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"))
+ {
+ // JBP removed this message for 2.11: May be reinstated in future version
+ // message.append("
...Checking latest version...");
}
- // TODO: update this text for each release or centrally store it for lite
- // and application
- message.append("\nAuthors: Jim Procter, Jan Engelhardt, Lauren Lui, Andrew Waterhouse, 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;
}
/**
@@ -1078,24 +1377,21 @@ 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++)
{
@@ -1106,19 +1402,28 @@ 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();
}
}
+ @Override
public void raiseRelated_actionPerformed(ActionEvent e)
{
reorderAssociatedWindows(false, false);
}
+ @Override
public void minimizeAssociated_actionPerformed(ActionEvent e)
{
reorderAssociatedWindows(true, false);
@@ -1135,6 +1440,7 @@ 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
@@ -1150,6 +1456,7 @@ 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());
@@ -1162,6 +1469,7 @@ 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());
@@ -1178,8 +1486,8 @@ 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);
}
@@ -1191,7 +1499,7 @@ 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();
@@ -1266,106 +1574,165 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void preferences_actionPerformed(ActionEvent e)
{
new Preferences();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Shows a file chooser dialog and writes out the current session as a Jalview
+ * project file
*/
- public void saveState_actionPerformed(ActionEvent e)
+ @Override
+ public void saveState_actionPerformed()
{
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jar" }, new String[]
- { "Jalview Project" }, "Jalview Project");
+ saveState_actionPerformed(false);
+ }
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save State");
+ public void saveState_actionPerformed(boolean saveAs)
+ {
+ java.io.File projectFile = getProjectFile();
+ // autoSave indicates we already have a file and don't need to ask
+ boolean autoSave = projectFile != null && !saveAs
+ && BackupFiles.getEnabled();
- int value = chooser.showSaveDialog(this);
+ // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
+ // saveAs="+saveAs+", Backups
+ // "+(BackupFiles.getEnabled()?"enabled":"disabled"));
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ boolean approveSave = false;
+ if (!autoSave)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser("jvp",
+ "Jalview Project");
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager.getString("label.save_state"));
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ projectFile = chooser.getSelectedFile();
+ setProjectFile(projectFile);
+ approveSave = true;
+ }
+ }
+
+ if (approveSave || autoSave)
{
final Desktop me = this;
- final java.io.File choice = chooser.getSelectedFile();
+ final java.io.File chosenFile = projectFile;
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[]
+ { chosenFile.getName() }), chosenFile.hashCode());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chosenFile.getParent());
+ // TODO catch and handle errors for savestate
+ // TODO prevent user from messing with the Desktop whilst we're saving
+ try
+ {
+ BackupFiles backupfiles = new BackupFiles(chosenFile);
- setProgressBar("Saving jalview project " + choice.getName(),
- choice.hashCode());
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- // TODO catch and handle errors for savestate
- // TODO prevent user from messing with the Desktop whilst we're saving
- try
- {
- new Jalview2XML().SaveState(choice);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning(
- "Whilst saving current state to " + choice.getName(), oom);
- } catch (Exception ex)
- {
- Cache.log
- .error("Problems whilst trying to save to "
- + choice.getName(), ex);
- JOptionPane.showMessageDialog(me,
- "Error whilst saving current state to " + choice.getName(),
- "Couldn't save project", JOptionPane.WARNING_MESSAGE);
- }
- setProgressBar(null, choice.hashCode());
+ new Jalview2XML().saveState(backupfiles.getTempFile());
+
+ backupfiles.setWriteSuccess(true);
+ backupfiles.rollBackupsAndRenameTempFile();
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Whilst saving current state to "
+ + chosenFile.getName(), oom);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Problems whilst trying to save to "
+ + chosenFile.getName(), ex);
+ JvOptionPane.showMessageDialog(me,
+ MessageManager.formatMessage(
+ "label.error_whilst_saving_current_state_to",
