+ while (st.hasMoreTokens())
+ {
+ history.addItem(st.nextElement());
+ }
+ }
+
+ int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
+ "Input Alignment From URL", JOptionPane.OK_CANCEL_OPTION);
+
+ if (reply != JOptionPane.OK_OPTION)
+ {
+ return;
+ }
+
+ String url = history.getSelectedItem().toString();
+
+ if (url.toLowerCase().endsWith(".jar"))
+ {
+ if (viewport != null)
+ {
+ new FileLoader().LoadFile(viewport, url, FormatAdapter.URL,
+ "Jalview");
+ }
+ else
+ {
+ new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
+ }
+ }
+ else
+ {
+ String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
+
+ if (format.equals("URL NOT FOUND"))
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Couldn't locate " + url, "URL not found",
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+
+ if (viewport != null)
+ {
+ new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
+ }
+ else
+ {
+ new FileLoader().LoadFile(url, FormatAdapter.URL, format);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(viewport);
+ Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+ }
+
+ /*
+ * Exit the program
+ */
+ public void quit()
+ {
+ Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+ jalview.bin.Cache
+ .setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
+ jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height
+ + "");
+ storeLastKnownDimensions("", new Rectangle(getBounds().x,
+ getBounds().y, getWidth(), getHeight()));
+
+ if (jconsole != null)
+ {
+ storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
+ jconsole.stopConsole();
+ }
+ if (jvnews!=null)
+ {
+ storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
+
+ }
+
+ System.exit(0);
+ }
+
+ private void storeLastKnownDimensions(String string, Rectangle jc)
+ {
+ jalview.bin.Cache.log.debug("Storing last known dimensions for "
+ + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+ + " height:" + jc.height);
+
+ jalview.bin.Cache.setProperty(string + "SCREEN_X", jc.x + "");
+ jalview.bin.Cache.setProperty(string + "SCREEN_Y", jc.y + "");
+ jalview.bin.Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
+ jalview.bin.Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void aboutMenuItem_actionPerformed(ActionEvent e)
+ {
+ StringBuffer message = new StringBuffer("Jalview version "
+ + jalview.bin.Cache.getProperty("VERSION") + "; last updated: "
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+
+ if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
+ jalview.bin.Cache.getProperty("VERSION")))
+ {
+ message.append("\n\n!! Jalview version "
+ + jalview.bin.Cache.getProperty("LATEST_VERSION")
+ + " is available for download from "+jalview.bin.Cache.getDefault("www.jalview.org","http://www.jalview.org")+" !!\n");
+
+ }
+ // TODO: update this text for each release or centrally store it for lite
+ // and application
+ message.append("\nAuthors: Jim Procter, 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,
+
+ message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ 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);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ public void closeAll_actionPerformed(ActionEvent e)
+ {
+ JInternalFrame[] frames = desktop.getAllFrames();
+ for (int i = 0; i < frames.length; i++)
+ {
+ try
+ {
+ frames[i].setClosed(true);
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
+ }
+ System.out.println("ALL CLOSED");
+ if (v_client != null)
+ {
+ // TODO clear binding to vamsas document objects on close_all
+
+ }
+ }
+
+ public void raiseRelated_actionPerformed(ActionEvent e)
+ {
+ reorderAssociatedWindows(false, false);
+ }
+
+ public void minimizeAssociated_actionPerformed(ActionEvent e)
+ {
+ reorderAssociatedWindows(true, false);
+ }
+
+ void closeAssociatedWindows()
+ {
+ reorderAssociatedWindows(false, true);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.
