progpanel);
+ 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);
+ 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());
+ }
+ }).start();
}
}
+ private void setProjectFile(File choice)
+ {
+ this.projectFile = choice;
+ }
+
+ public File getProjectFile()
+ {
+ return this.projectFile;
+ }
+
/**
* DOCUMENT ME!
*
* @param e
* 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(
+ 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();
- setProgressBar("loading jalview project "
- + chooser.getSelectedFile().getName(), choice.hashCode());
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
- new Jalview2XML().LoadJalviewAlign(choice);
- setProgressBar(null, choice.hashCode());
- }
- }
-
- public void inputSequence_actionPerformed(ActionEvent e)
- {
+ final File selectedFile = chooser.getSelectedFile();
+ setProjectFile(selectedFile);
+ final String choice = selectedFile.getAbsolutePath();
+ 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);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.error_whilst_loading_project_from",
+ new Object[]
+ { choice }),
+ MessageManager.getString("label.couldnt_load_project"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ setProgressBar(null, choice.hashCode());
+ }
+ }).start();
+ }
+ }
+
+ @Override
+ public void inputSequence_actionPerformed(ActionEvent e)
+ {
new SequenceFetcher(this);
}
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();
@@ -1274,51 +1756,50 @@ 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);
+ 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;
if (Desktop.desktop == null)
{
// no frames created and in headless mode
// TODO: verify that frames are recoverable when in headless mode
return null;
}
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- ArrayList aps = new ArrayList();
- for (int t = 0; t < frames.length; t++)
+ 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);
}
}
}
@@ -1326,11 +1807,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
return null;
}
- AlignmentPanel[] vap = new AlignmentPanel[aps.size()];
- for (int t = 0; t < vap.length; t++)
- {
- vap[t] = (AlignmentPanel) aps.get(t);
- }
+ AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]);
return vap;
}
@@ -1338,53 +1815,53 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* get all the viewports on an alignment.
*
* @param sequenceSetId
- * unique alignment id
+ * unique alignment id (may be null - all viewports returned in that
+ * case)
* @return all viewports on the alignment bound to sequenceSetId
*/
- public static AlignViewport[] getViewports(String sequenceSetId)
+ public static AlignmentViewport[] getViewports(String sequenceSetId)
{
- Vector viewp = new Vector();
+ List viewp = new ArrayList<>();
if (desktop != null)
{
- javax.swing.JInternalFrame[] frames = instance.getAllFrames();
+ AlignFrame[] frames = Desktop.getAlignFrames();
- for (int t = 0; t < frames.length; t++)
+ 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)
@@ -1394,15 +1871,21 @@ 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);
@@ -1413,12 +1896,20 @@ 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++)
{
@@ -1428,12 +1919,12 @@ 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);
}
}
@@ -1450,18 +1941,20 @@ 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);
@@ -1470,17 +1963,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements
String fle = chooser.getSelectedFile().toString();
if (!vamsasImport(chooser.getSelectedFile()))
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't import '" + fle + "' as a new vamsas session.",
- "Vamsas Document Import Failed",
- JOptionPane.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.");
}
}
@@ -1496,8 +1993,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
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;
}
@@ -1516,13 +2013,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
bis.close();
fos.close();
- v_client = new jalview.gui.VamsasApplication(this, file, url
- .toExternalForm());
+ 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);
+ + url,
+ ex);
return false;
}
setupVamsasConnectedGui();
@@ -1541,28 +2039,31 @@ public class Desktop extends jalview.jbgui.GDesktop implements
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("Importing VAMSAS session from " + file.getName(), file
- .hashCode());
+ 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("Importing VAMSAS session from " + file.getName(),
- file.hashCode());
+ 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("Importing VAMSAS session from " + file.getName(), file
- .hashCode());
+ setProgressBar(MessageManager.formatMessage(
+ "status.importing_vamsas_session_from", new Object[]
+ { file.getName() }), file.hashCode());
return v_client.inSession();
}
@@ -1570,12 +2071,13 @@ 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();
@@ -1583,6 +2085,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
return (v_client.inSession());
}
+ @Override
public void vamsasStart_actionPerformed(ActionEvent e)
{
if (v_client == null)
@@ -1615,7 +2118,7 @@ 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
@@ -1627,9 +2130,11 @@ 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)
@@ -1650,25 +2155,28 @@ public class Desktop extends jalview.jbgui.GDesktop implements
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("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)
@@ -1676,6 +2184,7 @@ 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);
@@ -1708,27 +2217,28 @@ 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");
+ // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+ JalviewFileChooser chooser = new JalviewFileChooser("vdj",
+ "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();
- JProgressBar progpanel = addProgressPanel("Saving VAMSAS Document to "
- + choice.getName());
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+ 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;
try
@@ -1738,29 +2248,29 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
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);
if (warnmsg != null)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- warnmsg, warnttl, JOptionPane.ERROR_MESSAGE);
+ warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
}
}
}
}
- JProgressBar vamUpdate = null;
+ JPanel vamUpdate = null;
/**
* hide vamsas user gui bits when a vamsas document event is being handled.