+ new Object[]
+ { chosenFile.getName() }),
+ MessageManager.getString("label.couldnt_save_project"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ setProgressBar(null, chosenFile.hashCode());
}
}).start();
}
}
+ @Override
+ public void saveAsState_actionPerformed(ActionEvent e)
+ {
+ saveState_actionPerformed(true);
+ }
+
+ private void setProjectFile(File choice)
+ {
+ this.projectFile = choice;
+ }
+
+ public File getProjectFile()
+ {
+ return this.projectFile;
+ }
+
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Shows a file chooser dialog and tries to read in the selected file as a
+ * Jalview project
*/
- public void loadState_actionPerformed(ActionEvent e)
+ @Override
+ public void loadState_actionPerformed()
{
+ final String[] suffix = new String[] { "jvp", "jar" };
+ final String[] desc = new String[] { "Jalview Project",
+ "Jalview Project (old)" };
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jar" }, new String[]
- { "Jalview Project" }, "Jalview Project");
+ Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
+ "Jalview Project", true, BackupFiles.getEnabled()); // last two booleans: allFiles,
+ // allowBackupFiles
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Restore state");
+ chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
int value = chooser.showOpenDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- final String choice = chooser.getSelectedFile().getAbsolutePath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
+ final File selectedFile = chooser.getSelectedFile();
+ setProjectFile(selectedFile);
+ final String choice = selectedFile.getAbsolutePath();
+ Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
new Thread(new Runnable()
{
+ @Override
public void run()
{
- setProgressBar("loading jalview project " + choice,
- choice.hashCode());
+ setProgressBar(MessageManager.formatMessage(
+ "label.loading_jalview_project", new Object[]
+ { choice }), choice.hashCode());
try
{
- new Jalview2XML().LoadJalviewAlign(choice);
+ new Jalview2XML().loadJalviewAlign(choice);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Whilst loading project from " + choice, oom);
} catch (Exception ex)
{
- Cache.log.error("Problems whilst loading project from "
- + choice, ex);
- JOptionPane.showMessageDialog(Desktop.desktop,
- "Error whilst loading project from " + choice,
- "Couldn't load project", JOptionPane.WARNING_MESSAGE);
+ 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());
}
@@ -1373,18 +1740,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
+ @Override
public void inputSequence_actionPerformed(ActionEvent e)
{
new SequenceFetcher(this);
}
JPanel progressPanel;
- ArrayList fileLoadingPanels=new ArrayList();
+
+ ArrayList fileLoadingPanels = new ArrayList<>();
+
public void startLoading(final String fileName)
{
if (fileLoadingCount == 0)
{
- fileLoadingPanels.add(addProgressPanel("Loading File: " + fileName + " "));
+ fileLoadingPanels.add(addProgressPanel(MessageManager
+ .formatMessage("label.loading_file", new Object[]
+ { fileName })));
}
fileLoadingCount++;
}
@@ -1393,11 +1765,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
if (progressPanel == null)
{
- progressPanel = new JPanel(new GridLayout(1,1));
+ progressPanel = new JPanel(new GridLayout(1, 1));
totalProgressCount = 0;
instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
}
- JPanel thisprogress=new JPanel(new BorderLayout(10,5));
+ JPanel thisprogress = new JPanel(new BorderLayout(10, 5));
JProgressBar progressBar = new JProgressBar();
progressBar.setIndeterminate(true);
@@ -1405,7 +1777,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
thisprogress.add(progressBar, BorderLayout.CENTER);
progressPanel.add(thisprogress);
- ((GridLayout)progressPanel.getLayout()).setRows(((GridLayout)progressPanel.getLayout()).getRows()+1);
+ ((GridLayout) progressPanel.getLayout()).setRows(
+ ((GridLayout) progressPanel.getLayout()).getRows() + 1);
++totalProgressCount;
instance.validate();
return thisprogress;
@@ -1417,13 +1790,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
if (progressPanel != null)
{
- progressPanel.remove(progbar);
- GridLayout gl = (GridLayout) progressPanel.getLayout();
- gl.setRows(gl.getRows()-1);
- if (--totalProgressCount < 1)
+ synchronized (progressPanel)
{
- this.getContentPane().remove(progressPanel);
- progressPanel = null;
+ progressPanel.remove(progbar);
+ GridLayout gl = (GridLayout) progressPanel.getLayout();
+ gl.setRows(gl.getRows() - 1);
+ if (--totalProgressCount < 1)
