-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.gui;
-
-import java.util.regex.*;
-import java.util.*;
-import java.awt.*;
-import javax.swing.*;
-import javax.swing.event.*;
-import java.awt.event.*;
-import java.io.*;
-
-import jalview.jbgui.GStructureViewer;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.structure.*;
-import jalview.datamodel.PDBEntry;
-import jalview.io.*;
-import jalview.schemes.*;
-import jalview.ws.ebi.EBIFetchClient;
-
-import org.jmol.api.*;
-import org.jmol.adapter.smarter.SmarterJmolAdapter;
-import org.jmol.popup.*;
-
-public class AppJmol extends GStructureViewer implements StructureListener,
- JmolStatusListener, Runnable
-
-{
- JmolViewer viewer;
-
- JmolPopup jmolpopup;
-
- ScriptWindow scriptWindow;
-
- PDBEntry pdbentry;
-
- SequenceI[] sequence;
-
- String[] chains;
-
- StructureSelectionManager ssm;
-
- JSplitPane splitPane;
-
- RenderPanel renderPanel;
-
- AlignmentPanel ap;
-
- String fileLoadingError;
-
- boolean colourBySequence = true;
-
- boolean loadingFromArchive = false;
-
- Vector atomsPicked = new Vector();
-
- public AppJmol(String file, String id, SequenceI[] seq,
- AlignmentPanel ap, String loadStatus, Rectangle bounds)
- {
- this(file, id, seq, ap, loadStatus, bounds, null);
- }
-
- public AppJmol(String file, String id, SequenceI[] seq,
- AlignmentPanel ap, String loadStatus, Rectangle bounds,
- String viewid)
- {
- loadingFromArchive = true;
- pdbentry = new PDBEntry();
- pdbentry.setFile(file);
- pdbentry.setId(id);
- this.chains = chains;
- this.sequence = seq;
- this.ap = ap;
- this.setBounds(bounds);
- colourBySequence = false;
- seqColour.setSelected(false);
- viewId = viewid;
- // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
- // bounds.width,bounds.height);
-
- initJmol(loadStatus);
-
- this.addInternalFrameListener(new InternalFrameAdapter()
- {
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
- {
- closeViewer();
- }
- });
- }
-
- public synchronized void addSequence(SequenceI[] seq)
- {
- Vector v = new Vector();
- for (int i = 0; i < sequence.length; i++)
- v.addElement(sequence[i]);
-
- for (int i = 0; i < seq.length; i++)
- if (!v.contains(seq[i]))
- v.addElement(seq[i]);
-
- SequenceI[] tmp = new SequenceI[v.size()];
- v.copyInto(tmp);
- sequence = tmp;
- }
-
- public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap)
- {
- // ////////////////////////////////
- // Is the pdb file already loaded?
- String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager().alreadyMappedToFile(
- pdbentry.getId());
-
- if (alreadyMapped != null)
- {
- int option = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- pdbentry.getId()
- + " is already displayed."
- + "\nDo you want to map sequences to the visible structure?",
- "Map Sequences to Visible Window: "
- + pdbentry.getId(), JOptionPane.YES_NO_OPTION);
-
- if (option == JOptionPane.YES_OPTION)
- {
- StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, chains, alreadyMapped,
- AppletFormatAdapter.FILE);
- if (ap.seqPanel.seqCanvas.fr != null)
- {
- ap.seqPanel.seqCanvas.fr.featuresAdded();
- ap.paintAlignment(true);
- }
-
- // Now this AppJmol is mapped to new sequences. We must add them to
- // the exisiting array
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
- for (int i = 0; i < frames.length; i++)
- {
- if (frames[i] instanceof AppJmol)
- {
- AppJmol topJmol = ((AppJmol) frames[i]);
- if (topJmol.pdbentry.getFile().equals(alreadyMapped))
- {
- topJmol.addSequence(seq);
- break;
- }
- }
- }
-
- return;
- }
- }
- // /////////////////////////////////
-
- this.ap = ap;
- this.pdbentry = pdbentry;
- this.sequence = seq;
- this.setSize(400, 400);
- // jalview.gui.Desktop.addInternalFrame(this, "Jmol
- // View"+(pdbentry.getId()!=null ? "for "+pdbentry.getId()
- // : ""), 400, 400);
-
- if (pdbentry.getFile() != null)
- {
- initJmol("load \"" + pdbentry.getFile() + "\"");
- }
- else
- {
- Thread worker = new Thread(this);
- worker.start();
- }
-
- this.addInternalFrameListener(new InternalFrameAdapter()
- {
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
- {
- closeViewer();
- }
- });
- }
-
- void initJmol(String command)
- {
- renderPanel = new RenderPanel();
-
- this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
-
- StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
- + pdbentry.getId());
-
- if (pdbentry.getProperty() != null)
- {
- if (pdbentry.getProperty().get("method") != null)
- {
- title.append(" Method: ");
- title.append(pdbentry.getProperty().get("method"));
- }
- if (pdbentry.getProperty().get("chains") != null)
- {
- title.append(" Chain:");
- title.append(pdbentry.getProperty().get("chains"));
- }
- }
-
- this.setTitle(title.toString());
- jalview.gui.Desktop.addInternalFrame(this, title.toString(),
- getBounds().width, getBounds().height);
-
- viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
- new SmarterJmolAdapter());
-
- viewer.setAppletContext("", null, null, "");
-
- viewer.setJmolStatusListener(this);
-
- jmolpopup = JmolPopup.newJmolPopup(viewer);
-
- viewer.evalStringQuiet(command);
- }
-
- void setChainMenuItems(Vector chains)
- {
- chainMenu.removeAll();
-
- JMenuItem menuItem = new JMenuItem("All");
- menuItem.addActionListener(new ActionListener()
- {
- 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 (int c = 0; c < chains.size(); c++)
- {
- menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
- menuItem.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent evt)
- {
- if (!allChainsSelected)
- centerViewer();
- }
- });
-
- chainMenu.add(menuItem);
- }
- }
-
- boolean allChainsSelected = false;
-
- void centerViewer()
- {
- StringBuffer cmd = new StringBuffer();
- for (int i = 0; i < chainMenu.getItemCount(); i++)
- {
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
- {
- JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
- if (item.isSelected())
- cmd.append(":" + item.getText() + " or ");
- }
- }
-
- if (cmd.length() > 0)
- cmd.setLength(cmd.length() - 4);
-
- viewer.evalStringQuiet("select *;restrict " + cmd + ";cartoon;center "
- + cmd);
- }
-
- void closeViewer()
- {
- viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
- viewer.evalStringQuiet("zap");
- viewer.setJmolStatusListener(null);
- viewer = null;
-
- // We'll need to find out what other
- // listeners need to be shut down in Jmol
- StructureSelectionManager.getStructureSelectionManager()
- .removeStructureViewerListener(this, pdbentry.getFile());
- }
-
- public void run()
- {
- try
- {
- // TODO: replace with reference fetching/transfer code (validate PDBentry as a DBRef?)
- jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
- AlignmentI pdbseq;
- if ((pdbseq=pdbclient.getSequenceRecords(pdbentry.getId())) != null)
- {
- // just transfer the file name from the first seuqence's first PDBEntry
- pdbentry.setFile(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId().elementAt(0)).getFile());
- initJmol("load " + pdbentry.getFile());
- }
- else
- {
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- pdbentry.getId()
- + " could not be retrieved. Please try downloading the file manually.",
- "Couldn't load file", JOptionPane.ERROR_MESSAGE);
-
- }
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("Retrieving PDB id " + pdbentry.getId() + " from MSD",
- oomerror);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- public void pdbFile_actionPerformed(ActionEvent actionEvent)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save PDB File");
- chooser.setToolTipText("Save");
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- try
- {
- BufferedReader in = new BufferedReader(new FileReader(pdbentry
- .getFile()));
- File outFile = chooser.getSelectedFile();
-
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- String data;
- while ((data = in.readLine()) != null)
- {
- if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
- {
- out.println(data);
- }
- }
- out.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- }
-
- public void viewMapping_actionPerformed(ActionEvent actionEvent)
- {
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
- 550, 600);
- cap.setText(StructureSelectionManager.getStructureSelectionManager()
- .printMapping(pdbentry.getFile()));
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void eps_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.EPS);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void png_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.PNG);
- }
-
- void makePDBImage(int type)
- {
- int width = getWidth();
- int height = getHeight();
-
- jalview.util.ImageMaker im;
-
- if (type == jalview.util.ImageMaker.PNG)
- {
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
- "Make PNG image from view", width, height, null, null);
- }
- else
- {
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
- "Make EPS file from view", width, height, null, this
- .getTitle());
- }
-
- if (im.getGraphics() != null)
- {
- Rectangle rect = new Rectangle(width, height);
- viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
- im.writeImage();
- }
- }
-
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- lastCommand = null;
- colourBySequence = seqColour.isSelected();
- colourBySequence(ap.alignFrame.alignPanel);
- }
-
- public void chainColour_actionPerformed(ActionEvent actionEvent)
- {
- colourBySequence = false;
- seqColour.setSelected(false);
- viewer.evalStringQuiet("select *;color chain");
- }
-
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
- {
- colourBySequence = false;
- seqColour.setSelected(false);
- viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
- + "select LYS,ARG;color blue;select CYS;color yellow");
- }
-
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new ZappoColourScheme());
- }
-
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new TaylorColourScheme());
- }
-
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new HydrophobicColourScheme());
- }
-
- public void helixColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new HelixColourScheme());
- }
-
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new StrandColourScheme());
- }
-
- public void turnColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new TurnColourScheme());
- }
-
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new BuriedColourScheme());
- }
-
- public void setJalviewColourScheme(ColourSchemeI cs)
- {
- colourBySequence = false;
- seqColour.setSelected(false);
-
- if (cs == null)
- return;
-
- String res;
- int index;
- Color col;
-
- Enumeration en = ResidueProperties.aa3Hash.keys();
- StringBuffer command = new StringBuffer("select *;color white;");
- while (en.hasMoreElements())
- {
- res = en.nextElement().toString();
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
- if (index > 20)
- continue;
-
- col = cs.findColour(ResidueProperties.aa[index].charAt(0));
-
- command.append("select " + res + ";color[" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
- }
-
- viewer.evalStringQuiet(command.toString());
- }
-
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
- new UserDefinedColours(this, null);
- }
-
- public void backGround_actionPerformed(ActionEvent actionEvent)
- {
- java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour", null);
-
- if (col != null)
- {
- viewer.evalStringQuiet("background [" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
- }
- }
-
- public void jmolHelp_actionPerformed(ActionEvent actionEvent)
- {
- try
- {
- jalview.util.BrowserLauncher
- .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
- } catch (Exception ex)
- {
- }
- }
-
- // ////////////////////////////////
- // /StructureListener
- public String getPdbFile()
- {
- return pdbentry.getFile();
- }
-
- Pattern pattern = Pattern
- .compile("\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?");
-
- String lastMessage;
-
- public void mouseOverStructure(int atomIndex, String strInfo)
- {
- Matcher matcher = pattern.matcher(strInfo);
- matcher.find();
- matcher.group(1);
- int pdbResNum = Integer.parseInt(matcher.group(2));
- String chainId = matcher.group(3);
-
- if (chainId != null)
- chainId = chainId.substring(1, chainId.length());
- else
- {
- chainId = " ";
- }
-
- if (lastMessage == null || !lastMessage.equals(strInfo))
- {
- ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
- }
- lastMessage = strInfo;
- }
-
- StringBuffer resetLastRes = new StringBuffer();
-
- StringBuffer eval = new StringBuffer();
-
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- // TODO: rna: remove CA dependency in select string
- if (!pdbfile.equals(pdbentry.getFile()))
- return;
-
- if (resetLastRes.length() > 0)
- {
- viewer.evalStringQuiet(resetLastRes.toString());
- }
-
- eval.setLength(0);
- eval.append("select " + pdbResNum);
-
- resetLastRes.setLength(0);
- resetLastRes.append("select " + pdbResNum);
-
- eval.append(":");
- resetLastRes.append(":");
- if (!chain.equals(" "))
- {
- eval.append(chain);
- resetLastRes.append(chain);
- }
-
- eval.append(";wireframe 100;" + eval.toString() + " and not hetero;"); // ".*;");
-
- resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
- //+ ".*;spacefill 0;");
- + " and not hetero;spacefill 0;");
-
- eval.append("spacefill 200;select none");
-// System.out.println("jmol:\n"+eval+"\n");
- viewer.evalStringQuiet(eval.toString());
- }
-
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- if (!pdbfile.equals(pdbentry.getFile()))
- return null;
-
- return new Color(viewer.getAtomArgb(atomIndex));
- }
-
- public void updateColours(Object source)
- {
- colourBySequence((AlignmentPanel) source);
- }
-
- // End StructureListener
- // //////////////////////////
-
- String lastCommand;
-
- FeatureRenderer fr = null;
-
- public void colourBySequence(AlignmentPanel sourceap)
- {
- this.ap = sourceap;
-
- if (!colourBySequence || ap.alignFrame.getCurrentView() != ap.av)
- return;
-
- StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
-
- if (mapping.length < 1)
- return;
-
- SequenceRenderer sr = new SequenceRenderer(ap.av);
-
- boolean showFeatures = false;
-
- if (ap.av.showSequenceFeatures)
- {
- showFeatures = true;
- if (fr == null)
- {
- fr = new jalview.gui.FeatureRenderer(ap);
- }
-
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
- }
-
- StringBuffer command = new StringBuffer();
-
- int lastPos = -1;
- for (int sp, s = 0; s < sequence.length; s++)
- {
- for (int m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[s]
- && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
- {
- SequenceI asp = ap.av.alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // No mapping to gaps in sequence.