@@ -1770,7 +2280,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
*/
public void setVamsasUpdate(boolean b)
{
- jalview.bin.Cache.log.debug("Setting gui for Vamsas update "
+ Cache.log.debug("Setting gui for Vamsas update "
+ (b ? "in progress" : "finished"));
if (vamUpdate != null)
@@ -1779,7 +2289,8 @@ 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);
@@ -1804,6 +2315,85 @@ public class Desktop extends jalview.jbgui.GDesktop implements
new Thread(jvq).start();
}
+ public void checkURLLinks()
+ {
+ // Thread off the URL link checker
+ addDialogThread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ if (Cache.getDefault("CHECKURLLINKS", true))
+ {
+ // check what the actual links are - if it's just the default don't
+ // bother with the warning
+ List links = Preferences.sequenceUrlLinks
+ .getLinksForMenu();
+
+ // only need to check links if there is one with a
+ // SEQUENCE_ID which is not the default EMBL_EBI link
+ ListIterator li = links.listIterator();
+ boolean check = false;
+ List urls = new ArrayList<>();
+ while (li.hasNext())
+ {
+ String link = li.next();
+ if (link.contains(SEQUENCE_ID)
+ && !link.equals(UrlConstants.DEFAULT_STRING))
+ {
+ check = true;
+ int barPos = link.indexOf("|");
+ String urlMsg = barPos == -1 ? link
+ : link.substring(0, barPos) + ": "
+ + link.substring(barPos + 1);
+ urls.add(new JLabel(urlMsg));
+ }
+ }
+ if (!check)
+ {
+ return;
+ }
+
+ // ask user to check in case URL links use old style tokens
+ // ($SEQUENCE_ID$ for sequence id _or_ accession id)
+ 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"));
+ msgPanel.add(msg);
+ for (JLabel url : urls)
+ {
+ msgPanel.add(url);
+ }
+ msgPanel.add(msg2);
+
+ final JCheckBox jcb = new JCheckBox(
+ MessageManager.getString("label.do_not_display_again"));
+ jcb.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // update Cache settings for "don't show this again"
+ boolean showWarningAgain = !jcb.isSelected();
+ Cache.setProperty("CHECKURLLINKS",
+ Boolean.valueOf(showWarningAgain).toString());
+ }
+ });
+ msgPanel.add(jcb);
+
+ JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
+ MessageManager
+ .getString("label.SEQUENCE_ID_no_longer_used"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ }
+ });
+ }
+
/**
* Proxy class for JDesktopPane which optionally displays the current memory
* usage and highlights the desktop area with a red bar if free memory runs
@@ -1814,6 +2404,8 @@ 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;
@@ -1828,14 +2420,15 @@ 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();
}
+ repaint();
}
public boolean isShowMemoryUsage()
@@ -1843,6 +2436,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
return showMemoryUsage;
}
+ @Override
public void run()
{
df = java.text.NumberFormat.getNumberInstance();
@@ -1853,9 +2447,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
try
{
- 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;
@@ -1876,49 +2470,86 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
+ @Override
public void paintComponent(Graphics g)
{
if (showMemoryUsage && g != null && df != null)
{
if (percentUsage < 20)
+ {
g.setColor(Color.red);
+ }
FontMetrics fm = g.getFontMetrics();
if (fm != null)
{
- g.drawString("Total Free Memory: " + df.format(totalFreeMemory)
- + "MB; Max Memory: " + df.format(maxMemory) + "MB; "
- + 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());
}
}
}
-
}
- 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())
{
- groovyShell = new JMenuItem();
- groovyShell.setText("Groovy Console...");
- groovyShell.addActionListener(new ActionListener()
+ // 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--)
+ {
+ 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();
@@ -1926,99 +2557,161 @@ 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)
+ @Override
+ 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,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+ MessageManager.getString("label.couldnt_create_groovy_shell"),
+ MessageManager.getString("label.groovy_support_failed"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+ /**
+ * Open the Groovy console
+ */
+ void openGroovyConsole()
+ {
+ if (groovyConsole == null)
+ {
+ groovyConsole = new groovy.ui.Console();
+ groovyConsole.setVariable("Jalview", this);
+ groovyConsole.run();
+
+ /*
+ * 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()
+ {
+ @Override
+ public void windowClosed(WindowEvent e)
+ {
+ /*
+ * rebind CMD-Q from Groovy Console to Jalview Quit
