-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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 <http://www.gnu.org/licenses/>.
- */
-package jalview.gui;
-
-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.api.AlignmentViewPanel;
-import jalview.api.SequenceStructureBinding;
-import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.structure.*;
-import jalview.datamodel.PDBEntry;
-import jalview.io.*;
-import jalview.schemes.*;
-
-public class AppJmol extends GStructureViewer implements Runnable,
- SequenceStructureBinding, ViewSetProvider
-
-{
- AppJmolBinding jmb;
-
- JPanel scriptWindow;
-
- JSplitPane splitPane;
-
- RenderPanel renderPanel;
-
- AlignmentPanel ap;
-
- Vector atomsPicked = new Vector();
-
- private boolean addingStructures = false;
-
- /**
- *
- * @param file
- * @param id
- * @param seq
- * @param ap
- * @param loadStatus
- * @param bounds
- * @deprecated defaults to AppJmol(String[] files, ... , viewid);
- */
- public AppJmol(String file, String id, SequenceI[] seq,
- AlignmentPanel ap, String loadStatus, Rectangle bounds)
- {
- this(file, id, seq, ap, loadStatus, bounds, null);
- }
-
- /**
- * @deprecated
- */
- public AppJmol(String file, String id, SequenceI[] seq,
- AlignmentPanel ap, String loadStatus, Rectangle bounds,
- String viewid)
- {
- this(new String[]
- { file }, new String[]
- { id }, new SequenceI[][]
- { seq }, ap, true, true, false, loadStatus, bounds, viewid);
- }
-
- 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();
- pdbentry.setFile(files[i]);
- pdbentry.setId(ids[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);
- jmolColour.setSelected(true);
- }
- if (usetoColour)
- {
- useAlignmentPanelForColourbyseq(ap);
- jmb.setColourBySequence(true);
- seqColour.setSelected(true);
- jmolColour.setSelected(false);
- }
- this.setBounds(bounds);
- initMenus();
- viewId = viewid;
- // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
- // bounds.width,bounds.height);
-
- this.addInternalFrameListener(new InternalFrameAdapter()
- {
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
- {
- closeViewer();
- }
- });
- initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
-
- }
-
- private void initMenus()
- {
- seqColour.setSelected(jmb.isColourBySequence());
- jmolColour.setSelected(!jmb.isColourBySequence());
- if (_colourwith==null)
- {
- _colourwith=new Vector<AlignmentPanel>();
- }
- if (_alignwith==null)
- {
- _alignwith=new Vector<AlignmentPanel>();
- }
-
- seqColourBy = new ViewSelectionMenu("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("Superpose with ..", this,
- _alignwith, handler = new ItemListener()
- {
-
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText("Align structures using "
- + _alignwith.size() + " linked alignment views");
- }
- });
- handler.itemStateChanged(null);
- jmolActionMenu.add(alpanels);
- jmolActionMenu.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;
- // ////////////////////////////////
- // Is the pdb file already loaded?
- String alreadyMapped = ap.getStructureSelectionManager().alreadyMappedToFile(
- pdbentry.getId());
-
- if (alreadyMapped != null)
- {
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- pdbentry.getId() + " is already displayed."
- + "\nDo you want to re-use this viewer ?",
- "Map Sequences to Visible Window: " + pdbentry.getId(),
- JOptionPane.YES_NO_OPTION);
-
- if (option == JOptionPane.YES_OPTION)
- {
- // TODO : Fix multiple seq to one chain issue here.
