chainNames)
+ {
+ chainMenu.removeAll();
+ if (chainNames == null || chainNames.isEmpty())
+ {
+ return;
+ }
+ JMenuItem menuItem = new JMenuItem(
+ MessageManager.getString("label.all"));
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ allChainsSelected = true;
+ for (int i = 0; i < chainMenu.getItemCount(); i++)
+ {
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
+ ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
+ }
+ }
+ showSelectedChains();
+ allChainsSelected = false;
+ }
+ });
+
+ chainMenu.add(menuItem);
+
+ for (String chain : chainNames)
+ {
+ menuItem = new JCheckBoxMenuItem(chain, true);
+ menuItem.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (!allChainsSelected)
+ {
+ showSelectedChains();
+ }
+ }
+ });
+
+ chainMenu.add(menuItem);
+ }
+ }
+
/**
- * Check if the PDB file is already loaded, if so offer to add it to the
- * existing viewer
+ * Action on selecting one of Jalview's registered colour schemes
+ */
+ @Override
+ public void changeColour_actionPerformed(String colourSchemeName)
+ {
+ AlignmentI al = getAlignmentPanel().av.getAlignment();
+ ColourSchemeI cs = ColourSchemes.getInstance()
+ .getColourScheme(colourSchemeName, getAlignmentPanel().av, al,
+ null);
+ getBinding().colourByJalviewColourScheme(cs);
+ }
+
+ /**
+ * Builds the colour menu
+ */
+ protected void buildColourMenu()
+ {
+ colourMenu.removeAll();
+ AlignmentI al = getAlignmentPanel().av.getAlignment();
+
+ /*
+ * add colour by sequence, by chain, by charge and cysteine
+ */
+ colourMenu.add(seqColour);
+ colourMenu.add(chainColour);
+ colourMenu.add(chargeColour);
+ chargeColour.setEnabled(!al.isNucleotide());
+
+ /*
+ * add all 'simple' (per-residue) colour schemes registered to Jalview
+ */
+ ButtonGroup itemGroup = ColourMenuHelper.addMenuItems(colourMenu, this,
+ al, true);
+
+ /*
+ * add 'colour by viewer' (menu item text is set in subclasses)
+ */
+ viewerColour.setSelected(false);
+ viewerColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ viewerColour_actionPerformed();
+ }
+ });
+ colourMenu.add(viewerColour);
+
+ /*
+ * add 'set background colour'
+ */
+ JMenuItem backGround = new JMenuItem();
+ backGround
+ .setText(MessageManager.getString("action.background_colour"));
+ backGround.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ background_actionPerformed();
+ }
+ });
+ colourMenu.add(backGround);
+
+ /*
+ * add colour buttons to a group so their selection is
+ * mutually exclusive (background colour is a separate option)
+ */
+ itemGroup.add(seqColour);
+ itemGroup.add(chainColour);
+ itemGroup.add(chargeColour);
+ itemGroup.add(viewerColour);
+ }
+
+ /**
+ * Construct menu items
+ */
+ protected void initMenus()
+ {
+ AAStructureBindingModel binding = getBinding();
+
+ seqColour = new JRadioButtonMenuItem();
+ seqColour.setText(MessageManager.getString("action.by_sequence"));
+ seqColour.setName(ViewerColour.BySequence.name());
+ seqColour.setSelected(binding.isColourBySequence());
+ seqColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ seqColour_actionPerformed();
+ }
+ });
+
+ chainColour = new JRadioButtonMenuItem();
+ chainColour.setText(MessageManager.getString("action.by_chain"));
+ chainColour.setName(ViewerColour.ByChain.name());
+ chainColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ chainColour_actionPerformed();
+ }
+ });
+
+ chargeColour = new JRadioButtonMenuItem();
+ chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
+ chargeColour.setName(ViewerColour.ChargeCysteine.name());
+ chargeColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ chargeColour_actionPerformed();
+ }
+ });
+
+ viewerColour = new JRadioButtonMenuItem();
+ viewerColour
+ .setText(MessageManager.getString("label.colour_with_viewer"));
+ viewerColour.setToolTipText(MessageManager
+ .getString("label.let_viewer_manage_structure_colours"));
+ viewerColour.setName(ViewerColour.ByViewer.name());
+ viewerColour.setSelected(!binding.isColourBySequence());
+
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector<>();
+ }
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<>();
+ }
+
+ ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
+ MessageManager.getString("label.colour_by"), this, _colourwith,
+ new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (!seqColour.isSelected())
+ {
+ seqColour.doClick();
+ }
+ else
+ {
+ // update the viewer display now.