+ * ActionEvent)
+ */
+ protected void garbageCollect_actionPerformed(ActionEvent e)
+ {
+ // We simply collect the garbage
+ jalview.bin.Cache.log.debug("Collecting garbage...");
+ System.gc();
+ jalview.bin.Cache.log.debug("Finished garbage collection.");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
+ * )
+ */
+ protected void showMemusage_actionPerformed(ActionEvent e)
+ {
+ desktop.showMemoryUsage(showMemusage.isSelected());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent
+ * )
+ */
+ 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();
+ if (frames == null || frames.length < 1)
+ {
+ return;
+ }
+
+ AlignViewport source = null, target = null;
+ if (frames[0] instanceof AlignFrame)
+ {
+ source = ((AlignFrame) frames[0]).getCurrentView();
+ }
+ else if (frames[0] instanceof TreePanel)
+ {
+ source = ((TreePanel) frames[0]).getViewPort();
+ }
+ else if (frames[0] instanceof PCAPanel)
+ {
+ source = ((PCAPanel) frames[0]).av;
+ }
+ else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
+ {
+ source = ((PairwiseAlignPanel) frames[0].getContentPane()).av;
+ }
+
+ if (source != null)
+ {
+ for (int i = 0; i < frames.length; i++)
+ {
+ target = null;
+ if (frames[i] == null)
+ {
+ continue;
+ }
+ if (frames[i] instanceof AlignFrame)
+ {
+ target = ((AlignFrame) frames[i]).getCurrentView();
+ }
+ else if (frames[i] instanceof TreePanel)
+ {
+ target = ((TreePanel) frames[i]).getViewPort();
+ }
+ else if (frames[i] instanceof PCAPanel)
+ {
+ target = ((PCAPanel) frames[i]).av;
+ }
+ else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
+ {
+ target = ((PairwiseAlignPanel) frames[i].getContentPane()).av;
+ }
+
+ if (source == target)
+ {
+ try
+ {
+ if (close)
+ {
+ frames[i].setClosed(true);
+ }
+ else
+ {
+ frames[i].setIcon(minimize);
+ if (!minimize)
+ {
+ frames[i].toFront();
+ }
+ }
+
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void preferences_actionPerformed(ActionEvent e)
+ {
+ new Preferences();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ 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");
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save State");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ final Desktop me = this;
+ final java.io.File choice = chooser.getSelectedFile();
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+
+ 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());
+ }
+ }).start();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ 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");
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("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());
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ setProgressBar("loading jalview project " + choice,
+ choice.hashCode());
+ try
+ {
+ new Jalview2XML().LoadJalviewAlign(choice);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Whilst loading project from " + choice, oom);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Problems whilst loading project from "
+ + choice, ex);
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "Error whilst loading project from " + choice,
+ "Couldn't load project", JOptionPane.WARNING_MESSAGE);
+ }
+ setProgressBar(null, choice.hashCode());
+ }
+ }).start();
+ }
+ }
+
+ public void inputSequence_actionPerformed(ActionEvent e)
+ {
+ new SequenceFetcher(this);
+ }
+
+ JPanel progressPanel;
+ ArrayList<JPanel> fileLoadingPanels=new ArrayList<JPanel>();
+ public void startLoading(final String fileName)
+ {
+ if (fileLoadingCount == 0)
+ {
+ fileLoadingPanels.add(addProgressPanel("Loading File: " + fileName + " "));
+ }
+ fileLoadingCount++;
+ }
+
+ private JPanel addProgressPanel(String string)
+ {
+ if (progressPanel == null)
+ {
+ 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);
+
+ thisprogress.add(new JLabel(string), BorderLayout.WEST);
+
+ 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(JPanel progbar)
+ {
+ if (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)
+ {
+ for (JPanel flp : fileLoadingPanels)
+ {
+ removeProgressPanel(flp);
+ }
+ fileLoadingPanels.clear();
+ fileLoadingCount = 0;
+ }
+ validate();
+ }
+
+ public static int getViewCount(String alignmentId)
+ {
+ AlignViewport[] aps = getViewports(alignmentId);
+ return (aps == null) ? 0 : aps.length;
+ }
+
+ /**
+ *
+ * @param alignmentId
+ * @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++)
+ {
+ if (frames[t] instanceof AlignFrame)
+ {
+ AlignFrame af = (AlignFrame) frames[t];
+ for (int a = 0; a < af.alignPanels.size(); a++)
+ {
+ if (alignmentId
+ .equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av
+ .getSequenceSetId()))
+ {
+ aps.add(af.alignPanels.elementAt(a));
+ }
+ }
+ }
+ }
+ if (aps.size() == 0)
+ {
+ return null;
+ }
+ AlignmentPanel[] vap = new AlignmentPanel[aps.size()];
+ for (int t = 0; t < vap.length; t++)
+ {
+ vap[t] = (AlignmentPanel) aps.get(t);
+ }
+ return vap;
+ }
+
+ /**
+ * get all the viewports on an alignment.