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(asp, r);
-
- if (showFeatures)
- col = fr.findFeatureColour(col, asp, r);
-
- if (command.toString().endsWith(
- ":" + mapping[m].getChain() + ";color[" + col.getRed()
- + "," + col.getGreen() + "," + col.getBlue()
- + "]"))
- {
- command = condenseCommand(command, pos);
- continue;
- }
-
- command.append(";select " + pos);
-
- if (!mapping[m].getChain().equals(" "))
- {
- command.append(":" + mapping[m].getChain());
- }
-
- command.append(";color[" + col.getRed() + "," + col.getGreen()
- + "," + col.getBlue() + "]");
-
- }
- break;
- }
- }
- }
-
- if (lastCommand == null || !lastCommand.equals(command.toString()))
- {
- viewer.evalStringQuiet(command.toString());
- }
- lastCommand = command.toString();
- }
-
- StringBuffer condenseCommand(StringBuffer command, int pos)
- {
- StringBuffer sb = new StringBuffer(command.substring(0, command
- .lastIndexOf("select") + 7));
-
- command.delete(0, sb.length());
-
- String start;
-
- if (command.indexOf("-") > -1)
- {
- start = command.substring(0, command.indexOf("-"));
- }
- else
- {
- start = command.substring(0, command.indexOf(":"));
- }
-
- sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-
- return sb;
- }
-
- // ///////////////////////////////
- // JmolStatusListener
-
- public String eval(String strEval)
- {
- // System.out.println(strEval);
- // "# 'eval' is implemented only for the applet.";
- return null;
- }
-
- public void createImage(String file, String type, int quality)
- {
- System.out.println("JMOL CREATE IMAGE");
- }
-
- public void setCallbackFunction(String callbackType,
- String callbackFunction)
- {
- }
-
- public void notifyFileLoaded(String fullPathName, String fileName,
- String modelName, Object clientFile, String errorMsg)
- {
- if (errorMsg != null)
- {
- fileLoadingError = errorMsg;
- repaint();
- return;
- }
-
- fileLoadingError = null;
-
- if (fileName != null)
- {
-
- // FILE LOADED OK
- ssm = StructureSelectionManager.getStructureSelectionManager();
- MCview.PDBfile pdbFile = ssm.setMapping(sequence, chains, pdbentry
- .getFile(), AppletFormatAdapter.FILE);
- ssm.addStructureViewerListener(this);
- Vector chains = new Vector();
- for (int i = 0; i < pdbFile.chains.size(); i++)
- {
- chains
- .addElement(((MCview.PDBChain) pdbFile.chains.elementAt(i)).id);
- }
- setChainMenuItems(chains);
-
- jmolpopup.updateComputedMenus();
-
- if (!loadingFromArchive)
- {
- viewer
- .evalStringQuiet("select backbone;restrict;cartoon;wireframe off;spacefill off");
-
- colourBySequence(ap);
- }
- if (fr != null)
- fr.featuresAdded();
-
- loadingFromArchive = false;
- }
- else
- return;
- }
-
- public void notifyFrameChanged(int frameNo)
- {
- boolean isAnimationRunning = (frameNo <= -2);
- }
-
- public void notifyScriptStart(String statusMessage, String additionalInfo)
- {
- }
-
- public void sendConsoleEcho(String strEcho)
- {
- if (scriptWindow != null)
- scriptWindow.sendConsoleEcho(strEcho);
- }
-
- public void sendConsoleMessage(String strStatus)
- {
- if (scriptWindow != null)
- scriptWindow.sendConsoleMessage(strStatus);
- }
-
- public void notifyScriptTermination(String strStatus, int msWalltime)
- {
- if (scriptWindow != null)
- scriptWindow.notifyScriptTermination(strStatus, msWalltime);
- }
-
- public void handlePopupMenu(int x, int y)
- {
- jmolpopup.show(x, y);
- }
-
- public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
- {
- notifyAtomPicked(iatom, strMeasure);
- }
-
- public void notifyNewDefaultModeMeasurement(int count, String strInfo)
- {
- }
-
- public void notifyAtomPicked(int atomIndex, String strInfo)
- {
- Matcher matcher = pattern.matcher(strInfo);
- matcher.find();
-
- matcher.group(1);
- String resnum = new String(matcher.group(2));
- String chainId = matcher.group(3);
-
- String picked = resnum;
-
- if (chainId != null)
- picked += (":" + chainId.substring(1, chainId.length()));
-
- picked += ".CA";
-
- if (!atomsPicked.contains(picked))
- {
- if (chainId != null)
- viewer.evalString("select " + picked + ";label %n %r:%c");
- else
- viewer.evalString("select " + picked + ";label %n %r");
- atomsPicked.addElement(picked);
- }
- else
- {
- viewer.evalString("select " + picked + ";label off");
- atomsPicked.removeElement(picked);
- }
-
- if (scriptWindow != null)
- {
- scriptWindow.sendConsoleMessage(strInfo);
- scriptWindow.sendConsoleMessage("\n");
- }
- }
-
- public void notifyAtomHovered(int atomIndex, String strInfo)
- {
- mouseOverStructure(atomIndex, strInfo);
- }
-
- public void sendSyncScript(String script, String appletName)
- {
- }
-
- public void showUrl(String url)
- {
- }
-
- public void showConsole(boolean showConsole)
- {
- if (scriptWindow == null)
- scriptWindow = new ScriptWindow(this);
-
- 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);
- splitPane.validate();
- }
- else
- {
- if (splitPane != null)
- splitPane.setVisible(false);
-
- splitPane = null;
-
- this.getContentPane().add(renderPanel, BorderLayout.CENTER);
- }
-
- validate();
- }
-
- public float functionXY(String functionName, int x, int y)
- {
- return 0;
- }
-
- // /End JmolStatusListener
- // /////////////////////////////
-
- class RenderPanel extends JPanel
- {
- final Dimension currentSize = new Dimension();
-
- final Rectangle rectClip = new Rectangle();
-
- public void paintComponent(Graphics g)
- {
- getSize(currentSize);
- g.getClipBounds(rectClip);
-
- if (viewer == 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("Retrieving PDB data....", 20, currentSize.height / 2);
- }
- else if (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("Error loading file..." + pdbentry.getId(), 20,
- currentSize.height / 2);
- }
- else
- {
- viewer.renderScreenImage(g, currentSize, rectClip);
- }
- }
- }
-
- String viewId = null;
-
- public String getViewId()
- {
- if (viewId == null)
- {
- viewId = System.currentTimeMillis() + "." + this.hashCode();
- }
- return viewId;
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package jalview.gui;\r
+\r
+import java.util.*;\r
+import java.awt.*;\r
+import javax.swing.*;\r
+import javax.swing.event.*;\r
+\r
+import java.awt.event.*;\r
+import java.io.*;\r
+\r
+import jalview.jbgui.GStructureViewer;\r
+import jalview.api.SequenceStructureBinding;\r
+import jalview.bin.Cache;\r
+import jalview.datamodel.*;\r
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;\r
+import jalview.datamodel.PDBEntry;\r