+ */
+ addQuitHandler();
+ enableExecuteGroovy(false);
+ }
+ });
+ }
+
+ /*
+ * 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();
+ }
+ });
+ }
- "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.",
- "Jalview Groovy Support Failed",
- JOptionPane.ERROR_MESSAGE);
+ /**
+ * 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, progressBarHandlers;
+ 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();
+ progressBars = new Hashtable<>();
+ progressBarHandlers = new Hashtable<>();
}
if (progressBars.get(new Long(id)) != null)
{
- JProgressBar progressPanel = (JProgressBar) progressBars
- .remove(new Long(id));
+ JPanel panel = progressBars.remove(new Long(id));
if (progressBarHandlers.contains(new Long(id)))
{
progressBarHandlers.remove(new Long(id));
}
- removeProgressPanel(progressPanel);
+ removeProgressPanel(panel);
}
else
{
@@ -2032,28 +2725,34 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* @see jalview.gui.IProgressIndicator#registerHandler(long,
* jalview.gui.IProgressIndicatorHandler)
*/
+ @Override
public void registerHandler(final long id,
final IProgressIndicatorHandler handler)
{
- if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+ 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");
+ 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);
@@ -2061,20 +2760,36 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
/**
- * 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
+ */
+ @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(AlignViewport av)
+ public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
{
if (desktop != null)
{
- AlignmentPanel[] aps = getAlignmentPanels(av.getSequenceSetId());
+ AlignmentPanel[] aps = getAlignmentPanels(
+ viewport.getSequenceSetId());
for (int panel = 0; aps != null && panel < aps.length; panel++)
{
- if (aps[panel] != null && aps[panel].av == av)
+ if (aps[panel] != null && aps[panel].av == viewport)
{
return aps[panel].alignFrame;
}
@@ -2088,13 +2803,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements
return v_client;
}
+
/**
* flag set if jalview GUI is being operated programmatically
*/
- private boolean inBatchMode=false;
+ private boolean inBatchMode = false;
/**
* check if jalview GUI is being operated programmatically
+ *
* @return inBatchMode
*/
public boolean isInBatchMode()
@@ -2104,14 +2821,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
/**
* set flag if jalview GUI is being operated programmatically
- * @param inBatchMode
+ *
+ * @param inBatchMode
*/
public void setInBatchMode(boolean inBatchMode)
{
this.inBatchMode = inBatchMode;
}
-
public void startServiceDiscovery()
{
startServiceDiscovery(false);
@@ -2121,43 +2838,29 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
boolean alive = true;
Thread t0 = null, t1 = null, t2 = null;
-
- // todo: changesupport handlers need to be transferred
- if (discoverer == null)
- {
- discoverer = new jalview.ws.jws1.Discoverer();
- // register PCS handler for desktop.
- discoverer.addPropertyChangeListener(changeSupport);
- }
- if (Cache.getDefault("SHOW_JWS1_SERVICES", true))
+ // 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
(t0 = new Thread(discoverer)).start();
}
- try
- {
- if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
- {
- // EnfinEnvision web service menu entries are rebuild every time the
- // menu is shown, so no changeSupport events are needed.
- jalview.ws.EnfinEnvision2OneWay.getInstance();
- (t1 = new Thread(jalview.ws.EnfinEnvision2OneWay.getInstance()))
- .start();
- }
- } catch (Exception e)
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- Cache.log
- .info(
- "Exception when trying to launch Envision2 workflow discovery.",
- e);
- Cache.log.info(e.getStackTrace());
+ t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ .startDiscoverer(changeSupport);
}
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ Thread t3 = null;
{
- jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
- .addPropertyChangeListener(changeSupport);
- (t2 = new Thread(jalview.ws.jws2.Jws2Discoverer.getDiscoverer()))
- .start();
+ // TODO: do rest service discovery
}
if (blocking)
{
@@ -2169,46 +2872,531 @@ public class Desktop extends jalview.jbgui.GDesktop implements
} 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());
}
}
}
/**
- * start a thread to open a URL in the configured browser. Pops up a warning dialog to the user if there is an exception when calling out to the browser to open the URL.
