/* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.gui.StructureViewer.ViewerType; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.schemes.BuriedColourScheme; import jalview.schemes.ColourSchemeI; import jalview.schemes.HelixColourScheme; import jalview.schemes.HydrophobicColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; import jalview.schemes.StrandColourScheme; import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; import jalview.schemes.ZappoColourScheme; import jalview.structures.models.AAStructureBindingModel; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.ws.dbsources.Pdb; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.Font; import java.awt.Graphics; import java.awt.Rectangle; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; import java.io.FileReader; import java.io.IOException; import java.io.PrintWriter; import java.util.ArrayList; import java.util.List; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; import javax.swing.JColorChooser; import javax.swing.JInternalFrame; import javax.swing.JMenu; import javax.swing.JMenuItem; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JSplitPane; import javax.swing.SwingUtilities; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; public class AppJmol extends StructureViewerBase { // ms to wait for Jmol to load files private static final int JMOL_LOAD_TIMEOUT = 20000; private static final String SPACE = " "; private static final String BACKSLASH = "\""; AppJmolBinding jmb; JPanel scriptWindow; JSplitPane splitPane; RenderPanel renderPanel; ViewSelectionMenu seqColourBy; /** * * @param files * @param ids * @param seqs * @param ap * @param usetoColour * - add the alignment panel to the list used for colouring these * structures * @param useToAlign * - add the alignment panel to the list used for aligning these * structures * @param leaveColouringToJmol * - do not update the colours from any other source. Jmol is * handling them * @param loadStatus * @param bounds * @param viewid */ public AppJmol(String[] files, String[] ids, SequenceI[][] seqs, AlignmentPanel ap, boolean usetoColour, boolean useToAlign, boolean leaveColouringToJmol, String loadStatus, Rectangle bounds, String viewid) { PDBEntry[] pdbentrys = new PDBEntry[files.length]; for (int i = 0; i < pdbentrys.length; i++) { // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]); PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB, files[i]); pdbentrys[i] = pdbentry; } // / TODO: check if protocol is needed to be set, and if chains are // autodiscovered. jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null); jmb.setLoadingFromArchive(true); addAlignmentPanel(ap); if (useToAlign) { useAlignmentPanelForSuperposition(ap); } if (leaveColouringToJmol || !usetoColour) { jmb.setColourBySequence(false); seqColour.setSelected(false); viewerColour.setSelected(true); } else if (usetoColour) { useAlignmentPanelForColourbyseq(ap); jmb.setColourBySequence(true); seqColour.setSelected(true); viewerColour.setSelected(false); } this.setBounds(bounds); initMenus(); setViewId(viewid); // jalview.gui.Desktop.addInternalFrame(this, "Loading File", // bounds.width,bounds.height); this.addInternalFrameListener(new InternalFrameAdapter() { @Override public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { closeViewer(false); } }); initJmol(loadStatus); // pdbentry, seq, JBPCHECK! } private void initMenus() { seqColour.setSelected(jmb.isColourBySequence()); viewerColour.setSelected(!jmb.isColourBySequence()); if (_colourwith == null) { _colourwith = new Vector(); } if (_alignwith == null) { _alignwith = new Vector(); } 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 jmol display now. seqColour_actionPerformed(null); } } }); viewMenu.add(seqColourBy); final ItemListener handler; JMenu alpanels = new ViewSelectionMenu( MessageManager.getString("label.superpose_with"), this, _alignwith, handler = new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { alignStructs.setEnabled(_alignwith.size() > 0); alignStructs.setToolTipText(MessageManager .formatMessage( "label.align_structures_using_linked_alignment_views", new String[] { new Integer(_alignwith .size()).toString() })); } }); handler.itemStateChanged(null); viewerActionMenu.add(alpanels); viewerActionMenu.addMenuListener(new MenuListener() { @Override public void menuSelected(MenuEvent e) { handler.itemStateChanged(null); } @Override