+ {
+ this.getContentPane().remove(progressPanel);
+ progressPanel = null;
+ }
}
}
validate();
@@ -1434,9 +1810,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
fileLoadingCount--;
if (fileLoadingCount < 1)
{
- for (JPanel flp : fileLoadingPanels)
+ while (fileLoadingPanels.size() > 0)
{
- removeProgressPanel(flp);
+ removeProgressPanel(fileLoadingPanels.remove(0));
}
fileLoadingPanels.clear();
fileLoadingCount = 0;
@@ -1446,39 +1822,38 @@ public class Desktop extends jalview.jbgui.GDesktop implements
public static int getViewCount(String alignmentId)
{
- AlignViewport[] aps = getViewports(alignmentId);
+ 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)
{
- 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 (alignmentId
- .equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av
- .getSequenceSetId()))
- {
- aps.add(af.alignPanels.elementAt(a));
- }
+ aps.add(ap);
}
}
}
@@ -1486,11 +1861,7 @@ 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;
}
@@ -1498,53 +1869,53 @@ 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)
@@ -1552,34 +1923,73 @@ public class Desktop extends jalview.jbgui.GDesktop implements
return;
}
+ // FIXME: ideally should use UI interface API
+ FeatureSettings viewFeatureSettings = (af.featureSettings != null
+ && af.featureSettings.isOpen())
+ ? af.featureSettings
+ : null;
+ Rectangle fsBounds = af.getFeatureSettingsGeometry();
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()))
+
+ // transfer reference for existing feature settings to new alignFrame
+ if (ap == af.alignPanel)
+ {
+ if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap)
+ {
+ newaf.featureSettings = viewFeatureSettings;
+ }
+ newaf.setFeatureSettingsGeometry(fsBounds);
+ }
+
+ /*
+ * 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);
+ // and materialise a new feature settings dialog instance for the new alignframe
+ // (closes the old as if 'OK' was pressed)
+ if (ap == af.alignPanel && newaf.featureSettings != null
+ && newaf.featureSettings.isOpen()
+ && af.alignPanel.getAlignViewport().isShowSequenceFeatures())
+ {
+ newaf.showFeatureSettingsUI();
+ }
}
+ af.featureSettings = null;
af.alignPanels.clear();
af.closeMenuItem_actionPerformed(true);
}
+ /**
+ * 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++)
{
if (frames[t] instanceof AlignFrame && frames[t] != source)
@@ -1588,420 +1998,187 @@ 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);
}
}
if (gatherThis)
{
+ if (af.featureSettings != null && af.featureSettings.isOpen())
+ {
+ if (source.featureSettings == null)
+ {
+ // preserve the feature settings geometry for this frame
+ source.featureSettings = af.featureSettings;
+ source.setFeatureSettingsGeometry(
+ af.getFeatureSettingsGeometry());
+ }
+ else
+ {
+ // close it and forget
+ af.featureSettings.close();
+ }
+ }
af.alignPanels.clear();
af.closeMenuItem_actionPerformed(true);
}
}
}
+ // refresh the feature setting UI for the source frame if it exists
+ if (source.featureSettings != null
+ && source.featureSettings.isOpen())
+ {
+ source.showFeatureSettingsUI();
+ }
}
- jalview.gui.VamsasApplication v_client = null;
+ public JInternalFrame[] getAllFrames()
+ {
+ 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.
+ *
+ * @param url
+ */
+ public void checkForQuestionnaire(String url)
+ {
+ UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
+ // javax.swing.SwingUtilities.invokeLater(jvq);
+ new Thread(jvq).start();
+ }
- public void vamsasImport_actionPerformed(ActionEvent e)
+ public void checkURLLinks()
{
- if (v_client == null)
+ // Thread off the URL link checker
+ addDialogThread(new Runnable()
{
- // Load and try to start a session.
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ @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(jalview.util.UrlConstants.SEQUENCE_ID)
+ && !UrlConstants.isDefaultString(link))
+ {
+ 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;
+ }
- 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.");
+ // 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);
- int value = chooser.showOpenDialog(this);
+ 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);
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- 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.showMessageDialog(Desktop.desktop, msgPanel,
+ MessageManager
+ .getString("label.SEQUENCE_ID_no_longer_used"),
+ JvOptionPane.WARNING_MESSAGE);
}
}
- }
- 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)
+ * 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.