+ * called to check if the service discovery process completed successfully.
+ *
+ * @param evt
+ */
+ protected void JalviewServicesChanged(PropertyChangeEvent evt)
+ {
+ if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
+ {
+ final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ .getErrorMessages();
+ if (ermsg != null)
+ {
+ if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
+ {
+ if (serviceChangedDialog == null)
+ {
+ // only run if we aren't already displaying one of these.
+ addDialogThread(serviceChangedDialog = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+
+ /*
+ * JalviewDialog jd =new JalviewDialog() {
+ *
+ * @Override protected void cancelPressed() { // TODO
+ * Auto-generated method stub
+ *
+ * }@Override protected void okPressed() { // TODO
+ * Auto-generated method stub
+ *
+ * }@Override protected void raiseClosed() { // TODO
+ * Auto-generated method stub
+ *
+ * } }; jd.initDialogFrame(new
+ * JLabel("" + 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. |
"
+ * ), true, true, "Web Service Configuration Problem", 450,
+ * 400);
+ *
+ * jd.waitForInput();
+ */
+ JvOptionPane.showConfirmDialog(Desktop.desktop,
+ new JLabel(""
+ + "It may be that you have invalid JABA URLs
in your web service preferences,"
+ + "
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.
"),
+ "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"
+ + ermsg);
+ }
+ }
+ }
+ }
+
+ private Runnable serviceChangedDialog = null;
+
+ /**
+ * start a thread to open a URL in the configured browser. Pops up a warning
+ * dialog to the user if there is an exception when calling out to the browser
+ * to open the URL.
+ *
* @param url
*/
public static void showUrl(final String url)
{
- new Thread(new Runnable() {
- public void run() {
- try {
+ showUrl(url, Desktop.instance);
+ }
+
+ /**
+ * Like showUrl but allows progress handler to be specified
+ *
+ * @param url
+ * @param progress
+ * (null) or object implementing IProgressIndicator
+ */
+ public static void showUrl(final String url,
+ final IProgressIndicator progress)
+ {
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ if (progress != null)
+ {
+ progress.setProgressBar(MessageManager
+ .formatMessage("status.opening_params", new Object[]
+ { url }), this.hashCode());
+ }
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
- {
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- "Unixers: Couldn't find default web browser."
- + "\nAdd the full path to your browser in Preferences.",
- "Web browser not found", JOptionPane.WARNING_MESSAGE);
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
+ if (progress != null)
+ {
+ progress.setProgressBar(null, this.hashCode());
+ }
}
- }).start();
+ }).start();
}
public static WsParamSetManager wsparamManager = null;
+
public static ParamManager getUserParameterStore()
{
- if (wsparamManager==null)
+ if (wsparamManager == null)
{
wsparamManager = new WsParamSetManager();
}
return wsparamManager;
}
+ /**
+ * static hyperlink handler proxy method for use by Jalview's internal windows
+ *
+ * @param e
+ */
+ public static void hyperlinkUpdate(HyperlinkEvent e)
+ {
+ if (e.getEventType() == EventType.ACTIVATED)
+ {
+ String url = null;
+ try
+ {
+ url = e.getURL().toString();
+ Desktop.showUrl(url);
+ } catch (Exception x)
+ {
+ if (url != null)
+ {
+ if (Cache.log != null)
+ {
+ Cache.log.error("Couldn't handle string " + url + " as a URL.");
+ }
+ else
+ {
+ System.err.println(
+ "Couldn't handle string " + url + " as a URL.");
+ }
+ }
+ // ignore any exceptions due to dud links.
+ }
+
+ }
+ }
+
+ /**
+ * single thread that handles display of dialogs to user.
