X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=955ad7be3313eea63ca8ba721b74107deaa4ff95;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=7945fa7d7fe5e954b60f3823b394000e023d3020;hpb=ea990f32cf34a867377d25f7fc05bfbfb15f6fb3;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 7945fa7..955ad7b 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -17,46 +17,32 @@ */ 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.api.AlignmentViewPanel; +import jalview.api.SequenceStructureBinding; import jalview.bin.Cache; import jalview.datamodel.*; -import jalview.gui.*; +import jalview.gui.ViewSelectionMenu.ViewSetProvider; 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.*; -import org.jmol.viewer.JmolConstants; -public class AppJmol extends GStructureViewer implements StructureListener, - JmolStatusListener, Runnable +public class AppJmol extends GStructureViewer implements Runnable, + SequenceStructureBinding, ViewSetProvider { - JmolViewer viewer; - - JmolPopup jmolpopup; - - ScriptWindow scriptWindow; + AppJmolBinding jmb; - PDBEntry pdbentry; - - SequenceI[] sequence; - - String[] chains; - - StructureSelectionManager ssm; + JPanel scriptWindow; JSplitPane splitPane; @@ -64,39 +50,100 @@ public class AppJmol extends GStructureViewer implements StructureListener, AlignmentPanel ap; - String fileLoadingError; - - boolean colourBySequence = true; - - boolean loadingFromArchive = false; - 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) { - loadingFromArchive = true; - pdbentry = new PDBEntry(); - pdbentry.setFile(file); - pdbentry.setId(id); - this.sequence = seq; - this.ap = ap; + 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); - colourBySequence = false; - seqColour.setSelected(false); + initMenus(); viewId = viewid; // jalview.gui.Desktop.addInternalFrame(this, "Loading File", // bounds.width,bounds.height); - initJmol(loadStatus); - this.addInternalFrameListener(new InternalFrameAdapter() { public void internalFrameClosing(InternalFrameEvent internalFrameEvent) @@ -104,47 +151,111 @@ public class AppJmol extends GStructureViewer implements StructureListener, closeViewer(); } }); + initJmol(loadStatus); // pdbentry, seq, JBPCHECK! + } - public synchronized void addSequence(SequenceI[] seq) + private void initMenus() { - Vector v = new Vector(); - for (int i = 0; i < sequence.length; i++) - v.addElement(sequence[i]); + seqColour.setSelected(jmb.isColourBySequence()); + jmolColour.setSelected(!jmb.isColourBySequence()); + if (_colourwith==null) + { + _colourwith=new Vector(); + } + if (_alignwith==null) + { + _alignwith=new Vector(); + } + + 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 + + } - for (int i = 0; i < seq.length; i++) - if (!v.contains(seq[i])) - v.addElement(seq[i]); + @Override + public void menuCanceled(MenuEvent e) + { + // TODO Auto-generated method stub - SequenceI[] tmp = new SequenceI[v.size()]; - v.copyInto(tmp); - sequence = tmp; + } + }); } + 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, - AlignmentPanel ap) + final AlignmentPanel ap) { + progressBar = ap.alignFrame; // //////////////////////////////// // Is the pdb file already loaded? - String alreadyMapped = StructureSelectionManager - .getStructureSelectionManager().alreadyMappedToFile( + 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 map sequences to the visible structure?", - "Map Sequences to Visible Window: " - + pdbentry.getId(), JOptionPane.YES_NO_OPTION); + 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) { - StructureSelectionManager.getStructureSelectionManager() - .setMapping(seq, chains, alreadyMapped, + // TODO : Fix multiple seq to one chain issue here. + ap.getStructureSelectionManager().setMapping(seq, chains, alreadyMapped, AppletFormatAdapter.FILE); if (ap.seqPanel.seqCanvas.fr != null) { @@ -160,11 +271,21 @@ public class AppJmol extends GStructureViewer implements StructureListener, { if (frames[i] instanceof AppJmol) { - AppJmol topJmol = ((AppJmol) frames[i]); - if (topJmol.pdbentry.getFile().equals(alreadyMapped)) + 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++) { - topJmol.addSequence(seq); - break; + 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; + } } } } @@ -173,25 +294,65 @@ public class AppJmol extends GStructureViewer implements StructureListener, } } // ///////////////////////////////// - - 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) + // 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) { - initJmol("load \"" + pdbentry.getFile() + "\""); + 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; + } + } } - else + // ///////////////////////////////// + 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) { - Thread worker = new Thread(this); - worker.start(); + 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) @@ -199,49 +360,263 @@ public class AppJmol extends GStructureViewer implements StructureListener, closeViewer(); } }); + } - void initJmol(String command) + /** + * 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) { - renderPanel = new RenderPanel(); - - this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER); + openNewJmol(ap, pe, seqs); + } - StringBuffer title = new StringBuffer(sequence[0].getName() + ":" - + pdbentry.getId()); + /** + * list of sequenceSet ids associated with the view + */ + ArrayList _aps = new ArrayList(); - if (pdbentry.getProperty() != null) + public AlignmentPanel[] getAllAlignmentPanels() + { + AlignmentPanel[] t, list = new AlignmentPanel[0]; + for (String setid : _aps) { - if (pdbentry.getProperty().get("method") != null) + AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid); + if (panels != null) { - title.append(" Method: "); - title.append(pdbentry.getProperty().get("method")); + 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; } - if (pdbentry.getProperty().get("chains") != null) + } + + return list; + } + + /** + * list of alignment panels to use for superposition + */ + Vector _alignwith = new Vector(); + + /** + * list of alignment panels that are used for colouring structures by aligned + * sequences + */ + Vector _colourwith = new Vector(); + + /** + * 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) { - title.append(" Chain:"); - title.append(pdbentry.getProperty().get("chains")); + ap = null; + for (AlignmentPanel aps : getAllAlignmentPanels()) + { + if (aps != nap) + { + ap = aps; + break; + } + } } + } catch (Exception ex) + { + } + if (ap != null) + { + buildJmolActionMenu(); } + } - this.setTitle(title.toString()); - jalview.gui.Desktop.addInternalFrame(this, title.toString(), - getBounds().width, getBounds().height); - // * OK, but safer to assign htmlName, URL bases, comandOptions, and - // statusListener now. + 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; + } - viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel, - new SmarterJmolAdapter(), "", null, null, "", this); + 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(); - jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true); + 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; + } - viewer.evalStringQuiet(command); + 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() { @@ -278,78 +653,221 @@ public class AppJmol extends GStructureViewer implements StructureListener, boolean allChainsSelected = false; + private boolean alignAddedStructures = false; + void centerViewer() { - StringBuffer cmd = new StringBuffer(); + 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()) - cmd.append(":" + item.getText() + " or "); + { + toshow.addElement(item.getText()); + } } } - - if (cmd.length() > 0) - cmd.setLength(cmd.length() - 4); - - viewer.evalStringQuiet("select *;restrict " + cmd + ";cartoon;center " - + cmd); + jmb.centerViewer(toshow); } 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()); + 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(); - 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 + for (int pi = 0; pi < jmb.pdbentry.length; pi++) { - JOptionPane - .showInternalMessageDialog( - Desktop.desktop, - pdbentry.getId() - + " could not be retrieved. Please try downloading the file manually.", - "Couldn't load file", JOptionPane.ERROR_MESSAGE); - + 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 id " + pdbentry.getId() + " from MSD", - 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")); + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Save PDB File"); @@ -361,8 +879,9 @@ public class AppJmol extends GStructureViewer implements StructureListener, { try { - BufferedReader in = new BufferedReader(new FileReader(pdbentry - .getFile())); + // 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)); @@ -385,14 +904,28 @@ public class AppJmol extends GStructureViewer implements StructureListener, 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! + 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! @@ -428,107 +961,110 @@ public class AppJmol extends GStructureViewer implements StructureListener, else { im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS, - "Make EPS file from view", width, height, null, this - .getTitle()); + "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); + 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) { - lastCommand = null; - colourBySequence = seqColour.isSelected(); - colourBySequence(ap.alignFrame.alignPanel); + jmb.setColourBySequence(seqColour.isSelected()); + if (_colourwith == null) + { + _colourwith = new Vector(); + } + 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) { - colourBySequence = false; - seqColour.setSelected(false); - viewer.evalStringQuiet("select *;color