*
- * @param file
- * @return true if import was a success and a session was started.
+ * @author AMW
*/
- public boolean vamsasImport(URL url)
+ public class MyDesktopPane extends JDesktopPane implements Runnable
{
- // 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;
- }
+ private static final float ONE_MB = 1048576f;
- 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)
+ boolean showMemoryUsage = false;
+
+ Runtime runtime;
+
+ java.text.NumberFormat df;
+
+ float maxMemory, allocatedMemory, freeMemory, totalFreeMemory,
+ percentUsage;
+
+ public MyDesktopPane(boolean showMemoryUsage)
{
- jalview.bin.Cache.log.error(
- "Failed to create new vamsas session from contents of URL "
- + url, ex);
- return false;
+ showMemoryUsage(showMemoryUsage);
}
- 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)
+ public void showMemoryUsage(boolean showMemory)
{
-
- jalview.bin.Cache.log
- .error("Implementation error - load session from a running session is not supported.");
- return false;
+ this.showMemoryUsage = showMemory;
+ if (showMemory)
+ {
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+ repaint();
}
- setProgressBar("Importing VAMSAS session from " + file.getName(),
- file.hashCode());
- try
- {
- v_client = new jalview.gui.VamsasApplication(this, file, null);
- } catch (Exception ex)
+ public boolean isShowMemoryUsage()
{
- setProgressBar("Importing VAMSAS session from " + 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());
- return v_client.inSession();
- }
-
- public boolean joinVamsasSession(String mysesid)
- {
- if (v_client != null)
- {
- throw new Error(
- "Trying to join a vamsas session when another is already connected.");
- }
- if (mysesid == null)
- {
- throw new Error("Invalid vamsas session id.");
- }
- v_client = new VamsasApplication(this, mysesid);
- setupVamsasConnectedGui();
- v_client.initial_update();
- return (v_client.inSession());
- }
-
- public void vamsasStart_actionPerformed(ActionEvent e)
- {
- if (v_client == null)
- {
- // 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());
- */
- v_client = new VamsasApplication(this);
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- }
- else
- {
- // store current data in session.
- v_client.push_update(); // TODO: thread
- }
- }
-
- protected void setupVamsasConnectedGui()
- {
- vamsasStart.setText("Session Update");
- vamsasSave.setVisible(true);
- vamsasStop.setVisible(true);
- 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");
- }
-
- public void vamsasStop_actionPerformed(ActionEvent e)
- {
- if (v_client != null)
- {
- v_client.end_session();
- v_client = null;
- setupVamsasDisconnectedGui();
- }
- }
-
- protected void buildVamsasStMenu()
- {
- if (v_client == null)
- {
- String[] sess = null;
- try
- {
- sess = VamsasApplication.getSessionList();
- } catch (Exception 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.");
- 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]);
- final Desktop dsktp = this;
- final String mysesid = sess[i];
- sessit.addActionListener(new ActionListener()
- {
-
- public void actionPerformed(ActionEvent e)
- {
- if (dsktp.v_client == null)
- {
- Thread rthr = new Thread(new Runnable()
- {
-
- public void run()
- {
- dsktp.v_client = new VamsasApplication(dsktp, mysesid);
- dsktp.setupVamsasConnectedGui();
- dsktp.v_client.initial_update();
- }
-
- });
- rthr.start();
- }
- };
- });
- VamsasStMenu.add(sessit);
- }
- // don't show an empty menu.
- VamsasStMenu.setVisible(sess.length > 0);
-
- }
- else
- {
- jalview.bin.Cache.log.debug("No current vamsas sessions.");
- VamsasStMenu.removeAll();
- VamsasStMenu.setVisible(false);
- }
- }
- else
- {
- // Not interested in the content. Just hide ourselves.