+ */
+ ExecutorService dialogExecutor = Executors.newSingleThreadExecutor();
+
+ /**
+ * flag indicating if dialogExecutor should try to acquire a permit
+ */
+ private volatile boolean dialogPause = true;
+
+ /**
+ * pause the queue
+ */
+ private java.util.concurrent.Semaphore block = new Semaphore(0);
+
+ private static groovy.ui.Console groovyConsole;
+
+ /**
+ * add another dialog thread to the queue
+ *
+ * @param prompter
+ */
+ public void addDialogThread(final Runnable prompter)
+ {
+ dialogExecutor.submit(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ if (dialogPause)
+ {
+ try
+ {
+ block.acquire();
+ } catch (InterruptedException x)
+ {
+ }
+ ;
+ }
+ if (instance == null)
+ {
+ return;
+ }
+ try
+ {
+ SwingUtilities.invokeAndWait(prompter);
+ } catch (Exception q)
+ {
+ Cache.log.warn("Unexpected Exception in dialog thread.", q);
+ }
+ }
+ });
+ }
+
+ public void startDialogQueue()
+ {
+ // set the flag so we don't pause waiting for another permit and semaphore
+ // the current task to begin
+ dialogPause = false;
+ block.release();
+ }
+
+ @Override
+ protected void snapShotWindow_actionPerformed(ActionEvent e)
+ {
+ 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);
+ try
+ {
+ paintAll(im.getGraphics());
+ im.writeImage();
+ } catch (Exception q)
+ {
+ Cache.log.error("Couldn't write snapshot to " + of.getAbsolutePath(),
+ q);
+ return;
+ }
+ Cache.log.info("Successfully written snapshot to file "
+ + of.getAbsolutePath());
+ }
+
+ /**
+ * Explode the views in the given SplitFrame into separate SplitFrame windows.
+ * This respects (remembers) any previous 'exploded geometry' i.e. the size
+ * and location last time the view was expanded (if any). However it does not
+ * remember the split pane divider location - this is set to match the
+ * 'exploding' frame.
+ *
+ * @param sf
+ */
+ public void explodeViews(SplitFrame sf)
+ {
+ AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame();
+ AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame();
+ List extends AlignmentViewPanel> topPanels = oldTopFrame
+ .getAlignPanels();
+ List extends AlignmentViewPanel> bottomPanels = oldBottomFrame
+ .getAlignPanels();
+ int viewCount = topPanels.size();
+ if (viewCount < 2)
+ {
+ return;
+ }
+
+ /*
+ * Processing in reverse order works, forwards order leaves the first panels
+ * not visible. I don't know why!
+ */
+ for (int i = viewCount - 1; i >= 0; i--)
+ {
+ /*
+ * Make new top and bottom frames. These take over the respective
+ * AlignmentPanel objects, including their AlignmentViewports, so the
+ * cdna/protein relationships between the viewports is carried over to the
+ * new split frames.
+ *
+ * explodedGeometry holds the (x, y) position of the previously exploded
+ * SplitFrame, and the (width, height) of the AlignFrame component
+ */
+ AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i);
+ AlignFrame newTopFrame = new AlignFrame(topPanel);
+ newTopFrame.setSize(oldTopFrame.getSize());
+ newTopFrame.setVisible(true);
+ Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport())
+ .getExplodedGeometry();
+ if (geometry != null)
+ {
+ newTopFrame.setSize(geometry.getSize());
+ }
+
+ AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i);
+ AlignFrame newBottomFrame = new AlignFrame(bottomPanel);
+ newBottomFrame.setSize(oldBottomFrame.getSize());
+ newBottomFrame.setVisible(true);
+ geometry = ((AlignViewport) bottomPanel.getAlignViewport())
+ .getExplodedGeometry();
+ if (geometry != null)
+ {
+ newBottomFrame.setSize(geometry.getSize());
+ }
+
+ topPanel.av.setGatherViewsHere(false);
+ bottomPanel.av.setGatherViewsHere(false);
+ JInternalFrame splitFrame = new SplitFrame(newTopFrame,
+ newBottomFrame);
+ if (geometry != null)
+ {
+ splitFrame.setLocation(geometry.getLocation());
+ }
+ Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
+ }
+
+ /*
+ * Clear references to the panels (now relocated in the new SplitFrames)
+ * before closing the old SplitFrame.
+ */
+ topPanels.clear();
+ bottomPanels.clear();
+ sf.close();
+ }
+
+ /**
+ * Gather expanded split frames, sharing the same pairs of sequence set ids,
+ * back into the given SplitFrame as additional views. Note that the gathered
+ * frames may themselves have multiple views.