- ap.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)
- {
- final AppJmol topJmol = ((AppJmol) frames[i]);
- // JBPNOTE: this looks like a binding routine, rather than a gui
- // routine
- for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
- {
- if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
- {
- topJmol.jmb.addSequence(pe, seq);
- topJmol.addAlignmentPanel(ap);
- // add it to the set used for colouring
- topJmol.useAlignmentPanelForColourbyseq(ap);
- topJmol.buildJmolActionMenu();
- ap.getStructureSelectionManager().sequenceColoursChanged(ap);
- break;
- }
- }
- }
- }
-
- return;
- }
- }
- // /////////////////////////////////
- // Check if there are other Jmol views involving this alignment
- // and prompt user about adding this molecule to one of them
- Vector existingViews = getJmolsFor(ap);
- if (existingViews.size() > 0)
- {
- Enumeration jm = existingViews.elements();
- while (jm.hasMoreElements())
- {
- AppJmol topJmol = (AppJmol) jm.nextElement();
- // TODO: highlight topJmol in view somehow
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- "Do you want to add " + pdbentry.getId()
- + " to the view called\n'" + topJmol.getTitle()
- + "'\n", "Align to existing structure view",
- JOptionPane.YES_NO_OPTION);
- if (option == JOptionPane.YES_OPTION)
- {
- topJmol.useAlignmentPanelForSuperposition(ap);
- topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
- return;
- }
- }
- }
- // /////////////////////////////////
- openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
- }
- private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) {
- boolean promptUser=pdbentrys.length==1;
- 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();
- worker=null;
- String filelist="";
-// for (PDBEntry pe: pdbentrys)
-// {
-// if (pe.getFile()==null)
- {
- addingStructures = false;
- worker = new Thread(this);
- worker.start();
-// break;
- }
-// filelist+=" \""+pe.getFile()+"\"";
-
-/* }
- if (worker==null)
- {
- initJmol("load"+(pdbentrys.length>1 ? " APPEND" : "") + filelist);
- }
-*/
- this.addInternalFrameListener(new InternalFrameAdapter()
- {
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
- {
- closeViewer();
- }
- });
-
- }
-
- /**
- * 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);
- }
-
- /**
- * list of sequenceSet ids associated with the view
- */
- ArrayList<String> _aps = new ArrayList();
-
- public AlignmentPanel[] getAllAlignmentPanels()
- {
- AlignmentPanel[] t, list = new AlignmentPanel[0];
- for (String setid : _aps)
- {
- AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
- if (panels != null)
- {
- t = new AlignmentPanel[list.length + panels.length];
- System.arraycopy(list, 0, t, 0, list.length);
- System.arraycopy(panels, 0, t, list.length, panels.length);
- list = t;
- }
- }
-
- return list;
- }
-
- /**
- * list of alignment panels to use for superposition
- */
- Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
-
- /**
- * list of alignment panels that are used for colouring structures by aligned
- * sequences
- */
- Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
-
- /**
- * set the primary alignmentPanel reference and add another alignPanel to the
- * list of ones to use for colouring and aligning
- *
- * @param nap
- */
- public void addAlignmentPanel(AlignmentPanel nap)
- {
- if (ap == null)
- {
- ap = nap;
- }
- if (!_aps.contains(nap.av.getSequenceSetId()))
- {
- _aps.add(nap.av.getSequenceSetId());
- }
- }
-
- /**
- * remove any references held to the given alignment panel
- *
- * @param nap
- */
- public void removeAlignmentPanel(AlignmentPanel nap)
- {
- try
- {
- _alignwith.remove(nap);
- _colourwith.remove(nap);
- if (ap == nap)
- {
- ap = null;
- for (AlignmentPanel aps : getAllAlignmentPanels())
- {
- if (aps != nap)
- {
- ap = aps;
- break;
- }
- }
- }
- } catch (Exception ex)
- {
- }
- if (ap != null)
- {
- buildJmolActionMenu();
- }
- }
-
- public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
- {
- addAlignmentPanel(nap);
- if (!_alignwith.contains(nap))
- {
- _alignwith.add(nap);
- }
- }
-
- public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
- {
- if (_alignwith.contains(nap))
- {
- _alignwith.remove(nap);
- }
- }
-
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, boolean enableColourBySeq)
- {
- useAlignmentPanelForColourbyseq(nap);
- jmb.setColourBySequence(enableColourBySeq);
- seqColour.setSelected(enableColourBySeq);
- jmolColour.setSelected(!enableColourBySeq);
- }
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
- {
- addAlignmentPanel(nap);
- if (!_colourwith.contains(nap))
- {
- _colourwith.add(nap);
- }
- }
-
- public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
- {
- if (_colourwith.contains(nap))
- {
- _colourwith.remove(nap);
- }
- }
-
- /**
- * pdb retrieval thread.