- VamsasStMenu.setVisible(false);
- }
- }
-
- 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");
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save Vamsas Document Archive");
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- java.io.File choice = chooser.getSelectedFile();
- JPanel progpanel = addProgressPanel("Saving VAMSAS Document to "
- + choice.getName());
- 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);
-
- }
- removeProgressPanel(progpanel);
- if (warnmsg != null)
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
-
- warnmsg, warnttl, JOptionPane.ERROR_MESSAGE);
- }
- }
- }
- }
-
- 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
- */
- public void setVamsasUpdate(boolean b)
- {
- jalview.bin.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");
- }
- vamsasStart.setVisible(!b);
- vamsasStop.setVisible(!b);
- vamsasSave.setVisible(!b);
- }
-
- public JInternalFrame[] getAllFrames()
- {
- 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.
- *
- * @param url
- */
- public void checkForQuestionnaire(String url)
- {
- UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
- // javax.swing.SwingUtilities.invokeLater(jvq);
- new Thread(jvq).start();
- }
-
- /**
- * 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
- */
- public class MyDesktopPane extends JDesktopPane implements Runnable
- {
-
- boolean showMemoryUsage = false;
-
- Runtime runtime;
-
- java.text.NumberFormat df;
-
- float maxMemory, allocatedMemory, freeMemory, totalFreeMemory,
- percentUsage;
-
- public MyDesktopPane(boolean showMemoryUsage)
- {
- showMemoryUsage(showMemoryUsage);
- }
-
- public void showMemoryUsage(boolean showMemoryUsage)
- {
- this.showMemoryUsage = showMemoryUsage;
- if (showMemoryUsage)
- {
- Thread worker = new Thread(this);
- worker.start();
- }
- }
-
- public boolean isShowMemoryUsage()
- {
- return showMemoryUsage;
+ return showMemoryUsage;
}
+ @Override
public void run()
{
df = java.text.NumberFormat.getNumberInstance();
@@ -2012,9 +2189,9 @@ 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;
@@ -2035,94 +2212,85 @@ 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());
}
}
}
-
}
/**
- * fixes stacking order after a modal dialog to ensure windows that should be on top actually are
+ * Accessor method to quickly get all the AlignmentFrames loaded.
+ *
+ * @return an array of AlignFrame, or null if none found
*/
- public void relayerWindows()
- {
-
- }
-
- protected JMenuItem groovyShell;
-
- public void doGroovyCheck()
+ public static AlignFrame[] getAlignFrames()
{
- if (jalview.bin.Cache.groovyJarsPresent())
+ if (Jalview.isHeadlessMode())
{
- 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);
+ // Desktop.desktop is null in headless mode
+ return new AlignFrame[] { Jalview.currentAlignFrame };
}
- }
- /**
- * Accessor method to quickly get all the AlignmentFrames loaded.
- */
- public static AlignFrame[] getAlignframes()
- {
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
if (frames == null)
{
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 AlignFrame)
{
- if (frames[i] instanceof AlignFrame)
+ 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)
{
- AlignFrame af = (AlignFrame) frames[i];
- avp.addElement(af);
+ avp.add((AlignFrame) sf.getTopFrame());
+ }
+ if (sf.getBottomFrame() instanceof AlignFrame)
+ {
+ avp.add((AlignFrame) sf.getBottomFrame());
}
}
- } 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();
+ AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]);
return afs;
}
- public AppJmol[] getJmols()
+
+ /**
+ * Returns an array of any AppJmol frames in the Desktop (or null if none).