+ *
+ * @param sequenceSetId
+ * unique alignment id
+ * @return all viewports on the alignment bound to sequenceSetId
+ */
+ public static AlignViewport[] getViewports(String sequenceSetId)
+ {
+ Vector viewp = new Vector();
+ if (desktop != null)
+ {
+ javax.swing.JInternalFrame[] frames = instance.getAllFrames();
+
+ for (int t = 0; t < frames.length; t++)
+ {
+ if (frames[t] instanceof AlignFrame)
+ {
+ AlignFrame afr = ((AlignFrame) frames[t]);
+ if (afr.getViewport().getSequenceSetId().equals(sequenceSetId))
+ {
+ if (afr.alignPanels != null)
+ {
+ for (int a = 0; a < afr.alignPanels.size(); a++)
+ {
+ if (sequenceSetId.equals(((AlignmentPanel) afr.alignPanels
+ .elementAt(a)).av.getSequenceSetId()))
+ {
+ viewp.addElement(((AlignmentPanel) afr.alignPanels
+ .elementAt(a)).av);
+ }
+ }
+ }
+ else
+ {
+ viewp.addElement(((AlignFrame) frames[t]).getViewport());
+ }
+ }
+ }
+ }
+ if (viewp.size() > 0)
+ {
+ AlignViewport[] vp = new AlignViewport[viewp.size()];
+ viewp.copyInto(vp);
+ return vp;
+ }
+ }
+ return null;
+ }
+
+ public void explodeViews(AlignFrame af)
+ {
+ int size = af.alignPanels.size();
+ if (size < 2)
+ {
+ return;
+ }
+
+ for (int i = 0; i < size; i++)
+ {
+ AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(i);
+ AlignFrame newaf = new AlignFrame(ap);
+ if (ap.av.explodedPosition != null
+ && !ap.av.explodedPosition.equals(af.getBounds()))
+ {
+ newaf.setBounds(ap.av.explodedPosition);
+ }
+
+ ap.av.gatherViewsHere = false;
+
+ addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
+
+ }
+
+ public void gatherViews(AlignFrame source)
+ {
+ source.viewport.gatherViewsHere = true;
+ source.viewport.explodedPosition = source.getBounds();
+ JInternalFrame[] frames = desktop.getAllFrames();
+ String viewId = source.viewport.sequenceSetID;
+
+ for (int t = 0; t < frames.length; t++)
+ {
+ if (frames[t] instanceof AlignFrame && frames[t] != source)
+ {
+ AlignFrame af = (AlignFrame) frames[t];
+ boolean gatherThis = false;
+ for (int a = 0; a < af.alignPanels.size(); a++)
+ {
+ AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a);
+ if (viewId.equals(ap.av.getSequenceSetId()))
+ {
+ gatherThis = true;
+ ap.av.gatherViewsHere = false;
+ ap.av.explodedPosition = af.getBounds();
+ source.addAlignmentPanel(ap, false);
+ }
+ }
+
+ if (gatherThis)
+ {
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
+ }
+ }
+ }
+
+ }
+
+ jalview.gui.VamsasApplication v_client = null;
+
+ public void vamsasImport_actionPerformed(ActionEvent e)
+ {
+ if (v_client == null)
+ {
+ // Load and try to start a session.
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+
+ 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.");