+ }
+ }
+ 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.");
+
+ int value = chooser.showOpenDialog(this);
+
+ 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);
+ }
+ }
+ }
+ 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("Importing VAMSAS session from " + file.getName(),
+ file.hashCode());
+ try
+ {
+ v_client = new jalview.gui.VamsasApplication(this, file, null);
+ } catch (Exception ex)
+ {
+ setProgressBar("Importing VAMSAS session from " + file.getName(),
+ file.hashCode());
+ 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,