Version "
+ + jalview.bin.Cache.getProperty("VERSION")
+ + "; last updated: "
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+ }
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ 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.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;
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @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)
+ {
}
- 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++)
{
try
{
frames[i].setClosed(true);
+ } catch (java.beans.PropertyVetoException ex)
+ {
}
- catch (java.beans.PropertyVetoException ex)
- {}
}
+ 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);
@@ -664,9 +1373,13 @@ public class Desktop
reorderAssociatedWindows(false, true);
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.ActionEvent)
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.
+ * ActionEvent)
*/
+ @Override
protected void garbageCollect_actionPerformed(ActionEvent e)
{
// We simply collect the garbage
@@ -675,14 +1388,48 @@ public class Desktop
jalview.bin.Cache.log.debug("Finished garbage collection.");
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent)
+ /*
+ * (non-Javadoc)
+ *
+ * @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();
@@ -691,22 +1438,22 @@ public class Desktop
return;
}
- AlignViewport source = null, target = null;
+ AlignmentViewport source = null, target = null;
if (frames[0] instanceof AlignFrame)
{
- source = ( (AlignFrame) frames[0]).getCurrentView();
+ source = ((AlignFrame) frames[0]).getCurrentView();
}
else if (frames[0] instanceof TreePanel)
{
- source = ( (TreePanel) frames[0]).getViewPort();
+ source = ((TreePanel) frames[0]).getViewPort();
}
else if (frames[0] instanceof PCAPanel)
{
- source = ( (PCAPanel) frames[0]).av;
+ source = ((PCAPanel) frames[0]).av;
}
else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
{
- source = ( (PairwiseAlignPanel) frames[0].getContentPane()).av;
+ source = ((PairwiseAlignPanel) frames[0].getContentPane()).av;
}
if (source != null)
@@ -720,19 +1467,19 @@ public class Desktop
}
if (frames[i] instanceof AlignFrame)
{
- target = ( (AlignFrame) frames[i]).getCurrentView();
+ target = ((AlignFrame) frames[i]).getCurrentView();
}
else if (frames[i] instanceof TreePanel)
{
- target = ( (TreePanel) frames[i]).getViewPort();
+ target = ((TreePanel) frames[i]).getViewPort();
}
else if (frames[i] instanceof PCAPanel)
{
- target = ( (PCAPanel) frames[i]).av;
+ target = ((PCAPanel) frames[i]).av;
}
else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
{
- target = ( (PairwiseAlignPanel) frames[i].getContentPane()).av;
+ target = ((PairwiseAlignPanel) frames[i].getContentPane()).av;
}
if (source == target)
@@ -752,18 +1499,21 @@ public class Desktop
}
}
+ } catch (java.beans.PropertyVetoException ex)
+ {
}
- catch (java.beans.PropertyVetoException ex)
- {}
}
}
}
}
+
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void preferences_actionPerformed(ActionEvent e)
{
new Preferences();
@@ -771,148 +1521,307 @@ public class Desktop
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @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(
+ Cache.getProperty("LAST_DIRECTORY"), "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();
- 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);
+ 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!
+ *
+ * @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();
- 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();
+ 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(null);
+ 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)
+ if (progressPanel == null)
{
- progressPanel = new JPanel(new BorderLayout());
- totalProgressCount=0;
+ 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)
+
+ int totalProgressCount = 0;
+
+ private void removeProgressPanel(JPanel progbar)
{
- if (progressPanel!=null)
+ 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();
}
+
public void stopLoading()
{
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)
{
- int count = 0;
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- for (int t = 0; t < frames.length; t++)
+ AlignmentViewport[] aps = getViewports(alignmentId);
+ return (aps == null) ? 0 : aps.length;
+ }
+
+ /**
+ *
+ * @param alignmentId
+ * - if null, all sets are returned
+ * @return all AlignmentPanels concerning the alignmentId sequence set
+ */
+ public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
+ {
+ 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()))
+ {
+ aps.add(ap);
+ }
+ }
+ }
+ if (aps.size() == 0)
+ {
+ return null;
+ }
+ AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]);
+ return vap;
+ }
+
+ /**
+ * get all the viewports on an alignment.
+ *
+ * @param sequenceSetId
+ * unique alignment id (may be null - all viewports returned in that
+ * case)
+ * @return all viewports on the alignment bound to sequenceSetId
+ */
+ public static AlignmentViewport[] getViewports(String sequenceSetId)
+ {
+ List viewp = new ArrayList();
+ if (desktop != null)
+ {
+ AlignFrame[] frames = Desktop.getAlignFrames();
+
+ for (AlignFrame afr : frames)
+ {
+ if (sequenceSetId == null
+ || afr.getViewport().getSequenceSetId()
+ .equals(sequenceSetId))
{
- if (viewId.equals(
- ( (AlignmentPanel) af.alignPanels.elementAt(a)).av.