+import jalview.io.*;\r
+import jalview.schemes.*;\r
+import jalview.util.MessageManager;\r
+import jalview.util.Platform;\r
+\r
+public class AppJmol extends GStructureViewer implements Runnable,\r
+ SequenceStructureBinding, ViewSetProvider\r
+\r
+{\r
+ AppJmolBinding jmb;\r
+\r
+ JPanel scriptWindow;\r
+\r
+ JSplitPane splitPane;\r
+\r
+ RenderPanel renderPanel;\r
+\r
+ AlignmentPanel ap;\r
+\r
+ Vector atomsPicked = new Vector();\r
+\r
+ private boolean addingStructures = false;\r
+\r
+ /**\r
+ * \r
+ * @param file\r
+ * @param id\r
+ * @param seq\r
+ * @param ap\r
+ * @param loadStatus\r
+ * @param bounds\r
+ * @deprecated defaults to AppJmol(String[] files, ... , viewid);\r
+ */\r
+ public AppJmol(String file, String id, SequenceI[] seq,\r
+ AlignmentPanel ap, String loadStatus, Rectangle bounds)\r
+ {\r
+ this(file, id, seq, ap, loadStatus, bounds, null);\r
+ }\r
+\r
+ /**\r
+ * @deprecated\r
+ */\r
+ public AppJmol(String file, String id, SequenceI[] seq,\r
+ AlignmentPanel ap, String loadStatus, Rectangle bounds,\r
+ String viewid)\r
+ {\r
+ this(new String[]\r
+ { file }, new String[]\r
+ { id }, new SequenceI[][]\r
+ { seq }, ap, true, true, false, loadStatus, bounds, viewid);\r
+ }\r
+\r
+ ViewSelectionMenu seqColourBy;\r
+\r
+ /**\r
+ * \r
+ * @param files\r
+ * @param ids\r
+ * @param seqs\r
+ * @param ap\r
+ * @param usetoColour\r
+ * - add the alignment panel to the list used for colouring these\r
+ * structures\r
+ * @param useToAlign\r
+ * - add the alignment panel to the list used for aligning these\r
+ * structures\r
+ * @param leaveColouringToJmol\r
+ * - do not update the colours from any other source. Jmol is\r
+ * handling them\r
+ * @param loadStatus\r
+ * @param bounds\r
+ * @param viewid\r
+ */\r
+ public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,\r
+ AlignmentPanel ap, boolean usetoColour, boolean useToAlign,\r
+ boolean leaveColouringToJmol, String loadStatus,\r
+ Rectangle bounds, String viewid)\r
+ {\r
+ PDBEntry[] pdbentrys = new PDBEntry[files.length];\r
+ for (int i = 0; i < pdbentrys.length; i++)\r
+ {\r
+ PDBEntry pdbentry = new PDBEntry();\r
+ pdbentry.setFile(files[i]);\r
+ pdbentry.setId(ids[i]);\r
+ pdbentrys[i] = pdbentry;\r
+ }\r
+ // / TODO: check if protocol is needed to be set, and if chains are\r
+ // autodiscovered.\r
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),\r
+ pdbentrys, seqs, null, null);\r
+\r
+ jmb.setLoadingFromArchive(true);\r
+ addAlignmentPanel(ap);\r
+ if (useToAlign)\r
+ {\r
+ useAlignmentPanelForSuperposition(ap);\r
+ }\r
+ if (leaveColouringToJmol || !usetoColour)\r
+ {\r
+ jmb.setColourBySequence(false);\r
+ seqColour.setSelected(false);\r
+ jmolColour.setSelected(true);\r
+ }\r
+ if (usetoColour)\r
+ {\r
+ useAlignmentPanelForColourbyseq(ap);\r
+ jmb.setColourBySequence(true);\r
+ seqColour.setSelected(true);\r
+ jmolColour.setSelected(false);\r
+ }\r
+ this.setBounds(bounds);\r
+ initMenus();\r
+ viewId = viewid;\r
+ // jalview.gui.Desktop.addInternalFrame(this, "Loading File",\r
+ // bounds.width,bounds.height);\r
+\r
+ this.addInternalFrameListener(new InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosing(InternalFrameEvent internalFrameEvent)\r
+ {\r
+ closeViewer();\r
+ }\r
+ });\r
+ initJmol(loadStatus); // pdbentry, seq, JBPCHECK!\r
+\r
+ }\r
+\r
+ private void initMenus()\r
+ {\r
+ seqColour.setSelected(jmb.isColourBySequence());\r
+ jmolColour.setSelected(!jmb.isColourBySequence());\r
+ if (_colourwith == null)\r
+ {\r
+ _colourwith = new Vector<AlignmentPanel>();\r
+ }\r
+ if (_alignwith == null)\r
+ {\r
+ _alignwith = new Vector<AlignmentPanel>();\r
+ }\r
+\r
+ seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,\r
+ new ItemListener()\r
+ {\r
+\r
+ @Override\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ if (!seqColour.isSelected())\r
+ {\r
+ seqColour.doClick();\r
+ }\r
+ else\r
+ {\r
+ // update the jmol display now.\r
+ seqColour_actionPerformed(null);\r
+ }\r
+ }\r
+ });\r
+ viewMenu.add(seqColourBy);\r
+ final ItemListener handler;\r
+ JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,\r
+ _alignwith, handler = new ItemListener()\r
+ {\r
+\r
+ @Override\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ alignStructs.setEnabled(_alignwith.size() > 0);\r
+ alignStructs.setToolTipText(MessageManager.formatMessage("label.align_structures_using_linked_alignment_views", new String[] {new Integer(_alignwith.size()).toString()}));\r
+ }\r
+ });\r
+ handler.itemStateChanged(null);\r
+ jmolActionMenu.add(alpanels);\r
+ jmolActionMenu.addMenuListener(new MenuListener()\r
+ {\r
+\r
+ @Override\r
+ public void menuSelected(MenuEvent e)\r
+ {\r
+ handler.itemStateChanged(null);\r
+ }\r
+\r
+ @Override\r
+ public void menuDeselected(MenuEvent e)\r
+ {\r
+ // TODO Auto-generated method stub\r
+\r
+ }\r
+\r
+ @Override\r
+ public void menuCanceled(MenuEvent e)\r
+ {\r
+ // TODO Auto-generated method stub\r
+\r
+ }\r
+ });\r
+ }\r
+\r
+ IProgressIndicator progressBar = null;\r
+\r
+ /**\r
+ * add a single PDB structure to a new or existing Jmol view\r
+ * \r
+ * @param pdbentry\r
+ * @param seq\r
+ * @param chains\r
+ * @param ap\r
+ */\r
+ public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,\r
+ final AlignmentPanel ap)\r
+ {\r
+ progressBar = ap.alignFrame;\r
+ // ////////////////////////////////\r
+ // Is the pdb file already loaded?\r
+ String alreadyMapped = ap.getStructureSelectionManager()\r
+ .alreadyMappedToFile(pdbentry.getId());\r
+\r
+ if (alreadyMapped != null)\r
+ {\r
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+ MessageManager.formatMessage("label.pdb_entry_is_already_displayed", new String[]{pdbentry.getId()}),\r
+ MessageManager.formatMessage("label.map_sequences_to_visible_window", new String[]{pdbentry.getId()}),\r
+ JOptionPane.YES_NO_OPTION);\r
+\r
+ if (option == JOptionPane.YES_OPTION)\r
+ {\r
+ // TODO : Fix multiple seq to one chain issue here.\r
+ ap.getStructureSelectionManager().setMapping(seq, chains,\r
+ alreadyMapped, AppletFormatAdapter.FILE);\r
+ if (ap.seqPanel.seqCanvas.fr != null)\r
+ {\r
+ ap.seqPanel.seqCanvas.fr.featuresAdded();\r
+ ap.paintAlignment(true);\r
+ }\r
+\r
+ // Now this AppJmol is mapped to new sequences. We must add them to\r
+ // the exisiting array\r
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();\r
+\r
+ for (int i = 0; i < frames.length; i++)\r
+ {\r
+ if (frames[i] instanceof AppJmol)\r
+ {\r