public void menuDeselected(MenuEvent e) { // TODO Auto-generated method stub } @Override public void menuCanceled(MenuEvent e) { // TODO Auto-generated method stub } }); } IProgressIndicator progressBar = null; /** * add a single PDB structure to a new or existing Jmol view * * @param pdbentry * @param seq * @param chains * @param ap */ public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains, final AlignmentPanel ap) { progressBar = ap.alignFrame; String pdbId = pdbentry.getId(); /* * If the PDB file is already loaded, the user may just choose to add to an * existing viewer (or cancel) */ if (addAlreadyLoadedFile(seq, chains, ap, pdbId)) { return; } /* * Check if there are other Jmol views involving this alignment and prompt * user about adding this molecule to one of them */ if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId)) { return; } /* * If the options above are declined or do not apply, open a new viewer */ openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq }); } /** * Answers true if this viewer already involves the given PDB ID */ @Override protected boolean hasPdbId(String pdbId) { return jmb.hasPdbId(pdbId); } private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) { progressBar = ap.alignFrame; jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); if (pdbentrys.length > 1) { alignAddedStructures = true; useAlignmentPanelForSuperposition(ap); } jmb.setColourBySequence(true); setSize(400, 400); // probably should be a configurable/dynamic default here initMenus(); addingStructures = false; worker = new Thread(this); worker.start(); this.addInternalFrameListener(new InternalFrameAdapter() { @Override public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { closeViewer(false); } }); } /** * create a new Jmol containing several structures superimposed using the * given alignPanel. * * @param ap * @param pe * @param seqs */ public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs) { openNewJmol(ap, pe, seqs); } /** * Returns a list of any Jmol viewers. The list is restricted to those linked * to the given alignment panel if it is not null. */ @Override protected List getViewersFor(AlignmentPanel apanel) { List result = new ArrayList(); JInternalFrame[] frames = Desktop.instance.getAllFrames(); for (JInternalFrame frame : frames) { if (frame instanceof AppJmol) { if (apanel == null || ((StructureViewerBase) frame).isLinkedWith(apanel)) { result.add((StructureViewerBase) frame); } } } return result; } void initJmol(String command) { jmb.setFinishedInit(false); renderPanel = new RenderPanel(); // TODO: consider waiting until the structure/view is fully loaded before // displaying this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER); jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(), getBounds().width, getBounds().height); if (scriptWindow == null) { BorderLayout bl = new BorderLayout(); bl.setHgap(0); bl.setVgap(0); scriptWindow = new JPanel(bl); scriptWindow.setVisible(false); } jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, null); // jmb.newJmolPopup("Jmol"); if (command == null) { command = ""; } jmb.evalStateCommand(command); jmb.evalStateCommand("set hoverDelay=0.1"); jmb.setFinishedInit(true); } void setChainMenuItems(Vector chains) { chainMenu.removeAll(); if (chains == null) { 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); } } centerViewer(); allChainsSelected = false; } }); chainMenu.add(menuItem); for (String chain : chains) { menuItem = new JCheckBoxMenuItem(chain, true); menuItem.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent evt) { if (!allChainsSelected) { centerViewer(); } } }); chainMenu.add(menuItem); } } boolean allChainsSelected = false; void centerViewer() { Vector toshow = new Vector(); for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) { JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i); if (item.isSelected()) { toshow.addElement(item.getText()); } } } jmb.centerViewer(toshow); } @Override public void closeViewer(boolean closeExternalViewer) { // Jmol does not use an external viewer if (jmb != null) { jmb.closeViewer(); } 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; } @Override public void run() { _started = true; try { List files = fetchPdbFiles(); if (files.size() > 0) { showFilesInViewer(files); } } finally { _started = false; worker = null; } } /** * Either adds the given files to a structure viewer or