- getSequenceSetId())
- )
+ if (afr.alignPanels != null)
+ {
+ for (AlignmentPanel ap : afr.alignPanels)
+ {
+ if (sequenceSetId == null
+ || sequenceSetId.equals(ap.av.getSequenceSetId()))
+ {
+ viewp.add(ap.av);
+ }
+ }
+ }
+ else
{
- count++;
+ viewp.add(afr.getViewport());
}
}
}
+ if (viewp.size() > 0)
+ {
+ return viewp.toArray(new AlignmentViewport[viewp.size()]);
+ }
}
-
- return count;
+ 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)
@@ -922,19 +1831,24 @@ public class Desktop
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);
+ addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
}
af.alignPanels.clear();
@@ -942,12 +1856,20 @@ public class Desktop
}
+ /**
+ * 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++)
{
@@ -957,12 +1879,12 @@ public class Desktop
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);
}
}
@@ -978,38 +1900,153 @@ public class Desktop
}
jalview.gui.VamsasApplication v_client = null;
+
+ @Override
public void vamsasImport_actionPerformed(ActionEvent e)
{
- if (v_client==null)
+ 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;
+ 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);
}
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
}
- }else {
- jalview.bin.Cache.log.error("Implementation error - load session from a running session is not supported.");
}
+ else
+ {
+ jalview.bin.Cache.log
+ .error("Implementation error - load session from a running session is not supported.");
+ }
+ }
+
+ /**
+ * 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)
@@ -1017,21 +2054,18 @@ public class Desktop
// Start a session.
// we just start a default session for moment.
/*
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Load Vamsas file");
- chooser.setToolTipText("Import");
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- v_client = new jalview.gui.VamsasApplication(this,
- chooser.getSelectedFile());
- *
- */
+ * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ * getProperty("LAST_DIRECTORY"));
+ *
+ * chooser.setFileView(new JalviewFileView());
+ * chooser.setDialogTitle("Load Vamsas file");
+ * chooser.setToolTipText("Import");
+ *
+ * int value = chooser.showOpenDialog(this);
+ *
+ * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
+ * jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
+ */
v_client = new VamsasApplication(this);
setupVamsasConnectedGui();
v_client.initial_update(); // TODO: thread ?
@@ -1045,19 +2079,23 @@ public class Desktop
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.
+ vamsasImport.setVisible(false); // Document import to existing session is
+ // not possible for vamsas-client-1.0.
}
+
protected void setupVamsasDisconnectedGui()
{
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)
@@ -1067,6 +2105,7 @@ public class Desktop
setupVamsasDisconnectedGui();
}
}
+
protected void buildVamsasStMenu()
{
if (v_client == null)
@@ -1090,25 +2129,29 @@ public class Desktop
{
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)
{
- Thread rthr = new Thread(new Runnable() {
+ Thread rthr = new Thread(new Runnable()
+ {
+ @Override
public void run()
{
dsktp.v_client = new VamsasApplication(dsktp, mysesid);
dsktp.setupVamsasConnectedGui();
dsktp.v_client.initial_update();
}
-
+
});
rthr.start();
}
@@ -1117,8 +2160,8 @@ public class Desktop
VamsasStMenu.add(sessit);
}
// don't show an empty menu.
- VamsasStMenu.setVisible(sess.length>0);
-
+ VamsasStMenu.setVisible(sess.length > 0);
+
}
else
{
@@ -1126,77 +2169,88 @@ public class Desktop
VamsasStMenu.removeAll();
VamsasStMenu.setVisible(false);
}
- } else {
+ }
+ else
+ {
// Not interested in the content. Just hide ourselves.