+ *
+ * @return
+ */
+ public GStructureViewer[] getJmols()
{
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
@@ -2130,104 +2298,165 @@ 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 AppJmol)
- {
- AppJmol af = (AppJmol) frames[i];
- avp.addElement(af);
- }
+ GStructureViewer af = (GStructureViewer) frames[i];
+ avp.add(af);
}
- } catch (Exception ex)
- {
- ex.printStackTrace();
}
if (avp.size() == 0)
{
return null;
}
- AppJmol afs[] = new AppJmol[avp.size()];
- for (int i = 0, j = avp.size(); i < j; i++)
- {
- afs[i] = (AppJmol) 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,
- "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.",
- "Jalview Groovy Support Failed",
- JOptionPane.ERROR_MESSAGE);
+ MessageManager.getString("label.couldnt_create_groovy_shell"),
+ MessageManager.getString("label.groovy_support_failed"),
+ 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,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()),
+ "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;
+ 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)
+ if (progressBars.get(Long.valueOf(id)) != null)
{
- JPanel progressPanel = progressBars
- .remove(new Long(id));
- if (progressBarHandlers.contains(new Long(id)))
+ JPanel panel = progressBars.remove(Long.valueOf(id));
+ if (progressBarHandlers.contains(Long.valueOf(id)))
{
- progressBarHandlers.remove(new Long(id));
+ progressBarHandlers.remove(Long.valueOf(id));
}
- removeProgressPanel(progressPanel);
+ removeProgressPanel(panel);
}
else
{
- progressBars.put(new Long(id), addProgressPanel(message));
+ progressBars.put(Long.valueOf(id), addProgressPanel(message));
}
}
@@ -2237,30 +2466,34 @@ 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(Long.valueOf(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));
+ progressBarHandlers.put(Long.valueOf(id), handler);
+ final JPanel progressPanel = progressBars.get(Long.valueOf(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);
@@ -2268,20 +2501,36 @@ 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
*/
- public static AlignFrame getAlignFrameFor(AlignViewport av)
+ @Override
+ public boolean operationInProgress()
+ {
+ if (progressBars != null && progressBars.size() > 0)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * This will return the first AlignFrame holding the given viewport instance.
+ * It will break if there are more than one AlignFrames viewing a particular
+ * av.
+ *
+ * @param viewport
+ * @return alignFrame for viewport
+ */
+ public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
{
if (desktop != null)
{
- AlignmentPanel[] aps = getAlignmentPanels(av.getSequenceSetId());
+ 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;
}
@@ -2292,7 +2541,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
public VamsasApplication getVamsasApplication()
{
- return v_client;
+ // TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS
+ return null;
}
@@ -2330,48 +2580,27 @@ 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);
- }
- // JAL-940 - disabled JWS1 service configuration - always start discoverer until we phase out completely
+ // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
if (true)
{
- (t0 = new Thread(discoverer)).start();
- }
-
- try
- {
- if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+ // todo: changesupport handlers need to be transferred
+ if (discoverer == null)
{
- // 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();
+ discoverer = new jalview.ws.jws1.Discoverer();
+ // register PCS handler for desktop.
+ discoverer.addPropertyChangeListener(changeSupport);
}
- } catch (Exception e)
- {
- Cache.log
- .info("Exception when trying to launch Envision2 workflow discovery.",
- e);
- Cache.log.info(e.getStackTrace());
+ // 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);
-
+ t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ .startDiscoverer(changeSupport);
}
- Thread t3=null;
+ Thread t3 = null;
{
// TODO: do rest service discovery
}
@@ -2385,8 +2614,7 @@ 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());
}
@@ -2408,32 +2636,59 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
{
- if (serviceChangedDialog == null)
- {
- // only run if we aren't already displaying one of these.
- javax.swing.SwingUtilities
- .invokeLater(serviceChangedDialog = new Runnable()
- {
- public void run()
- {
-
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- ermsg
- + "It may be that you have invalid JABA URLs\nin your web service preferences.\n\nGo to the Web services tab of the\nTools->Preferences dialog box to change them.\n",
- "Preferences Problem",
- JOptionPane.WARNING_MESSAGE);
- serviceChangedDialog = null;
-
- }
- });
+ 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"
+ Cache.log.error(
+ "Errors reported by JABA discovery service. Check web services preferences.\n"
+ ermsg);
}
}
@@ -2453,36 +2708,43 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
showUrl(url, Desktop.instance);
}
+
/**
* Like showUrl but allows progress handler to be specified
+ *
* @param url
- * @param progress (null) or object implementing IProgressIndicator
+ * @param progress
+ * (null) or object implementing IProgressIndicator
*/
- public static void showUrl(final String url, final IProgressIndicator progress)
+ public static void showUrl(final String url,
+ final IProgressIndicator progress)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
try
{
- if (progress!=null) {
- progress.setProgressBar("Opening "+url, this.hashCode());
+ 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) {
+ if (progress != null)
+ {
progress.setProgressBar(null, this.hashCode());
}
}
@@ -2500,5 +2762,525 @@ public class Desktop extends jalview.jbgui.GDesktop implements
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;
+ }
+
+ /**
+ * handles the payload of a drag and drop event.