opens a new viewer to * show them * * @param files * list of absolute paths to structure files */ void showFilesInViewer(List files) { long lastnotify = jmb.getLoadNotifiesHandled(); StringBuilder fileList = new StringBuilder(); for (String s : files) { fileList.append(SPACE).append(BACKSLASH) .append(Platform.escapeString(s)).append(BACKSLASH); } String filesString = fileList.toString(); if (!addingStructures) { try { initJmol("load FILES " + filesString); } catch (OutOfMemoryError oomerror) { new OOMWarning("When trying to open the Jmol viewer!", oomerror); Cache.log.debug("File locations are " + filesString); } catch (Exception ex) { Cache.log.error("Couldn't open Jmol viewer!", ex); } } else { StringBuilder cmd = new StringBuilder(); cmd.append("loadingJalviewdata=true\nload APPEND "); cmd.append(filesString); cmd.append("\nloadingJalviewdata=null"); final String command = cmd.toString(); lastnotify = jmb.getLoadNotifiesHandled(); try { jmb.evalStateCommand(command); } catch (OutOfMemoryError oomerror) { new OOMWarning("When trying to add structures to the Jmol viewer!", oomerror); Cache.log.debug("File locations are " + filesString); } catch (Exception ex) { Cache.log.error("Couldn't add files to Jmol viewer!", ex); } } // need to wait around until script has finished int waitMax = JMOL_LOAD_TIMEOUT; int waitFor = 35; int waitTotal = 0; while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled() : !(jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb .getPdbFile().length == files.size())) { try { Cache.log.debug("Waiting around for jmb notify."); Thread.sleep(waitFor); waitTotal += waitFor; } catch (Exception e) { } if (waitTotal > waitMax) { System.err .println("Timed out waiting for Jmol to load files after " + waitTotal + "ms"); // System.err.println("finished: " + jmb.isFinishedInit() // + "; loaded: " + Arrays.toString(jmb.getPdbFile()) // + "; files: " + files.toString()); jmb.getPdbFile(); break; } } // refresh the sequence colours for the new structure(s) for (AlignmentPanel ap : _colourwith) { jmb.updateColours(ap); } // do superposition if asked to if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures) { alignAddedStructures(); } addingStructures = false; } /** * Queues a thread to align structures with Jalview alignments */ void alignAddedStructures() { javax.swing.SwingUtilities.invokeLater(new Runnable() { @Override public void run() { if (jmb.viewer.isScriptExecuting()) { SwingUtilities.invokeLater(this); try { Thread.sleep(5); } catch (InterruptedException q) { } return; } else { alignStructs_withAllAlignPanels(); } } }); alignAddedStructures = false; } /** * Retrieves and saves as file any modelled PDB entries for which we do not * already have a file saved. Returns a list of absolute paths to structure * files which were either retrieved, or already stored but not modelled in * the structure viewer (i.e. files to add to the viewer display). * * @return */ List fetchPdbFiles() { // todo - record which pdbids were successfully imported. StringBuilder errormsgs = new StringBuilder(); List files = new ArrayList(); String pdbid = ""; try { String[] filesInViewer = jmb.getPdbFile(); // TODO: replace with reference fetching/transfer code (validate PDBentry // as a DBRef?) Pdb pdbclient = new Pdb(); for (int pi = 0; pi < jmb.getPdbCount(); pi++) { String file = jmb.getPdbEntry(pi).getFile(); if (file == null) { // retrieve the pdb and store it locally AlignmentI pdbseq = null; pdbid = jmb.getPdbEntry(pi).getId(); long hdl = pdbid.hashCode() - System.currentTimeMillis(); if (progressBar != null) { progressBar.setProgressBar(MessageManager.formatMessage( "status.fetching_pdb", new String[] { pdbid }), hdl); } try { pdbseq = pdbclient.getSequenceRecords(pdbid); } catch (OutOfMemoryError oomerror) { new OOMWarning("Retrieving PDB id " + pdbid, oomerror); } catch (Exception ex) { ex.printStackTrace(); errormsgs.append("'").append(pdbid).append("'"); } finally { if (progressBar != null) { progressBar.setProgressBar( MessageManager.getString("label.state_completed"), hdl); } } if (pdbseq != null) { // just transfer the file name from the first sequence's first // PDBEntry file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries() .elementAt(0).getFile()).getAbsolutePath(); jmb.getPdbEntry(pi).setFile(file); files.add(file); } else { errormsgs.append("'").append(pdbid).append("' "); } } else { if (filesInViewer != null && filesInViewer.length > 0) { addingStructures = true; // already files loaded. for (int c = 0; c < filesInViewer.length; c++) { if (filesInViewer[c].equals(file)) { file = null; break; } } } if (file != null) { files.add(file); } } } } catch (OutOfMemoryError oomerror) { new OOMWarning("Retrieving PDB files: " + pdbid, oomerror); } catch (Exception ex) { ex.printStackTrace(); errormsgs.append("When retrieving pdbfiles : current was: '") .append(pdbid).append("'"); } if (errormsgs.length() > 0) { JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.pdb_entries_couldnt_be_retrieved", new String[] { errormsgs.toString() }), MessageManager.getString("label.couldnt_load_file"), JOptionPane.ERROR_MESSAGE); } return files; } @Override public void pdbFile_actionPerformed(ActionEvent actionEvent) { JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.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(jmb.getPdbFile()[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(ActionEvent actionEvent) { jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); try { cap.appendText(jmb.printMappings()); } catch (OutOfMemoryError e) { new OOMWarning( "composing sequence-structure alignments for display in text box.", e); cap.dispose(); return; } jalview.gui.Desktop.addInternalFrame(cap, MessageManager.getString("label.pdb_sequence_mapping"), 550, 600); } @Override public void eps_actionPerformed(ActionEvent e) { makePDBImage(jalview.util.ImageMaker.TYPE.EPS); } @Override public void png_actionPerformed(ActionEvent e) { makePDBImage(jalview.util.ImageMaker.TYPE.PNG); } void makePDBImage(jalview.util.ImageMaker.TYPE type) { int width = getWidth(); int height = getHeight(); jalview.util.ImageMaker im; if (type == jalview.util.ImageMaker.TYPE.PNG) { im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view", width, height, null, null, null, 0, false); } else if (type == jalview.util.ImageMaker.TYPE.EPS) { im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view", width, height, null, this.getTitle(), null, 0, false); } else { im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA", width, height, null, this.getTitle(), null, 0, false); } if (im.getGraphics() != null) { jmb.viewer.renderScreenImage(im.getGraphics(), width, height); im.writeImage(); } } @Override public void viewerColour_actionPerformed(ActionEvent actionEvent) { if (viewerColour.isSelected()) { // disable automatic sequence colouring. jmb.setColourBySequence(false); } } @Override public void seqColour_actionPerformed(ActionEvent actionEvent) { jmb.setColourBySequence(seqColour.isSelected()); if (_colourwith == null) { _colourwith = new Vector(); } if (jmb.isColourBySequence()) { if (!jmb.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 (AlignmentPanel ap : _colourwith) { jmb.colourBySequence(ap); } } } @Override public void chainColour_actionPerformed(ActionEvent actionEvent) { chainColour.setSelected(true); jmb.colourByChain(); } @Override public void chargeColour_actionPerformed(ActionEvent actionEvent) { chargeColour.setSelected(true); jmb.colourByCharge(); } @Override public void zappoColour_actionPerformed(ActionEvent actionEvent) { zappoColour.setSelected(true); jmb.setJalviewColourScheme(new ZappoColourScheme()); } @Override public void taylorColour_actionPerformed(ActionEvent actionEvent) { taylorColour.setSelected(true); jmb.setJalviewColourScheme(new TaylorColourScheme()); } @Override public void hydroColour_actionPerformed(ActionEvent actionEvent) { hydroColour.setSelected(true); jmb.setJalviewColourScheme(new HydrophobicColourScheme()); } @Override public void helixColour_actionPerformed(ActionEvent actionEvent) { helixColour.setSelected(true); jmb.setJalviewColourScheme(new HelixColourScheme()); } @Override public void strandColour_actionPerformed(ActionEvent actionEvent) { strandColour.setSelected(true); jmb.setJalviewColourScheme(new StrandColourScheme()); } @Override public void turnColour_actionPerformed(ActionEvent actionEvent) { turnColour.setSelected(true); jmb.setJalviewColourScheme(new TurnColourScheme()); } @Override public void buriedColour_actionPerformed(ActionEvent actionEvent) { buriedColour.setSelected(true); jmb.setJalviewColourScheme(new BuriedColourScheme()); } @Override public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent) { setJalviewColourScheme(new PurinePyrimidineColourScheme()); } @Override public void userColour_actionPerformed(ActionEvent actionEvent) { userColour.setSelected(true); new UserDefinedColours(this, null); } @Override public void backGround_actionPerformed(ActionEvent actionEvent) { java.awt.Color col = JColorChooser .showDialog(this, MessageManager .getString("label.select_backgroud_colour"), null); if (col != null) { jmb.setBackgroundColour(col); } } @Override public void showHelp_actionPerformed(ActionEvent actionEvent) { try { jalview.util.BrowserLauncher .