VamsasStMenu.setVisible(false);
}
}
+
+ @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(
+ Cache.getProperty("LAST_DIRECTORY"), "vdj",// TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+ "Vamsas Document");
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_vamsas_document_archive"));
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save Vamsas Document Archive");
+ int value = chooser.showSaveDialog(this);
- 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() }));
+ Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+ String warnmsg = null;
+ String warnttl = null;
+ try
+ {
+ v_client.vclient.storeDocument(choice);
+ } catch (Error ex)
+ {
+ warnttl = "Serious Problem saving Vamsas Document";
+ warnmsg = ex.toString();
+ jalview.bin.Cache.log.error("Error Whilst saving document to "
+ + choice, ex);
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ } catch (Exception ex)
{
- java.io.File choice = chooser.getSelectedFile();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- String warnmsg=null;
- String warnttl=null;
- try {
- v_client.vclient.storeDocument(choice);
- }
- catch (Error ex)
- {
- warnttl = "Serious Problem saving Vamsas Document";
- warnmsg = ex.toString();
- 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);
-
- }
- if (warnmsg!=null)
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ warnttl = "Problem saving Vamsas Document.";
+ warnmsg = ex.toString();
+ jalview.bin.Cache.log.warn("Exception Whilst saving document to "
+ + choice, ex);
- warnmsg, warnttl,
- JOptionPane.ERROR_MESSAGE);
- }
}
+ removeProgressPanel(progpanel);
+ if (warnmsg != null)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+ warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
+ }
+ }
}
}
- 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
+ *
+ * @param b
+ * true to hide gui, false to reveal gui
*/
public void setVamsasUpdate(boolean b)
{
- jalview.bin.Cache.log.debug("Setting gui for Vamsas update " +
- (b ? "in progress" : "finished"));
-
- if (vamUpdate!=null)
+ Cache.log.debug("Setting gui for Vamsas update "
+ + (b ? "in progress" : "finished"));
+
+ if (vamUpdate != null)
{
this.removeProgressPanel(vamUpdate);
}
if (b)
{
- vamUpdate = this.addProgressPanel("Updating vamsas session");
+ vamUpdate = this.addProgressPanel(MessageManager
+ .getString("label.updating_vamsas_session"));
}
vamsasStart.setVisible(!b);
vamsasStop.setVisible(!b);
@@ -1208,47 +2262,139 @@ public class Desktop
return desktop.getAllFrames();
}
-
/**
- * Checks the given url to see if it gives a response indicating that
- * the user should be informed of a new questionnaire.
+ * Checks the given url to see if it gives a response indicating that the user
+ * should be informed of a new questionnaire.
+ *
* @param url
*/
public void checkForQuestionnaire(String url)
{
UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
- javax.swing.SwingUtilities.invokeLater(jvq);
+ // javax.swing.SwingUtilities.invokeLater(jvq);
+ 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
+ Vector links = Preferences.sequenceURLLinks;
+
+ // 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(EMBLEBI_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 low.
+ * Proxy class for JDesktopPane which optionally displays the current memory
+ * usage and highlights the desktop area with a red bar if free memory runs
+ * low.
+ *
* @author AMW
*/
- class MyDesktopPane extends JDesktopPane implements Runnable
+ public class MyDesktopPane extends JDesktopPane implements Runnable
{
-
+
+ private static final float ONE_MB = 1048576f;
+
boolean showMemoryUsage = false;
+
Runtime runtime;
+
java.text.NumberFormat df;
- float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, percentUsage;
+ float maxMemory, allocatedMemory, freeMemory, totalFreeMemory,
+ percentUsage;
public MyDesktopPane(boolean showMemoryUsage)
{
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();
}
}
+ public boolean isShowMemoryUsage()
+ {
+ return showMemoryUsage;
+ }
+
+ @Override
public void run()
{
df = java.text.NumberFormat.getNumberInstance();
@@ -1259,127 +2405,964 @@ public class Desktop
{
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;
- // if (percentUsage < 20)
+ // if (percentUsage < 20)
{
- // border1 = BorderFactory.createMatteBorder(12, 12, 12, 12, Color.red);
- // instance.set.setBorder(border1);
+ // border1 = BorderFactory.createMatteBorder(12, 12, 12, 12,
+ // Color.red);
+ // instance.set.setBorder(border1);
}
repaint();
-
- }
- catch (Exception ex)
+ // sleep after showing usage
+ Thread.sleep(3000);
+ } catch (Exception ex)
{
ex.printStackTrace();
}
}
}
+ @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() {
- if (jalview.bin.Cache.groovyJarsPresent())
- {
- groovyShell = new JMenuItem();
- groovyShell.setText("Groovy Console...");
- groovyShell.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e) {
- groovyShell_actionPerformed(e);
- }
- });
- toolsMenu.add(groovyShell);
- groovyShell.setVisible(true);
- }
- }
+
/**
- * Accessor method to quickly get all the AlignmentFrames
- * loaded.
+ * Accessor method to quickly get all the AlignmentFrames loaded.
+ *
+ * @return an array of AlignFrame, or null if none found
*/
- public static AlignFrame[] getAlignframes() {
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-
+ public static AlignFrame[] getAlignFrames()
+ {
+ 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--)
+ {
+ if (frames[i] instanceof AlignFrame)
+ {
+ avp.add((AlignFrame) frames[i]);
}
- Vector avp=new Vector();
- try
+ 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)
+ {
+ avp.add((AlignFrame) sf.getTopFrame());
+ }
+ 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;
+ }
+
+ /**
+ * Returns an array of any AppJmol frames in the Desktop (or null if none).