- */
- private Thread worker = null;
-
- /**
- * add a new structure (with associated sequences and chains) to this viewer,
- * retrieving it if necessary first.
- *
- * @param pdbentry
- * @param seq
- * @param chains
- * @param alignFrame
- * @param align
- * if true, new structure(s) will be align using associated alignment
- */
- private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
- final String[] chains, final boolean b,
- final IProgressIndicator alignFrame)
- {
- if (pdbentry.getFile() == null)
- {
- if (worker != null && worker.isAlive())
- {
- // a retrieval is in progress, wait around and add ourselves to the
- // queue.
- new Thread(new Runnable()
- {
- public void run()
- {
- while (worker != null && worker.isAlive() && _started)
- {
- try
- {
- Thread.sleep(100 + ((int) Math.random() * 100));
-
- } catch (Exception e)
- {
- }
-
- }
- // and call ourselves again.
- addStructure(pdbentry, seq, chains, b, alignFrame);
- }
- }).start();
- return;
- }
- }
- // otherwise, start adding the structure.
- jmb.addSequenceAndChain(new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, new String[][]
- { chains });
- addingStructures = true;
- _started = false;
- alignAddedStructures = b;
- progressBar = alignFrame; // visual indication happens on caller frame.
- (worker = new Thread(this)).start();
- return;
- }
-
- private Vector getJmolsFor(AlignmentPanel ap2)
- {
- Vector otherJmols = new Vector();
- // 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.isLinkedWith(ap2))
- {
- otherJmols.addElement(topJmol);
- }
- }
- }
- return otherJmols;
- }
-
- 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(true, "Jmol", true);
- if (command==null)
- {
- command="";
- }
- jmb.evalStateCommand(command);
- jmb.setFinishedInit(true);
- }
-
- void setChainMenuItems(Vector chains)
- {
- chainMenu.removeAll();
- if (chains == null)
- {
- return;
- }
- 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;
-
- private boolean alignAddedStructures = false;
-
- void centerViewer()
- {
- Vector toshow = new Vector();
- String lbl;
- int mlength, p, mnum;
- 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);
- }
-
- void closeViewer()
- {
- jmb.closeViewer();
- ap = 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;
- }
-
- /**
- * state flag for PDB retrieval thread
- */
- private boolean _started = false;
-
- public void run()
- {
- _started = true;
- String pdbid = "";
- // todo - record which pdbids were successfuly imported.
- StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
- try
- {
- String[] curfiles = jmb.getPdbFile(); // files currently in viewer
- // TODO: replace with reference fetching/transfer code (validate PDBentry
- // as a DBRef?)
- jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
- for (int pi = 0; pi < jmb.pdbentry.length; pi++)
- {
- String file = jmb.pdbentry[pi].getFile();
- if (file == null)
- {
- // retrieve the pdb and store it locally
- AlignmentI pdbseq = null;
- pdbid = jmb.pdbentry[pi].getId();
- long hdl = pdbid.hashCode() - System.currentTimeMillis();
- if (progressBar != null)
- {
- progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);
- }
- try
- {
- pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
- .getId());
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- errormsgs.append("'" + pdbid + "'");
- }
- if (progressBar != null)
- {
- progressBar.setProgressBar("Finished.", hdl);
- }
- if (pdbseq != null)
- {
- // just transfer the file name from the first sequence's first
- // PDBEntry
- jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq
- .getSequenceAt(0).getPDBId().elementAt(0)).getFile());
- files.append(" \"" + file + "\"");
- }
- else
- {
- errormsgs.append("'" + pdbid + "' ");
- }
- }
- else
- {
- if (curfiles != null && curfiles.length > 0)
- {
- addingStructures = true; // already files loaded.