+ seqColour_actionPerformed();
+ }
+ }
+ });
+ viewMenu.add(seqColourBy);
+
+ final ItemListener handler = new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (_alignwith.isEmpty())
+ {
+ alignStructs.setEnabled(false);
+ alignStructs.setToolTipText(null);
+ }
+ else
+ {
+ alignStructs.setEnabled(true);
+ alignStructs.setToolTipText(MessageManager.formatMessage(
+ "label.align_structures_using_linked_alignment_views",
+ _alignwith.size()));
+ }
+ }
+ };
+ viewSelectionMenu = new ViewSelectionMenu(
+ MessageManager.getString("label.superpose_with"), this,
+ _alignwith, handler);
+ handler.itemStateChanged(null);
+ viewerActionMenu.add(viewSelectionMenu, 0);
+ viewerActionMenu.addMenuListener(new MenuListener()
+ {
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
+ handler.itemStateChanged(null);
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent e)
+ {
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent e)
+ {
+ }
+ });
+
+ viewerActionMenu.setText(getViewerName());
+ helpItem.setText(MessageManager.formatMessage("label.viewer_help",
+ getViewerName()));
+
+ buildColourMenu();
+ }
+
+ /**
+ * Sends commands to the structure viewer to superimpose structures based on
+ * currently associated alignments. May optionally return an error message for
+ * the operation.
+ */
+ @Override
+ protected String alignStructsWithAllAlignPanels()
+ {
+ if (getAlignmentPanel() == null)
+ {
+ return null;
+ }
+
+ if (_alignwith.size() == 0)
+ {
+ _alignwith.add(getAlignmentPanel());
+ }
+
+ String reply = null;
+ try
+ {
+ reply = getBinding().superposeStructures(_alignwith);
+ if (reply != null && !reply.isEmpty())
+ {
+ String text = MessageManager
+ .formatMessage("error.superposition_failed", reply);
+ statusBar.setText(text);
+ }
+ } catch (Exception e)
+ {
+ StringBuffer sp = new StringBuffer();
+ for (AlignmentViewPanel alignPanel : _alignwith)
+ {
+ sp.append("'" + alignPanel.getViewName() + "' ");
+ }
+ Console.info("Couldn't align structures with the " + sp.toString()
+ + "associated alignment panels.", e);
+ }
+ return reply;
+ }
+
+ /**
+ * Opens a colour chooser dialog, and applies the chosen colour to the
+ * background of the structure viewer
+ */
+ @Override
+ public void background_actionPerformed()
+ {
+ String ttl = MessageManager.getString("label.select_background_colour");
+ ColourChooserListener listener = new ColourChooserListener()
+ {
+ @Override
+ public void colourSelected(Color c)
+ {
+ getBinding().setBackgroundColour(c);
+ }
+ };
+ JalviewColourChooser.showColourChooser(this, ttl, null, listener);
+ }
+
+ @Override
+ public void viewerColour_actionPerformed()
+ {
+ if (viewerColour.isSelected())
+ {
+ // disable automatic sequence colouring.