chain"); + chainColour.setSelected(true); + jmb.colourByChain(); } 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"); + chargeColour.setSelected(true); + jmb.colourByCharge(); } public void zappoColour_actionPerformed(ActionEvent actionEvent) { - setJalviewColourScheme(new ZappoColourScheme()); + zappoColour.setSelected(true); + jmb.setJalviewColourScheme(new ZappoColourScheme()); } public void taylorColour_actionPerformed(ActionEvent actionEvent) { - setJalviewColourScheme(new TaylorColourScheme()); + taylorColour.setSelected(true); + jmb.setJalviewColourScheme(new TaylorColourScheme()); } public void hydroColour_actionPerformed(ActionEvent actionEvent) { - setJalviewColourScheme(new HydrophobicColourScheme()); + hydroColour.setSelected(true); + jmb.setJalviewColourScheme(new HydrophobicColourScheme()); } public void helixColour_actionPerformed(ActionEvent actionEvent) { - setJalviewColourScheme(new HelixColourScheme()); + helixColour.setSelected(true); + jmb.setJalviewColourScheme(new HelixColourScheme()); } public void strandColour_actionPerformed(ActionEvent actionEvent) { - setJalviewColourScheme(new StrandColourScheme()); + strandColour.setSelected(true); + jmb.setJalviewColourScheme(new StrandColourScheme()); } public void turnColour_actionPerformed(ActionEvent actionEvent) { - setJalviewColourScheme(new TurnColourScheme()); + turnColour.setSelected(true); + jmb.setJalviewColourScheme(new TurnColourScheme()); } public void buriedColour_actionPerformed(ActionEvent actionEvent) { - setJalviewColourScheme(new BuriedColourScheme()); + buriedColour.setSelected(true); + jmb.setJalviewColourScheme(new BuriedColourScheme()); } - - public void setJalviewColourScheme(ColourSchemeI cs) + + public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent) { - 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()); + setJalviewColourScheme(new PurinePyrimidineColourScheme()); } - + public void userColour_actionPerformed(ActionEvent actionEvent) { + userColour.setSelected(true); new UserDefinedColours(this, null); } @@ -536,11 +1072,9 @@ public class AppJmol extends GStructureViewer implements StructureListener, { java.awt.Color col = JColorChooser.showDialog(this, "Select Background Colour", null); - if (col != null) { - viewer.evalStringQuiet("background [" + col.getRed() + "," - + col.getGreen() + "," + col.getBlue() + "];"); + jmb.setBackgroundColour(col); } } @@ -555,369 +1089,8 @@ public class AppJmol extends GStructureViewer implements StructureListener, } } - // //////////////////////////////// - // /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 notifyFileLoaded(String fullPathName, String fileName, - String modelName, String errorMsg, int modelParts) - { - if (errorMsg != null) - { - fileLoadingError = errorMsg; - repaint(); - return; - } - - fileLoadingError = null; - - if (fileName != null) - { - // TODO: do some checking using the modelPts number of parts against our own estimate of the number of chains - // 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 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, null); - } - - public void notifyAtomPicked(int atomIndex, String strInfo, String strData) - { - if (strData!=null) - { - Cache.log.info("Non null pick data string: "+strData+" (other info: '"+strInfo+"' pos "+atomIndex+")"); - } - 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 = "(("+picked+".CA" + ")|("+picked+".P"+"))"; - - 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, String data) - { - if (data!=null) - { - Cache.log.info("Non null hover data string: "+data+" (other info: '"+strInfo+"' pos "+atomIndex+")"); - } - mouseOverStructure(atomIndex, strInfo); - } - - @Override - public void showUrl(String url) - { - try { - jalview.util.BrowserLauncher.openURL(url); - } catch (IOException e) - { - Cache.log.error("Failed to launch Jmol-associated url "+url,e); - // TODO: 2.6 : warn user if browser was not configured. - } - } - public void showConsole(boolean showConsole) { - if (scriptWindow == null) - scriptWindow = new ScriptWindow(this); if (showConsole) { @@ -927,15 +1100,19 @@ public class AppJmol extends GStructureViewer implements StructureListener, splitPane.setTopComponent(renderPanel); splitPane.setBottomComponent(scriptWindow); this.getContentPane().add(splitPane, BorderLayout.CENTER); + splitPane.setDividerLocation(getHeight() - 200); + scriptWindow.setVisible(true); + scriptWindow.validate(); + splitPane.validate(); } - splitPane.setDividerLocation(getHeight() - 200); - splitPane.validate(); } else { if (splitPane != null) + { splitPane.setVisible(false); + } splitPane = null; @@ -945,14 +1122,6 @@ public class AppJmol extends GStructureViewer implements StructureListener, validate(); } - public float[][] functionXY(String functionName, int x, int y) - { - return null; - } - - // /End