- for (int c = 0; c < curfiles.length; c++)
- {
- if (curfiles[c].equals(file))
- {
- file = null;
- break;
- }
- }
- }
- if (file != null)
- {
- files.append(" \"" + file + "\"");
- }
- }
- }
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
- + "'");
- }
- if (errormsgs.length() > 0)
- {
-
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "The following pdb entries could not be retrieved from the PDB:\n"
- + errormsgs.toString()
- + "\nPlease try downloading them manually.",
- "Couldn't load file", JOptionPane.ERROR_MESSAGE);
-
- }
- long lastnotify = jmb.getLoadNotifiesHandled();
- if (files.length() > 0)
- {
- if (!addingStructures)
- {
-
- try
- {
- initJmol("load FILES " + files.toString());
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("When trying to open the Jmol viewer!", oomerror);
- Cache.log.debug("File locations are " + files);
- } catch (Exception ex)
- {
- Cache.log.error("Couldn't open Jmol viewer!", ex);
- }
- }
- else
- {
- StringBuffer cmd = new StringBuffer();
- cmd.append("loadingJalviewdata=true\nload APPEND ");
- cmd.append(files.toString());
- cmd.append("\nloadingJalviewdata=null");
- final String command = cmd.toString();
- cmd = null;
- 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 " + files);
- } catch (Exception ex)
- {
- Cache.log.error("Couldn't add files to Jmol viewer!", ex);
- }
- }
-
- // need to wait around until script has finished
- while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
- : (jmb.isFinishedInit() && jmb.getPdbFile().length!=jmb.pdbentry.length))
- {
- try
- {
- Cache.log.debug("Waiting around for jmb notify.");
- Thread.sleep(35);
- } catch (Exception e)
- {
- }
- }
- // refresh the sequence colours for the new structure(s)
- for (AlignmentPanel ap : _colourwith)
- {
- jmb.updateColours(ap);
- }
- // do superposition if asked to
- if (alignAddedStructures)
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- alignStructs_withAllAlignPanels();
- // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
- }
- });
- alignAddedStructures = false;
- }
- addingStructures = false;
-
- }
- _started = false;
- worker = null;
- }
-
- 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
- {
- // TODO: cope with multiple PDB files in view
- BufferedReader 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("<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();
- try
- {
- for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
- {
- cap.appendText(jmb.printMapping(
- jmb.pdbentry[pdbe].getFile()));
- cap.appendText("\n");
- }
- } catch (OutOfMemoryError e)
- {
- new OOMWarning(
- "composing sequence-structure alignments for display in text box.",
- e);
- cap.dispose();
- return;
- }
- jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
- 550, 600);
- }
-
- /**
- * 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);
- jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
- im.writeImage();
- }
- }
- public void jmolColour_actionPerformed(ActionEvent actionEvent)
- {
- if (jmolColour.isSelected()) {
- // disable automatic sequence colouring.