+ final AppJmol topJmol = ((AppJmol) frames[i]);\r
+ // JBPNOTE: this looks like a binding routine, rather than a gui\r
+ // routine\r
+ for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)\r
+ {\r
+ if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))\r
+ {\r
+ topJmol.jmb.addSequence(pe, seq);\r
+ topJmol.addAlignmentPanel(ap);\r
+ // add it to the set used for colouring\r
+ topJmol.useAlignmentPanelForColourbyseq(ap);\r
+ topJmol.buildJmolActionMenu();\r
+ ap.getStructureSelectionManager()\r
+ .sequenceColoursChanged(ap);\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ return;\r
+ }\r
+ }\r
+ // /////////////////////////////////\r
+ // Check if there are other Jmol views involving this alignment\r
+ // and prompt user about adding this molecule to one of them\r
+ Vector existingViews = getJmolsFor(ap);\r
+ if (existingViews.size() > 0)\r
+ {\r
+ Enumeration jm = existingViews.elements();\r
+ while (jm.hasMoreElements())\r
+ {\r
+ AppJmol topJmol = (AppJmol) jm.nextElement();\r
+ // TODO: highlight topJmol in view somehow\r
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+ MessageManager.formatMessage("label.add_pdbentry_to_view", new String[]{pdbentry.getId(),topJmol.getTitle()}),\r
+ MessageManager.getString("label.align_to_existing_structure_view"),\r
+ JOptionPane.YES_NO_OPTION);\r
+ if (option == JOptionPane.YES_OPTION)\r
+ {\r
+ topJmol.useAlignmentPanelForSuperposition(ap);\r
+ topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);\r
+ return;\r
+ }\r
+ }\r
+ }\r
+ // /////////////////////////////////\r
+ openNewJmol(ap, new PDBEntry[]\r
+ { pdbentry }, new SequenceI[][]\r
+ { seq });\r
+ }\r
+\r
+ private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,\r
+ SequenceI[][] seqs)\r
+ {\r
+ progressBar = ap.alignFrame;\r
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),\r
+ pdbentrys, seqs, null, null);\r
+ addAlignmentPanel(ap);\r
+ useAlignmentPanelForColourbyseq(ap);\r
+ if (pdbentrys.length > 1)\r
+ {\r
+ alignAddedStructures = true;\r
+ useAlignmentPanelForSuperposition(ap);\r
+ }\r
+ jmb.setColourBySequence(true);\r
+ setSize(400, 400); // probably should be a configurable/dynamic default here\r
+ initMenus();\r
+ worker = null;\r
+ {\r
+ addingStructures = false;\r
+ worker = new Thread(this);\r
+ worker.start();\r
+ }\r
+ this.addInternalFrameListener(new InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosing(InternalFrameEvent internalFrameEvent)\r
+ {\r
+ closeViewer();\r
+ }\r
+ });\r
+\r
+ }\r
+\r
+ /**\r
+ * create a new Jmol containing several structures superimposed using the\r
+ * given alignPanel.\r
+ * \r
+ * @param ap\r
+ * @param pe\r
+ * @param seqs\r
+ */\r
+ public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)\r
+ {\r
+ openNewJmol(ap, pe, seqs);\r
+ }\r
+\r
+ /**\r
+ * list of sequenceSet ids associated with the view\r
+ */\r
+ ArrayList<String> _aps = new ArrayList();\r
+\r
+ public AlignmentPanel[] getAllAlignmentPanels()\r
+ {\r
+ AlignmentPanel[] t, list = new AlignmentPanel[0];\r
+ for (String setid : _aps)\r
+ {\r
+ AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);\r
+ if (panels != null)\r
+ {\r
+ t = new AlignmentPanel[list.length + panels.length];\r
+ System.arraycopy(list, 0, t, 0, list.length);\r
+ System.arraycopy(panels, 0, t, list.length, panels.length);\r
+ list = t;\r
+ }\r
+ }\r
+\r
+ return list;\r
+ }\r
+\r
+ /**\r
+ * list of alignment panels to use for superposition\r
+ */\r
+ Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();\r
+\r
+ /**\r
+ * list of alignment panels that are used for colouring structures by aligned\r
+ * sequences\r
+ */\r
+ Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();\r
+\r
+ /**\r
+ * set the primary alignmentPanel reference and add another alignPanel to the\r
+ * list of ones to use for colouring and aligning\r
+ * \r
+ * @param nap\r
+ */\r
+ public void addAlignmentPanel(AlignmentPanel nap)\r
+ {\r
+ if (ap == null)\r
+ {\r
+ ap = nap;\r
+ }\r
+ if (!_aps.contains(nap.av.getSequenceSetId()))\r
+ {\r
+ _aps.add(nap.av.getSequenceSetId());\r
+ }\r
+ }\r
+\r
+ /**\r
+ * remove any references held to the given alignment panel\r
+ * \r
+ * @param nap\r
+ */\r
+ public void removeAlignmentPanel(AlignmentPanel nap)\r
+ {\r
+ try\r
+ {\r
+ _alignwith.remove(nap);\r
+ _colourwith.remove(nap);\r
+ if (ap == nap)\r
+ {\r
+ ap = null;\r
+ for (AlignmentPanel aps : getAllAlignmentPanels())\r
+ {\r
+ if (aps != nap)\r
+ {\r
+ ap = aps;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ } catch (Exception ex)\r
+ {\r
+ }\r
+ if (ap != null)\r
+ {\r
+ buildJmolActionMenu();\r
+ }\r
+ }\r
+\r
+ public void useAlignmentPanelForSuperposition(AlignmentPanel nap)\r
+ {\r
+ addAlignmentPanel(nap);\r
+ if (!_alignwith.contains(nap))\r
+ {\r
+ _alignwith.add(nap);\r
+ }\r
+ }\r
+\r
+ public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)\r
+ {\r
+ if (_alignwith.contains(nap))\r
+ {\r
+ _alignwith.remove(nap);\r
+ }\r
+ }\r
+\r
+ public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,\r
+ boolean enableColourBySeq)\r
+ {\r
+ useAlignmentPanelForColourbyseq(nap);\r
+ jmb.setColourBySequence(enableColourBySeq);\r
+ seqColour.setSelected(enableColourBySeq);\r
+ jmolColour.setSelected(!enableColourBySeq);\r
+ }\r
+\r
+ public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)\r
+ {\r
+ addAlignmentPanel(nap);\r
+ if (!_colourwith.contains(nap))\r
+ {\r
+ _colourwith.add(nap);\r
+ }\r
+ }\r
+\r
+ public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)\r
+ {\r
+ if (_colourwith.contains(nap))\r
+ {\r
+ _colourwith.remove(nap);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * pdb retrieval thread.\r
+ */\r
+ private Thread worker = null;\r
+\r
+ /**\r
+ * add a new structure (with associated sequences and chains) to this viewer,\r
+ * retrieving it if necessary first.\r
+ * \r
+ * @param pdbentry\r
+ * @param seq\r
+ * @param chains\r
+ * @param alignFrame\r
+ * @param align\r
+ * if true, new structure(s) will be align using associated alignment\r
+ */\r
+ private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,\r
+ final String[] chains, final boolean b,\r
+ final IProgressIndicator alignFrame)\r
+ {\r
+ if (pdbentry.getFile() == null)\r
+ {\r
+ if (worker != null && worker.isAlive())\r
+ {\r
+ // a retrieval is in progress, wait around and add ourselves to the\r
+ // queue.\r
+ new Thread(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ while (worker != null && worker.isAlive() && _started)\r