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/"); } catch (Exception ex) { } } public void showConsole(boolean showConsole) { if (showConsole) { if (splitPane == null) { splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT); splitPane.setTopComponent(renderPanel); splitPane.setBottomComponent(scriptWindow); this.getContentPane().add(splitPane, BorderLayout.CENTER); splitPane.setDividerLocation(getHeight() - 200); scriptWindow.setVisible(true); scriptWindow.validate(); splitPane.validate(); } } else { if (splitPane != null) { splitPane.setVisible(false); } splitPane = null; this.getContentPane().add(renderPanel, BorderLayout.CENTER); } validate(); } class RenderPanel extends JPanel { final Dimension currentSize = new Dimension(); @Override public void paintComponent(Graphics g) { getSize(currentSize); if (jmb != null && jmb.fileLoadingError != null) { g.setColor(Color.black); g.fillRect(0, 0, currentSize.width, currentSize.height); g.setColor(Color.white); g.setFont(new Font("Verdana", Font.BOLD, 14)); g.drawString(MessageManager.getString("label.error_loading_file") + "...", 20, currentSize.height / 2); StringBuffer sb = new StringBuffer(); int lines = 0; for (int e = 0; e < jmb.getPdbCount(); e++) { sb.append(jmb.getPdbEntry(e).getId()); if (e < jmb.getPdbCount() - 1) { sb.append(","); } if (e == jmb.getPdbCount() - 1 || sb.length() > 20) { lines++; g.drawString(sb.toString(), 20, currentSize.height / 2 - lines * g.getFontMetrics().getHeight()); } } } else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit()) { g.setColor(Color.black); g.fillRect(0, 0, currentSize.width, currentSize.height); g.setColor(Color.white); g.setFont(new Font("Verdana", Font.BOLD, 14)); g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2); } else { jmb.viewer.renderScreenImage(g, currentSize.width, currentSize.height); } } } public void updateTitleAndMenus() { if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) { repaint(); return; } setChainMenuItems(jmb.chainNames); this.setTitle(jmb.getViewerTitle()); if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1) { viewerActionMenu.setVisible(true); } if (!jmb.isLoadingFromArchive()) { seqColour_actionPerformed(null); } } /* * (non-Javadoc) * * @see * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event * .ActionEvent) */ @Override protected void alignStructs_actionPerformed(ActionEvent actionEvent) { alignStructs_withAllAlignPanels(); } private void alignStructs_withAllAlignPanels() { if (getAlignmentPanel() == null) { return; } ; if (_alignwith.size() == 0) { _alignwith.add(getAlignmentPanel()); } ; try { AlignmentI[] als = new Alignment[_alignwith.size()]; ColumnSelection[] alc = new ColumnSelection[_alignwith.size()]; int[] alm = new int[_alignwith.size()]; int a = 0; for (AlignmentPanel ap : _alignwith) { als[a] = ap.av.getAlignment(); alm[a] = -1; alc[a++] = ap.av.getColumnSelection(); } jmb.superposeStructures(als, alm, alc); } catch (Exception e) { StringBuffer sp = new StringBuffer(); for (AlignmentPanel ap : _alignwith) { sp.append("'" + ap.alignFrame.getTitle() + "' "); } Cache.log.info("Couldn't align structures with the " + sp.toString() + "associated alignment panels.", e); } } @Override public void setJalviewColourScheme(ColourSchemeI ucs) { jmb.setJalviewColourScheme(ucs); } /** * * @param alignment * @return first alignment panel displaying given alignment, or the default * alignment panel */ public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment) { for (AlignmentPanel ap : getAllAlignmentPanels()) { if (ap.av.getAlignment() == alignment) { return ap; } } return getAlignmentPanel(); } @Override public AAStructureBindingModel getBinding() { return this.jmb; } @Override public String getStateInfo() { return jmb == null ? null : jmb.viewer.getStateInfo(); } @Override public ViewerType getViewerType() { return ViewerType.JMOL; } @Override protected AAStructureBindingModel getBindingModel() { return jmb; } }