- jmb.setColourBySequence(false);
- }
- }
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- jmb.setColourBySequence(seqColour.isSelected());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
- }
- if (jmb.isColourBySequence())
- {
- if (!jmb.isLoadingFromArchive())
- {
- if (_colourwith.size()==0 && ap!=null) {
- // Make the currently displayed alignment panel the associated view
- _colourwith.add(ap.alignFrame.alignPanel);
- }
- }
- // Set the colour using the current view for the associated alignframe
- for (AlignmentPanel ap : _colourwith)
- {
- jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
- }
- }
- }
-
- public void chainColour_actionPerformed(ActionEvent actionEvent)
- {
- chainColour.setSelected(true);
- jmb.colourByChain();
- }
-
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
- {
- chargeColour.setSelected(true);
- jmb.colourByCharge();
- }
-
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
- zappoColour.setSelected(true);
- jmb.setJalviewColourScheme(new ZappoColourScheme());
- }
-
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
- taylorColour.setSelected(true);
- jmb.setJalviewColourScheme(new TaylorColourScheme());
- }
-
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
- {
- hydroColour.setSelected(true);
- jmb.setJalviewColourScheme(new HydrophobicColourScheme());
- }
-
- public void helixColour_actionPerformed(ActionEvent actionEvent)
- {
- helixColour.setSelected(true);
- jmb.setJalviewColourScheme(new HelixColourScheme());
- }
-
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
- strandColour.setSelected(true);
- jmb.setJalviewColourScheme(new StrandColourScheme());
- }
-
- public void turnColour_actionPerformed(ActionEvent actionEvent)
- {
- turnColour.setSelected(true);
- jmb.setJalviewColourScheme(new TurnColourScheme());
- }
-
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
- buriedColour.setSelected(true);
- jmb.setJalviewColourScheme(new BuriedColourScheme());
- }
-
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
- userColour.setSelected(true);
- new UserDefinedColours(this, null);
- }
-
- public void backGround_actionPerformed(ActionEvent actionEvent)
- {
- java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour", null);
- if (col != null)
- {
- jmb.setBackgroundColour(col);
- }
- }
-
- public void jmolHelp_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();
-
- final Rectangle rectClip = new Rectangle();
-
- public void paintComponent(Graphics g)
- {
- getSize(currentSize);
- g.getClipBounds(rectClip);
-
- if (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("Error loading file...", 20, currentSize.height / 2);
- StringBuffer sb = new StringBuffer();
- int lines = 0;
- for (int e = 0; e < jmb.pdbentry.length; e++)
- {
- sb.append(jmb.pdbentry[e].getId());
- if (e < jmb.pdbentry.length - 1)
- {
- sb.append(",");
- }
-
- if (e == jmb.pdbentry.length - 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("Retrieving PDB data....", 20, currentSize.height / 2);
- }
- else
- {
- jmb.viewer.renderScreenImage(g, currentSize, rectClip);
- }
- }
- }
-
- String viewId = null;
-
- public String getViewId()
- {
- if (viewId == null)
- {
- viewId = System.currentTimeMillis() + "." + this.hashCode();
- }
- return viewId;
- }
-
- 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.sequence.length > 1)
- {
- jmolActionMenu.setVisible(true);
- }
- if (!jmb.isLoadingFromArchive())
- {
- seqColour_actionPerformed(null);
- }
- }
-
- protected void buildJmolActionMenu()
- {
- if (_alignwith == null)
- {
- _alignwith = new Vector<AlignmentPanel>();
- }
- if (_alignwith.size() == 0 && ap != null)
- {
- _alignwith.add(ap);
- }
- ;
- for (Component c : jmolActionMenu.getMenuComponents())
- {
- if (c != alignStructs)
- {
- jmolActionMenu.remove((JMenuItem) c);
- }
- }
- final ItemListener handler;
- }
-
- /*
- * (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 (ap == null)
- {
- return;
- }
- ;
- if (_alignwith.size() == 0)
- {
- _alignwith.add(ap);
- }
- ;
- 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);
-
- }
-
- }
-
- 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 ap;
- }
-
- /**
- *
- * @param ap2
- * @return true if this Jmol instance is linked with the given alignPanel
- */
- public boolean isLinkedWith(AlignmentPanel ap2)
- {
- return _aps.contains(ap2.av.getSequenceSetId());
- }
-
- public boolean isUsedforaligment(AlignmentPanel ap2)
- {
-
- return (_alignwith != null) && _alignwith.contains(ap2);
- }
-
- public boolean isUsedforcolourby(AlignmentPanel ap2)
- {
- return (_colourwith != null) && _colourwith.contains(ap2);
- }
-
- /**
- *
- * @return TRUE if the view is NOT being coloured by sequence associations.
- */
- public boolean isColouredByJmol()
- {
- return !jmb.isColourBySequence();
- }
-
-
-}
+/*\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