+ {\r
+ try\r
+ {\r
+ Thread.sleep(100 + ((int) Math.random() * 100));\r
+\r
+ } catch (Exception e)\r
+ {\r
+ }\r
+\r
+ }\r
+ // and call ourselves again.\r
+ addStructure(pdbentry, seq, chains, b, alignFrame);\r
+ }\r
+ }).start();\r
+ return;\r
+ }\r
+ }\r
+ // otherwise, start adding the structure.\r
+ jmb.addSequenceAndChain(new PDBEntry[]\r
+ { pdbentry }, new SequenceI[][]\r
+ { seq }, new String[][]\r
+ { chains });\r
+ addingStructures = true;\r
+ _started = false;\r
+ alignAddedStructures = b;\r
+ progressBar = alignFrame; // visual indication happens on caller frame.\r
+ (worker = new Thread(this)).start();\r
+ return;\r
+ }\r
+\r
+ private Vector getJmolsFor(AlignmentPanel ap2)\r
+ {\r
+ Vector otherJmols = new Vector();\r
+ // Now this AppJmol is mapped to new sequences. We must add them to\r
+ // the exisiting array\r
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();\r
+\r
+ for (int i = 0; i < frames.length; i++)\r
+ {\r
+ if (frames[i] instanceof AppJmol)\r
+ {\r
+ AppJmol topJmol = ((AppJmol) frames[i]);\r
+ if (topJmol.isLinkedWith(ap2))\r
+ {\r
+ otherJmols.addElement(topJmol);\r
+ }\r
+ }\r
+ }\r
+ return otherJmols;\r
+ }\r
+\r
+ void initJmol(String command)\r
+ {\r
+ jmb.setFinishedInit(false);\r
+ renderPanel = new RenderPanel();\r
+ // TODO: consider waiting until the structure/view is fully loaded before\r
+ // displaying\r
+ this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);\r
+ jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),\r
+ getBounds().width, getBounds().height);\r
+ if (scriptWindow == null)\r
+ {\r
+ BorderLayout bl = new BorderLayout();\r
+ bl.setHgap(0);\r
+ bl.setVgap(0);\r
+ scriptWindow = new JPanel(bl);\r
+ scriptWindow.setVisible(false);\r
+ }\r
+ ;\r
+ jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,\r
+ null);\r
+ jmb.newJmolPopup(true, "Jmol", true);\r
+ if (command == null)\r
+ {\r
+ command = "";\r
+ }\r
+ jmb.evalStateCommand(command);\r
+ jmb.setFinishedInit(true);\r
+ }\r
+\r
+ void setChainMenuItems(Vector chains)\r
+ {\r
+ chainMenu.removeAll();\r
+ if (chains == null)\r
+ {\r
+ return;\r
+ }\r
+ JMenuItem menuItem = new JMenuItem(MessageManager.getString("label.all"));\r
+ menuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ allChainsSelected = true;\r
+ for (int i = 0; i < chainMenu.getItemCount(); i++)\r
+ {\r
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)\r
+ ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);\r
+ }\r
+ centerViewer();\r
+ allChainsSelected = false;\r
+ }\r
+ });\r
+\r
+ chainMenu.add(menuItem);\r
+\r
+ for (int c = 0; c < chains.size(); c++)\r
+ {\r
+ menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);\r
+ menuItem.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if (!allChainsSelected)\r
+ centerViewer();\r
+ }\r
+ });\r
+\r
+ chainMenu.add(menuItem);\r
+ }\r
+ }\r
+\r
+ boolean allChainsSelected = false;\r
+\r
+ private boolean alignAddedStructures = false;\r
+\r
+ void centerViewer()\r
+ {\r
+ Vector toshow = new Vector();\r
+ String lbl;\r
+ int mlength, p, mnum;\r
+ for (int i = 0; i < chainMenu.getItemCount(); i++)\r
+ {\r
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)\r
+ {\r
+ JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);\r
+ if (item.isSelected())\r
+ {\r
+ toshow.addElement(item.getText());\r
+ }\r
+ }\r
+ }\r
+ jmb.centerViewer(toshow);\r
+ }\r
+\r
+ void closeViewer()\r
+ {\r
+ jmb.closeViewer();\r
+ ap = null;\r
+ _aps.clear();\r
+ _alignwith.clear();\r
+ _colourwith.clear();\r
+ // TODO: check for memory leaks where instance isn't finalised because jmb\r
+ // holds a reference to the window\r
+ jmb = null;\r
+ }\r
+\r
+ /**\r
+ * state flag for PDB retrieval thread\r
+ */\r
+ private boolean _started = false;\r
+\r
+ public void run()\r
+ {\r
+ _started = true;\r
+ String pdbid = "";\r
+ // todo - record which pdbids were successfuly imported.\r
+ StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();\r
+ try\r
+ {\r
+ String[] curfiles = jmb.getPdbFile(); // files currently in viewer\r
+ // TODO: replace with reference fetching/transfer code (validate PDBentry\r
+ // as a DBRef?)\r
+ jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();\r
+ for (int pi = 0; pi < jmb.pdbentry.length; pi++)\r
+ {\r
+ String file = jmb.pdbentry[pi].getFile();\r
+ if (file == null)\r
+ {\r
+ // retrieve the pdb and store it locally\r
+ AlignmentI pdbseq = null;\r
+ pdbid = jmb.pdbentry[pi].getId();\r
+ long hdl = pdbid.hashCode() - System.currentTimeMillis();\r
+ if (progressBar != null)\r
+ {\r
+ progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);\r
+ }\r
+ try\r
+ {\r
+ pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]\r
+ .getId());\r
+ } catch (OutOfMemoryError oomerror)\r
+ {\r
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ errormsgs.append("'" + pdbid + "'");\r
+ }\r
+ if (progressBar != null)\r
+ {\r
+ progressBar.setProgressBar("Finished.", hdl);\r
+ }\r
+ if (pdbseq != null)\r
+ {\r
+ // just transfer the file name from the first sequence's first\r
+ // PDBEntry\r
+ file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()\r
+ .elementAt(0)).getFile()).getAbsolutePath();\r
+ jmb.pdbentry[pi].setFile(file);\r
+\r
+ files.append(" \"" + Platform.escapeString(file) + "\"");\r
+ }\r
+ else\r
+ {\r
+ errormsgs.append("'" + pdbid + "' ");\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (curfiles != null && curfiles.length > 0)\r
+ {\r
+ addingStructures = true; // already files loaded.\r
+ for (int c = 0; c < curfiles.length; c++)\r
+ {\r
+ if (curfiles[c].equals(file))\r
+ {\r
+ file = null;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ if (file != null)\r
+ {\r
+ files.append(" \"" + Platform.escapeString(file) + "\"");\r
+ }\r
+ }\r
+ }\r
+ } catch (OutOfMemoryError oomerror)\r
+ {\r
+ new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid\r
+ + "'");\r
+ }\r
+ if (errormsgs.length() > 0)\r
+ {\r
+\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ MessageManager.formatMessage("label.pdb_entries_couldnt_be_retrieved", new String[]{errormsgs.toString()}),\r
+ MessageManager.getString("label.couldnt_load_file"), JOptionPane.ERROR_MESSAGE);\r
+\r
+ }\r
+ long lastnotify = jmb.getLoadNotifiesHandled();\r
+ if (files.length() > 0)\r
+ {\r
+ if (!addingStructures)\r
+ {\r
+\r
+ try\r
+ {\r
+ initJmol("load FILES " + files.toString());\r
+ } catch (OutOfMemoryError oomerror)\r