+ getBinding().setColourBySequence(false);
+ }
+ }
+
+ @Override
+ public void chainColour_actionPerformed()
+ {
+ chainColour.setSelected(true);
+ getBinding().colourByChain();
+ }
+
+ @Override
+ public void chargeColour_actionPerformed()
+ {
+ chargeColour.setSelected(true);
+ getBinding().colourByCharge();
+ }
+
+ @Override
+ public void seqColour_actionPerformed()
+ {
+ AAStructureBindingModel binding = getBinding();
+ binding.setColourBySequence(seqColour.isSelected());
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector<>();
+ }
+ if (binding.isColourBySequence())
+ {
+ if (!binding.isLoadingFromArchive())
+ {
+ if (_colourwith.size() == 0 && getAlignmentPanel() != null)
+ {
+ // Make the currently displayed alignment panel the associated view
+ _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
+ }
+ }
+ // Set the colour using the current view for the associated alignframe
+ for (AlignmentViewPanel alignPanel : _colourwith)
+ {
+ binding.colourBySequence(alignPanel);
+ }
+ seqColoursApplied = true;
+ }
+ }
+
+ @Override
+ public void pdbFile_actionPerformed()
+ {
+ // TODO: JAL-3048 not needed for Jalview-JS - save PDB file
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ Cache.getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ BufferedReader in = null;
+ try
+ {
+ // TODO: cope with multiple PDB files in view
+ in = new BufferedReader(
+ new FileReader(getBinding().getStructureFiles()[0]));
+ File outFile = chooser.getSelectedFile();
+
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+ String data;
+ while ((data = in.readLine()) != null)
+ {
+ if (!(data.indexOf("") > -1 || data.indexOf("") > -1))
+ {
+ out.println(data);
+ }
+ }
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } finally
+ {
+ if (in != null)
+ {
+ try
+ {
+ in.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ }
+ }
+
+ @Override
+ public void viewMapping_actionPerformed()
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ try
+ {
+ cap.appendText(getBinding().printMappings());
+ } catch (OutOfMemoryError e)
+ {
+ new OOMWarning(
+ "composing sequence-structure alignments for display in text box.",
+ e);
+ cap.dispose();
+ return;
+ }
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
+ }
+
+ protected abstract String getViewerName();
+
+ /**
+ * Configures the title and menu items of the viewer panel.
+ */
+ @Override
+ public void updateTitleAndMenus()
+ {
+ AAStructureBindingModel binding = getBinding();
+ if (binding.hasFileLoadingError())
+ {
+ repaint();
+ return;
+ }
+ setChainMenuItems(binding.getChainNames());
+
+ this.setTitle(binding.getViewerTitle(getViewerName(), true));
+
+ /*
+ * enable 'Superpose with' if more than one mapped structure
+ */
+ viewSelectionMenu.setEnabled(false);
+ if (getBinding().getMappedStructureCount() > 1
+ && getBinding().getSequence().length > 1)
+ {
+ viewSelectionMenu.setEnabled(true);
+ }
+
+ /*
+ * Show action menu if it has any enabled items
+ */
+ viewerActionMenu.setVisible(false);
+ for (int i = 0; i < viewerActionMenu.getItemCount(); i++)
+ {
+ if (viewerActionMenu.getItem(i).isEnabled())
+ {
+ viewerActionMenu.setVisible(true);
+ break;
+ }
+ }
+
+ if (!binding.isLoadingFromArchive())
+ {
+ seqColour_actionPerformed();
+ }
+ }
+
+ @Override
+ public String toString()
+ {
+ return getTitle();
+ }
+
+ @Override
+ public boolean hasMapping()
+ {
+ if (worker != null && (addingStructures || _started))
+ {
+ return false;
+ }
+ if (getBinding() == null)
+ {
+ if (_aps == null || _aps.size() == 0)
+ {
+ // viewer has been closed, but we did at some point run.