+ *
+ * @return
+ */
+ public GStructureViewer[] getJmols()
+ {
+ 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 AppJmol)
+ {
+ GStructureViewer af = (GStructureViewer) frames[i];
+ avp.add(af);
+ }
+ }
+ if (avp.size() == 0)
+ {
+ return null;
+ }
+ GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]);
+ return afs;
+ }
+
+ /**
+ * Add Groovy Support to Jalview
+ */
+ public void groovyShell_actionPerformed()
+ {
+ try
+ {
+ openGroovyConsole();
+ } catch (Exception ex)
+ {
+ jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
+ 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();
+ }
+ });
+ }
+
+ /**
+ * 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(
+ MessageManager
+ .getString("error.call_setprogressbar_before_registering_handler"));
+ }
+ progressBarHandlers.put(new Long(id), handler);
+ final JPanel progressPanel = progressBars.get(new Long(id));
+ if (handler.canCancel())
+ {
+ 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(MessageManager.formatMessage(
+ "label.cancelled_params",
+ new Object[] { ((JLabel) progressPanel.getComponent(0))
+ .getText() }), id);
+ }
+ });
+ progressPanel.add(cancel, BorderLayout.EAST);
+ }
+ }
+
+ /**
+ *
+ * @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(AlignViewportI viewport)
+ {
+ if (desktop != null)
+ {
+ AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId());
+ for (int panel = 0; aps != null && panel < aps.length; panel++)
{
- //REVERSE ORDER
- for (int i = frames.length - 1; i > -1; i--)
+ if (aps[panel] != null && aps[panel].av == viewport)
+ {
+ return aps[panel].alignFrame;
+ }
+ }
+ }
+ return null;
+ }
+
+ public VamsasApplication getVamsasApplication()
+ {
+ return v_client;
+
+ }
+
+ /**
+ * flag set if jalview GUI is being operated programmatically
+ */
+ private boolean inBatchMode = false;
+
+ /**
+ * check if jalview GUI is being operated programmatically
+ *
+ * @return inBatchMode
+ */
+ public boolean isInBatchMode()
+ {
+ return inBatchMode;
+ }
+
+ /**
+ * set flag if jalview GUI is being operated programmatically
+ *
+ * @param inBatchMode
+ */
+ public void setInBatchMode(boolean inBatchMode)
+ {
+ this.inBatchMode = inBatchMode;
+ }
+
+ public void startServiceDiscovery()
+ {
+ startServiceDiscovery(false);
+ }
+
+ public void startServiceDiscovery(boolean blocking)
+ {
+ boolean alive = true;
+ Thread t0 = null, t1 = null, t2 = null;
+ // 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();
+ }
+
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
+ if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning())
+ {
+ jalview.ws.jws2.Jws2Discoverer.getDiscoverer().setAborted(true);
+ }
+ t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(
+ changeSupport);
+
+ }
+ Thread t3 = null;
+ {
+ // TODO: do rest service discovery
+ }
+ if (blocking)
+ {
+ while (alive)
+ {
+ try
+ {
+ Thread.sleep(15);
+ } catch (Exception e)
+ {
+ }
+ alive = (t1 != null && t1.isAlive())
+ || (t2 != null && t2.isAlive())
+ || (t3 != null && t3.isAlive())
+ || (t0 != null && t0.isAlive());
+ }
+ }
+ }
+
+ /**
+ * 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)
{
- if (frames[i] instanceof AlignFrame)
+ // only run if we aren't already displaying one of these.
+ addDialogThread(serviceChangedDialog = new Runnable()
+ {
+ @Override
+ public void run()
{
- AlignFrame af = (AlignFrame) frames[i];
- avp.addElement(af);
+
+ /*
+ * 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);
+ }
}
- catch (Exception ex)
+ }
+ }
+
+ 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)
+ {
+ 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)
+ {
+ 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());
+ }
}
- if (avp.size()==0)
+ }).start();
+ }
+
+ public static WsParamSetManager wsparamManager = null;
+
+ public static ParamManager getUserParameterStore()
+ {
+ 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
{
- return null;
+ 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.
}
- AlignFrame afs[] = new AlignFrame[avp.size()];
- for (int i=0,j=avp.size(); i topPanels = oldTopFrame
+ .getAlignPanels();
+ List 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");
+ }
+ }
+ }
+ }
}
}
}