+ *
+ * @param source
+ */
+ public void gatherViews(GSplitFrame source)
+ {
+ /*
+ * special handling of explodedGeometry for a view within a SplitFrame: - it
+ * holds the (x, y) position of the enclosing SplitFrame, and the (width,
+ * height) of the AlignFrame component
+ */
+ AlignFrame myTopFrame = (AlignFrame) source.getTopFrame();
+ 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()));
+ myTopFrame.viewport.setGatherViewsHere(true);
+ myBottomFrame.viewport.setGatherViewsHere(true);
+ String topViewId = myTopFrame.viewport.getSequenceSetId();
+ String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
+
+ JInternalFrame[] frames = desktop.getAllFrames();
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof SplitFrame && frame != source)
+ {
+ SplitFrame sf = (SplitFrame) frame;
+ AlignFrame topFrame = (AlignFrame) sf.getTopFrame();
+ AlignFrame bottomFrame = (AlignFrame) sf.getBottomFrame();
+ boolean gatherThis = false;
+ for (int a = 0; a < topFrame.alignPanels.size(); a++)
+ {
+ AlignmentPanel topPanel = topFrame.alignPanels.get(a);
+ AlignmentPanel bottomPanel = bottomFrame.alignPanels.get(a);
+ if (topViewId.equals(topPanel.av.getSequenceSetId())
+ && bottomViewId.equals(bottomPanel.av.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()));
+ myTopFrame.addAlignmentPanel(topPanel, false);
+ myBottomFrame.addAlignmentPanel(bottomPanel, false);
+ }
+ }
+
+ if (gatherThis)
+ {
+ topFrame.getAlignPanels().clear();
+ bottomFrame.getAlignPanels().clear();
+ sf.close();
+ }
+ }
+ }
+
+ /*
+ * The dust settles...give focus to the tab we did this from.
+ */
+ myTopFrame.setDisplayedView(myTopFrame.alignPanel);
+ }
+
+ public static groovy.ui.Console getGroovyConsole()
+ {
+ return groovyConsole;
+ }
+
+ public static void transferFromDropTarget(List files,
+ List protocols, DropTargetDropEvent evt,
+ Transferable t) throws Exception
+ {
+
+ DataFlavor uriListFlavor = new DataFlavor(
+ "text/uri-list;class=java.lang.String");
+ if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+ {
+ // Works on Windows and MacOSX
+ Cache.log.debug("Drop handled as javaFileListFlavor");
+ for (Object file : (List) t
+ .getTransferData(DataFlavor.javaFileListFlavor))
+ {
+ files.add(((File) file).toString());
+ protocols.add(DataSourceType.FILE);
+ }
+ }
+ else
+ {
+ // Unix like behaviour
+ boolean added = false;
+ String data = null;
+ if (t.isDataFlavorSupported(uriListFlavor))
+ {
+ Cache.log.debug("Drop handled as uriListFlavor");
+ // This is used by Unix drag system
+ data = (String) t.getTransferData(uriListFlavor);
+ }
+ if (data == null)
+ {
+ // 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"));
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("fallback returned " + data);
+ }
+ }
+ while (protocols.size() < files.size())
+ {
+ Cache.log.debug("Adding missing FILE protocol for "
+ + files.get(protocols.size()));
+ protocols.add(DataSourceType.FILE);
+ }
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+ data, "\r\n"); st.hasMoreTokens();)
+ {
+ added = true;
+ String s = st.nextToken();
+ if (s.startsWith("#"))
+ {
+ // the line is a comment (as per the RFC 2483)
+ continue;
+ }
+ java.net.URI uri = new java.net.URI(s);
+ if (uri.getScheme().toLowerCase().startsWith("http"))
+ {
+ protocols.add(DataSourceType.URL);
+ files.add(uri.toString());
+ }
+ else
+ {
+ // otherwise preserve old behaviour: catch all for file objects
+ java.io.File file = new java.io.File(uri);
+ protocols.add(DataSourceType.FILE);
+ files.add(file.toString());
+ }
+ }
+ if (Cache.log.isDebugEnabled())
+ {
+ if (data == null || !added)
+ {
+ 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());
+ Object df = t.getTransferData(fl);
+ if (df != null)
+ {
+ Cache.log.debug("Retrieves: " + df);
+ }
+ else
+ {
+ Cache.log.debug("Retrieved nothing");
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Sets the Preferences property for experimental features to True or False
+ * depending on the state of the controlling menu item
+ */
+ @Override
+ protected void showExperimental_actionPerformed(boolean selected)
+ {
+ Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));
+ }
}