+ {\r
+ new OOMWarning("When trying to open the Jmol viewer!", oomerror);\r
+ Cache.log.debug("File locations are " + files);\r
+ } catch (Exception ex)\r
+ {\r
+ Cache.log.error("Couldn't open Jmol viewer!", ex);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ StringBuffer cmd = new StringBuffer();\r
+ cmd.append("loadingJalviewdata=true\nload APPEND ");\r
+ cmd.append(files.toString());\r
+ cmd.append("\nloadingJalviewdata=null");\r
+ final String command = cmd.toString();\r
+ cmd = null;\r
+ lastnotify = jmb.getLoadNotifiesHandled();\r
+\r
+ try\r
+ {\r
+ jmb.evalStateCommand(command);\r
+ } catch (OutOfMemoryError oomerror)\r
+ {\r
+ new OOMWarning(\r
+ "When trying to add structures to the Jmol viewer!",\r
+ oomerror);\r
+ Cache.log.debug("File locations are " + files);\r
+ } catch (Exception ex)\r
+ {\r
+ Cache.log.error("Couldn't add files to Jmol viewer!", ex);\r
+ }\r
+ }\r
+\r
+ // need to wait around until script has finished\r
+ while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()\r
+ : (jmb.isFinishedInit() && jmb.getPdbFile().length != jmb.pdbentry.length))\r
+ {\r
+ try\r
+ {\r
+ Cache.log.debug("Waiting around for jmb notify.");\r
+ Thread.sleep(35);\r
+ } catch (Exception e)\r
+ {\r
+ }\r
+ }\r
+ // refresh the sequence colours for the new structure(s)\r
+ for (AlignmentPanel ap : _colourwith)\r
+ {\r
+ jmb.updateColours(ap);\r
+ }\r
+ // do superposition if asked to\r
+ if (alignAddedStructures)\r
+ {\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ alignStructs_withAllAlignPanels();\r
+ // jmb.superposeStructures(ap.av.getAlignment(), -1, null);\r
+ }\r
+ });\r
+ alignAddedStructures = false;\r
+ }\r
+ addingStructures = false;\r
+\r
+ }\r
+ _started = false;\r
+ worker = null;\r
+ }\r
+\r
+ public void pdbFile_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Save PDB File");\r
+ chooser.setToolTipText(MessageManager.getString("action.save"));\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ try\r
+ {\r
+ // TODO: cope with multiple PDB files in view\r
+ BufferedReader in = new BufferedReader(new FileReader(\r
+ jmb.getPdbFile()[0]));\r
+ File outFile = chooser.getSelectedFile();\r
+\r
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
+ String data;\r
+ while ((data = in.readLine()) != null)\r
+ {\r
+ if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))\r
+ {\r
+ out.println(data);\r
+ }\r
+ }\r
+ out.close();\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+ public void viewMapping_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();\r
+ try\r
+ {\r
+ for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)\r
+ {\r
+ cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile()));\r
+ cap.appendText("\n");\r
+ }\r
+ } catch (OutOfMemoryError e)\r
+ {\r
+ new OOMWarning(\r
+ "composing sequence-structure alignments for display in text box.",\r
+ e);\r
+ cap.dispose();\r
+ return;\r
+ }\r
+ jalview.gui.Desktop.addInternalFrame(cap, MessageManager.getString("label.pdb_sequence_mapping"),\r
+ 550, 600);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ public void eps_actionPerformed(ActionEvent e)\r
+ {\r
+ makePDBImage(jalview.util.ImageMaker.EPS);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ public void png_actionPerformed(ActionEvent e)\r
+ {\r
+ makePDBImage(jalview.util.ImageMaker.PNG);\r
+ }\r
+\r
+ void makePDBImage(int type)\r
+ {\r
+ int width = getWidth();\r
+ int height = getHeight();\r
+\r
+ jalview.util.ImageMaker im;\r
+\r
+ if (type == jalview.util.ImageMaker.PNG)\r
+ {\r
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,\r
+ "Make PNG image from view", width, height, null, null);\r
+ }\r
+ else\r
+ {\r
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,\r
+ "Make EPS file from view", width, height, null,\r
+ this.getTitle());\r
+ }\r
+\r
+ if (im.getGraphics() != null)\r
+ {\r
+ Rectangle rect = new Rectangle(width, height);\r
+ jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);\r
+ im.writeImage();\r
+ }\r
+ }\r
+\r
+ public void jmolColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ if (jmolColour.isSelected())\r
+ {\r
+ // disable automatic sequence colouring.\r
+ jmb.setColourBySequence(false);\r
+ }\r
+ }\r
+\r
+ public void seqColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ jmb.setColourBySequence(seqColour.isSelected());\r
+ if (_colourwith == null)\r
+ {\r
+ _colourwith = new Vector<AlignmentPanel>();\r
+ }\r
+ if (jmb.isColourBySequence())\r
+ {\r
+ if (!jmb.isLoadingFromArchive())\r
+ {\r
+ if (_colourwith.size() == 0 && ap != null)\r
+ {\r
+ // Make the currently displayed alignment panel the associated view\r
+ _colourwith.add(ap.alignFrame.alignPanel);\r
+ }\r
+ }\r
+ // Set the colour using the current view for the associated alignframe\r
+ for (AlignmentPanel ap : _colourwith)\r
+ {\r
+ jmb.colourBySequence(ap.av.showSequenceFeatures, ap);\r
+ }\r
+ }\r
+ }\r
+\r
+ public void chainColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ chainColour.setSelected(true);\r
+ jmb.colourByChain();\r
+ }\r
+\r
+ public void chargeColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ chargeColour.setSelected(true);\r
+ jmb.colourByCharge();\r
+ }\r
+\r
+ public void zappoColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ zappoColour.setSelected(true);\r
+ jmb.setJalviewColourScheme(new ZappoColourScheme());\r
+ }\r
+\r
+ public void taylorColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ taylorColour.setSelected(true);\r
+ jmb.setJalviewColourScheme(new TaylorColourScheme());\r
+ }\r
+\r
+ public void hydroColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ hydroColour.setSelected(true);\r
+ jmb.setJalviewColourScheme(new HydrophobicColourScheme());\r
+ }\r
+\r
+ public void helixColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ helixColour.setSelected(true);\r
+ jmb.setJalviewColourScheme(new HelixColourScheme());\r
+ }\r
+\r
+ public void strandColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ strandColour.setSelected(true);\r
+ jmb.setJalviewColourScheme(new StrandColourScheme());\r
+ }\r
+\r
+ public void turnColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ turnColour.setSelected(true);\r
+ jmb.setJalviewColourScheme(new TurnColourScheme());\r
+ }\r
+\r
+ public void buriedColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ buriedColour.setSelected(true);\r
+ jmb.setJalviewColourScheme(new BuriedColourScheme());\r