+ *
+ * TODO refactor to desktop utilities class
+ *
+ * @param files
+ * - Data source strings extracted from the drop event
+ * @param protocols
+ * - protocol for each data source extracted from the drop event
+ * @param evt
+ * - the drop event
+ * @param t
+ * - the payload from the drop event
+ * @throws Exception
+ */
+ 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"), urlFlavour = null;
+ try
+ {
+ urlFlavour = new DataFlavor(
+ "application/x-java-url; class=java.net.URL");
+ } catch (ClassNotFoundException cfe)
+ {
+ Cache.log.debug("Couldn't instantiate the URL dataflavor.", cfe);
+ }
+
+ if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour))
+ {
+
+ try
+ {
+ java.net.URL url = (URL) t.getTransferData(urlFlavour);
+ // nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099
+ // means url may be null.
+ if (url != null)
+ {
+ protocols.add(DataSourceType.URL);
+ files.add(url.toString());
+ Cache.log.debug("Drop handled as URL dataflavor "
+ + files.get(files.size() - 1));
+ return;
+ }
+ else
+ {
+ if (Platform.isAMac())
+ {
+ System.err.println(
+ "Please ignore plist error - occurs due to problem with java 8 on OSX");
+ }
+ ;
+ }
+ } catch (Throwable ex)
+ {
+ Cache.log.debug("URL drop handler failed.", ex);
+ }
+ }
+ 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
+ DataFlavor textDf = new DataFlavor(
+ "text/plain;class=java.lang.String");
+ if (t.isDataFlavorSupported(textDf))
+ {
+ data = (String) t.getTransferData(textDf);
+ }
+
+ Cache.log.debug("Plain text drop content returned "
+ + (data == null ? "Null - failed" : data));
+
+ }
+ if (data != null)
+ {
+ 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)
+ {
+
+ if (t.getTransferDataFlavors() != null
+ && t.getTransferDataFlavors().length > 0)
+ {
+ 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");
+ }
+ }
+ }
+ else
+ {
+ Cache.log.debug("Couldn't resolve dataflavor for drop: "
+ + t.toString());
+ }
+ }
+ }
+ }
+ if (Platform.isWindows())
+
+ {
+ Cache.log.debug("Scanning dropped content for Windows Link Files");
+
+ // resolve any .lnk files in the file drop
+ for (int f = 0; f < files.size(); f++)
+ {
+ String source = files.get(f).toLowerCase();
+ if (protocols.get(f).equals(DataSourceType.FILE)
+ && (source.endsWith(".lnk") || source.endsWith(".url")
+ || source.endsWith(".site")))
+ {
+ try
+ {
+ File lf = new File(files.get(f));
+ // process link file to get a URL
+ Cache.log.debug("Found potential link file: " + lf);
+ WindowsShortcut wscfile = new WindowsShortcut(lf);
+ String fullname = wscfile.getRealFilename();
+ protocols.set(f, FormatAdapter.checkProtocol(fullname));
+ files.set(f, fullname);
+ Cache.log.debug("Parsed real filename " + fullname
+ + " to extract protocol: " + protocols.get(f));
+ } catch (Exception ex)
+ {
+ Cache.log.error(
+ "Couldn't parse " + files.get(f) + " as a link file.",
+ ex);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * 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));
+ }
+
+ /**
+ * Answers a (possibly empty) list of any structure viewer frames (currently
+ * for either Jmol or Chimera) which are currently open. This may optionally
+ * be restricted to viewers of a specified class, or viewers linked to a
+ * specified alignment panel.
+ *
+ * @param apanel
+ * if not null, only return viewers linked to this panel
+ * @param structureViewerClass
+ * if not null, only return viewers of this class
+ * @return
+ */
+ public List getStructureViewers(
+ AlignmentPanel apanel,
+ Class extends StructureViewerBase> structureViewerClass)
+ {
+ List result = new ArrayList<>();
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof StructureViewerBase)
+ {
+ if (structureViewerClass == null
+ || structureViewerClass.isInstance(frame))
+ {
+ if (apanel == null
+ || ((StructureViewerBase) frame).isLinkedWith(apanel))
+ {
+ result.add((StructureViewerBase) frame);
+ }
+ }
+ }
+ }
+ return result;
+ }
}