JmolStatusListener - // ///////////////////////////// - class RenderPanel extends JPanel { final Dimension currentSize = new Dimension(); @@ -964,26 +1133,42 @@ public class AppJmol extends GStructureViewer implements StructureListener, getSize(currentSize); g.getClipBounds(rectClip); - if (viewer == null) + 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("Retrieving PDB data....", 20, currentSize.height / 2); + 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 (fileLoadingError != null) + 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("Error loading file..." + pdbentry.getId(), 20, - currentSize.height / 2); + g.drawString("Retrieving PDB data....", 20, currentSize.height / 2); } else { - viewer.renderScreenImage(g, currentSize, rectClip); + jmb.viewer.renderScreenImage(g, currentSize, rectClip); } } } @@ -999,96 +1184,153 @@ public class AppJmol extends GStructureViewer implements StructureListener, return viewId; } - @Override - public String createImage(String fileName, String type, - Object textOrBytes, int quality) + public void updateTitleAndMenus() { - // TODO Auto-generated method stub - return null; + 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); + } } - @Override - public float[][][] functionXYZ(String functionName, int nx, int ny, int nz) + protected void buildJmolActionMenu() { - // TODO Auto-generated method stub - return null; + if (_alignwith == null) + { + _alignwith = new Vector(); + } + 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 - public Hashtable getRegistryInfo() + protected void alignStructs_actionPerformed(ActionEvent actionEvent) { - // TODO Auto-generated method stub - return null; + alignStructs_withAllAlignPanels(); } - @Override - public void notifyCallback(int type, Object[] data) + private void alignStructs_withAllAlignPanels() { - try { - switch (type) + if (ap == null) { - case JmolConstants.CALLBACK_LOADSTRUCT: - notifyFileLoaded((String) data[1], (String) data[2], - (String) data[3], (String) data[4], ((Integer) data[5]).intValue()); - - break; - case JmolConstants.CALLBACK_PICK: - notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]); - // also highlight in alignment - case JmolConstants.CALLBACK_HOVER: - notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]); - break; - case JmolConstants.CALLBACK_SCRIPT: - notifyScriptTermination((String)data[2], ((Integer)data[3]).intValue()); - break; - case JmolConstants.CALLBACK_ECHO: - sendConsoleEcho((String)data[1]); - break; - case JmolConstants.CALLBACK_MESSAGE: - sendConsoleMessage((data==null) ? ((String) null) : (String)data[1]); - break; - case JmolConstants.CALLBACK_MEASURE: - case JmolConstants.CALLBACK_CLICK: - default: - System.err.println("Unhandled callback "+type+" "+data); - break; + return; } + ; + if (_alignwith.size() == 0) + { + _alignwith.add(ap); } - catch (Exception e) + ; + try { - Cache.log.warn("Squashed Jmol callback handler error: ",e); + AlignmentI[] als = new Alignment[_alignwith.size()]; + ColumnSelection[] alc = new ColumnSelection[_alignwith.size()]; + int[] alm = new int[_alignwith.size()]; + int a = 0; + + for (AlignmentPanel ap : _alignwith) + { + als[a] = ap.av.getAlignment(); + alm[a] = -1; + alc[a++] = ap.av.getColumnSelection(); + } + jmb.superposeStructures(als, alm, alc); + } catch (Exception e) + { + StringBuffer sp = new StringBuffer(); + for (AlignmentPanel ap : _alignwith) + { + sp.append("'" + ap.alignFrame.getTitle() + "' "); + } + Cache.log.info("Couldn't align structures with the " + sp.toString() + + "associated alignment panels.", e); + } + } - @Override - public boolean notifyEnabled(int callbackPick) + 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) { - switch (callbackPick) + for (AlignmentPanel ap : getAllAlignmentPanels()) { - case JmolConstants.CALLBACK_ECHO: - case JmolConstants.CALLBACK_LOADSTRUCT: - case JmolConstants.CALLBACK_MEASURE: - case JmolConstants.CALLBACK_MESSAGE: - case JmolConstants.CALLBACK_PICK: - case JmolConstants.CALLBACK_SCRIPT: - case JmolConstants.CALLBACK_HOVER: - case JmolConstants.CALLBACK_ERROR: - return true; - case JmolConstants.CALLBACK_CLICK: - case JmolConstants.CALLBACK_ANIMFRAME: - case JmolConstants.CALLBACK_MINIMIZATION: - case JmolConstants.CALLBACK_RESIZE: - case JmolConstants.CALLBACK_SYNC: + if (ap.av.getAlignment() == alignment) + { + return ap; + } } - return false; + return ap; } - @Override - public void setCallbackFunction(String callbackType, - String callbackFunction) + /** + * + * @param ap2 + * @return true if this Jmol instance is linked with the given alignPanel + */ + public boolean isLinkedWith(AlignmentPanel ap2) { - Cache.log.debug("Ignoring set-callback request to associate "+callbackType+" with function "+callbackFunction); - + 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(); + } + + }