+ }\r
+\r
+ public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ setJalviewColourScheme(new PurinePyrimidineColourScheme());\r
+ }\r
+\r
+ public void userColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ userColour.setSelected(true);\r
+ new UserDefinedColours(this, null);\r
+ }\r
+\r
+ public void backGround_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ java.awt.Color col = JColorChooser.showDialog(this,\r
+ "Select Background Colour", null);\r
+ if (col != null)\r
+ {\r
+ jmb.setBackgroundColour(col);\r
+ }\r
+ }\r
+\r
+ public void jmolHelp_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ try\r
+ {\r
+ jalview.util.BrowserLauncher\r
+ .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");\r
+ } catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ public void showConsole(boolean showConsole)\r
+ {\r
+\r
+ if (showConsole)\r
+ {\r
+ if (splitPane == null)\r
+ {\r
+ splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);\r
+ splitPane.setTopComponent(renderPanel);\r
+ splitPane.setBottomComponent(scriptWindow);\r
+ this.getContentPane().add(splitPane, BorderLayout.CENTER);\r
+ splitPane.setDividerLocation(getHeight() - 200);\r
+ scriptWindow.setVisible(true);\r
+ scriptWindow.validate();\r
+ splitPane.validate();\r
+ }\r
+\r
+ }\r
+ else\r
+ {\r
+ if (splitPane != null)\r
+ {\r
+ splitPane.setVisible(false);\r
+ }\r
+\r
+ splitPane = null;\r
+\r
+ this.getContentPane().add(renderPanel, BorderLayout.CENTER);\r
+ }\r
+\r
+ validate();\r
+ }\r
+\r
+ class RenderPanel extends JPanel\r
+ {\r
+ final Dimension currentSize = new Dimension();\r
+\r
+ final Rectangle rectClip = new Rectangle();\r
+\r
+ public void paintComponent(Graphics g)\r
+ {\r
+ getSize(currentSize);\r
+ g.getClipBounds(rectClip);\r
+\r
+ if (jmb.fileLoadingError != null)\r
+ {\r
+ g.setColor(Color.black);\r
+ g.fillRect(0, 0, currentSize.width, currentSize.height);\r
+ g.setColor(Color.white);\r
+ g.setFont(new Font("Verdana", Font.BOLD, 14));\r
+ g.drawString(MessageManager.getString("label.error_loading_file") + "...", 20, currentSize.height / 2);\r
+ StringBuffer sb = new StringBuffer();\r
+ int lines = 0;\r
+ for (int e = 0; e < jmb.pdbentry.length; e++)\r
+ {\r
+ sb.append(jmb.pdbentry[e].getId());\r
+ if (e < jmb.pdbentry.length - 1)\r
+ {\r
+ sb.append(",");\r
+ }\r
+\r
+ if (e == jmb.pdbentry.length - 1 || sb.length() > 20)\r
+ {\r
+ lines++;\r
+ g.drawString(sb.toString(), 20, currentSize.height / 2 - lines\r
+ * g.getFontMetrics().getHeight());\r
+ }\r
+ }\r
+ }\r
+ else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())\r
+ {\r
+ g.setColor(Color.black);\r
+ g.fillRect(0, 0, currentSize.width, currentSize.height);\r
+ g.setColor(Color.white);\r
+ g.setFont(new Font("Verdana", Font.BOLD, 14));\r
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2);\r
+ }\r
+ else\r
+ {\r
+ jmb.viewer.renderScreenImage(g, currentSize, rectClip);\r
+ }\r
+ }\r
+ }\r
+\r
+ String viewId = null;\r
+\r
+ public String getViewId()\r
+ {\r
+ if (viewId == null)\r
+ {\r
+ viewId = System.currentTimeMillis() + "." + this.hashCode();\r
+ }\r
+ return viewId;\r
+ }\r
+\r
+ public void updateTitleAndMenus()\r
+ {\r
+ if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)\r
+ {\r
+ repaint();\r
+ return;\r
+ }\r
+ setChainMenuItems(jmb.chainNames);\r
+\r
+ this.setTitle(jmb.getViewerTitle());\r
+ if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)\r
+ {\r
+ jmolActionMenu.setVisible(true);\r
+ }\r
+ if (!jmb.isLoadingFromArchive())\r
+ {\r
+ seqColour_actionPerformed(null);\r
+ }\r
+ }\r
+\r
+ protected void buildJmolActionMenu()\r
+ {\r
+ if (_alignwith == null)\r
+ {\r
+ _alignwith = new Vector<AlignmentPanel>();\r
+ }\r
+ if (_alignwith.size() == 0 && ap != null)\r
+ {\r
+ _alignwith.add(ap);\r
+ }\r
+ ;\r
+ for (Component c : jmolActionMenu.getMenuComponents())\r
+ {\r
+ if (c != alignStructs)\r
+ {\r
+ jmolActionMenu.remove((JMenuItem) c);\r
+ }\r
+ }\r
+ final ItemListener handler;\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event\r
+ * .ActionEvent)\r
+ */\r
+ @Override\r
+ protected void alignStructs_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ alignStructs_withAllAlignPanels();\r
+ }\r
+\r
+ private void alignStructs_withAllAlignPanels()\r
+ {\r
+ if (ap == null)\r
+ {\r
+ return;\r
+ }\r
+ ;\r
+ if (_alignwith.size() == 0)\r
+ {\r
+ _alignwith.add(ap);\r
+ }\r
+ ;\r
+ try\r
+ {\r
+ AlignmentI[] als = new Alignment[_alignwith.size()];\r
+ ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];\r
+ int[] alm = new int[_alignwith.size()];\r
+ int a = 0;\r
+\r
+ for (AlignmentPanel ap : _alignwith)\r
+ {\r
+ als[a] = ap.av.getAlignment();\r
+ alm[a] = -1;\r
+ alc[a++] = ap.av.getColumnSelection();\r
+ }\r
+ jmb.superposeStructures(als, alm, alc);\r
+ } catch (Exception e)\r
+ {\r
+ StringBuffer sp = new StringBuffer();\r
+ for (AlignmentPanel ap : _alignwith)\r
+ {\r
+ sp.append("'" + ap.alignFrame.getTitle() + "' ");\r
+ }\r
+ Cache.log.info("Couldn't align structures with the " + sp.toString()\r
+ + "associated alignment panels.", e);\r
+\r
+ }\r
+\r
+ }\r
+\r
+ public void setJalviewColourScheme(ColourSchemeI ucs)\r
+ {\r
+ jmb.setJalviewColourScheme(ucs);\r
+\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param alignment\r
+ * @return first alignment panel displaying given alignment, or the default\r
+ * alignment panel\r
+ */\r
+ public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)\r
+ {\r
+ for (AlignmentPanel ap : getAllAlignmentPanels())\r
+ {\r
+ if (ap.av.getAlignment() == alignment)\r
+ {\r
+ return ap;\r
+ }\r
+ }\r
+ return ap;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param ap2\r
+ * @return true if this Jmol instance is linked with the given alignPanel\r
+ */\r
+ public boolean isLinkedWith(AlignmentPanel ap2)\r
+ {\r
+ return _aps.contains(ap2.av.getSequenceSetId());\r
+ }\r
+\r
+ public boolean isUsedforaligment(AlignmentPanel ap2)\r
+ {\r
+\r
+ return (_alignwith != null) && _alignwith.contains(ap2);\r
+ }\r
+\r
+ public boolean isUsedforcolourby(AlignmentPanel ap2)\r
+ {\r
+ return (_colourwith != null) && _colourwith.contains(ap2);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return TRUE if the view is NOT being coloured by sequence associations.\r
+ */\r
+ public boolean isColouredByJmol()\r
+ {\r
+ return !jmb.isColourBySequence();\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalview.git / blobdiff