+ return true;
+ }
+ return false;
+ }
+ String[] pdbids = getBinding().getStructureFiles();
+ if (pdbids == null)
+ {
+ return false;
+ }
+ int p=0;
+ for (String pdbid:pdbids) {
+ StructureMapping sm[] = getBinding().getSsm().getMapping(pdbid);
+ if (sm!=null && sm.length>0 && sm[0]!=null) {
+ p++;
+ }
+ }
+ // only return true if there is a mapping for every structure file we have loaded
+ if (p == 0 || p != pdbids.length)
+ {
+ return false;
+ }
+ // and that coloring has been applied
+ return seqColoursApplied;
+ }
+
+ @Override
+ public void raiseViewer()
+ {
+ toFront();
+ }
+
+ @Override
+ public long startProgressBar(String msg)
+ {
+ // TODO would rather have startProgress/stopProgress as the
+ // IProgressIndicator interface
+ long tm = random.nextLong();
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(msg, tm);
+ }
+ return tm;
+ }
+
+ @Override
+ public void stopProgressBar(String msg, long handle)
+ {
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(msg, handle);
+ }
+ }
+
+ protected IProgressIndicator getProgressIndicator()
+ {
+ return progressBar;
+ }
+
+ protected void setProgressIndicator(IProgressIndicator pi)
+ {
+ progressBar = pi;
+ }
+
+ public void setProgressMessage(String message, long id)
+ {
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(message, id);
+ }
+ }
+
+ @Override
+ public void showConsole(boolean show)
+ {
+ // default does nothing
+ }
+
+ /**
+ * Show only the selected chain(s) in the viewer
+ */
+ protected void showSelectedChains()
+ {
+ List toshow = new ArrayList<>();
+ for (int i = 0; i < chainMenu.getItemCount(); i++)
+ {
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
+ JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
+ if (item.isSelected())
+ {
+ toshow.add(item.getText());
+ }
+ }
+ }
+ getBinding().showChains(toshow);
+ }
+
+ /**
+ * Tries to fetch a PDB file and save to a temporary local file. Returns the
+ * saved file path if successful, or null if not.
*
- * @param seq
- * @param chains
- * @param apanel
- * @param pdbId
- * @return true if the user chooses to add to a viewer, or to cancel entirely
+ * @param processingEntry
+ * @return
*/
- protected boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
- final AlignmentPanel apanel, String pdbId)
+ protected String fetchPdbFile(PDBEntry processingEntry)
{
- boolean finished = false;
- String alreadyMapped = apanel.getStructureSelectionManager()
- .alreadyMappedToFile(pdbId);
+ String filePath = null;
+ Pdb pdbclient = new Pdb();
+ EBIAlfaFold afclient = new EBIAlfaFold();
+ AlignmentI pdbseq = null;
+ String pdbid = processingEntry.getId();
+ long handle = System.currentTimeMillis()
+ + Thread.currentThread().hashCode();
- if (alreadyMapped != null)
- {
- /*
- * the PDB file is already loaded
- */
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.pdb_entry_is_already_displayed", new Object[]
- { pdbId }), MessageManager.formatMessage(
- "label.map_sequences_to_visible_window", new Object[]
- { pdbId }), JOptionPane.YES_NO_CANCEL_OPTION);
- if (option == JOptionPane.CANCEL_OPTION)
+ /*
+ * Write 'fetching PDB' progress on AlignFrame as we are not yet visible
+ */
+ String msg = MessageManager.formatMessage("status.fetching_pdb",
+ new Object[]
+ { pdbid });
+ getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
+ // long hdl = startProgressBar(MessageManager.formatMessage(
+ // "status.fetching_pdb", new Object[]
+ // { pdbid }));
+ try
+ {
+ if (afclient.isValidReference(pdbid))
+ {
+ pdbseq = afclient.getSequenceRecords(pdbid,processingEntry.getRetrievalUrl());
+ } else {
+ if (processingEntry.hasRetrievalUrl())
+ {
+ String safePDBId = java.net.URLEncoder.encode(pdbid,"UTF-8");
+
+ // retrieve from URL to new local tmpfile
+ File tmpFile = File.createTempFile(safePDBId,
+ "." + (PDBEntry.Type.MMCIF.toString().equals(
+ processingEntry.getType().toString()) ? "cif"
+ : "pdb"));
+ String fromUrl = processingEntry.getRetrievalUrl();
+ UrlDownloadClient.download(fromUrl, tmpFile);
+
+ // may not need this check ?
+ String file = tmpFile.getAbsolutePath();
+ if (file != null)
+ {
+ pdbseq = EBIAlfaFold.importDownloadedStructureFromUrl(fromUrl,tmpFile,pdbid,null,null,null);
+ }
+ } else {
+ pdbseq = pdbclient.getSequenceRecords(pdbid);
+ }
+ }
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Error retrieving PDB id " + pdbid + ": " + e.getMessage());
+ } finally
+ {
+ msg = pdbid + " " + MessageManager.getString("label.state_completed");
+ getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
+ // stopProgressBar(msg, hdl);
+ }
+ /*
+ * If PDB data were saved and are not invalid (empty alignment), return the
+ * file path.
+ */
+ if (pdbseq != null && pdbseq.getHeight() > 0)
+ {
+ // just use the file name from the first sequence's first PDBEntry
+ filePath = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
+ .elementAt(0).getFile()).getAbsolutePath();
+ processingEntry.setFile(filePath);
+ }
+ return filePath;
+ }
+
+ /**
+ * If supported, saves the state of the structure viewer to a temporary file
+ * and returns the file, else returns null
+ *
+ * @return
+ */
+ public File saveSession()
+ {
+ if (getBinding() == null) { return null;}
+ File session = getBinding().saveSession();
+ long l = session.length();
+ int wait=50;
+ do {
+ try {
+ Thread.sleep(5);
+ } catch (InterruptedException e) {
+ }
+ long nextl = session.length();
+ if (nextl!=l)
+ {
+ wait = 50;
+ l=nextl;
+ }
+ } while (--wait>0);
+ return session;
+ }
+
+ /**
+ * Close down this instance of Jalview's Chimera viewer, giving the user the
+ * option to close the associated Chimera window (process). They may wish to
+ * keep it open until they have had an opportunity to save any work.
+ *
+ * @param forceClose
+ * if true, close any linked Chimera process; if false, prompt first
+ */
+ @Override
+ public void closeViewer(boolean forceClose)
+ {
+ AAStructureBindingModel binding = getBinding();
+ if (binding != null && binding.isViewerRunning())
+ {
+ if (!forceClose)
{
- finished = true;
+ String viewerName = getViewerName();
+ String prompt = MessageManager
+ .formatMessage("label.confirm_close_viewer", new Object[]
+ { binding.getViewerTitle(viewerName, false), viewerName });
+ prompt = JvSwingUtils.wrapTooltip(true, prompt);
+ int confirm = JvOptionPane.showConfirmDialog(this, prompt,
+ MessageManager.getString("label.close_viewer"),
+ JvOptionPane.YES_NO_CANCEL_OPTION);
+ /*
+ * abort closure if user hits escape or Cancel
+ */
+ if (confirm == JvOptionPane.CANCEL_OPTION
+ || confirm == JvOptionPane.CLOSED_OPTION)
+ {
+ return;
+ }
+ forceClose = confirm == JvOptionPane.YES_OPTION;
}
- else if (option == JOptionPane.YES_OPTION)
+ }
+ if (binding != null)
+ {
+ binding.closeViewer(forceClose);
+ }
+ setAlignmentPanel(null);
+ _aps.clear();
+ _alignwith.clear();
+ _colourwith.clear();
+ // TODO: check for memory leaks where instance isn't finalised because jmb
+ // holds a reference to the window
+ // jmb = null;
+ dispose();
+ }
+
+ @Override
+ public void showHelp_actionPerformed()
+ {
+ try
+ {
+ String url = getBinding().getHelpURL();
+ if (url != null)
{
- addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
- finished = true;
+ BrowserLauncher.openURL(url);
}
+ } catch (IOException ex)
+ {
+ System.err
+ .println("Show " + getViewerName() + " failed with: "
+ + ex.getMessage());
}
- return finished;
+ }
+ @Override
+ public boolean hasViewerActionsMenu()
+ {
+ return viewerActionMenu != null && viewerActionMenu.isEnabled()
+ && viewerActionMenu.getItemCount() > 0
+ && viewerActionMenu.isVisible();
}
}