X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=64ea4dca9020017952cb47802aa6fa178a66f530;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=fcb31eb57504dc9c45e3060083abd1fe362b9f8f;hpb=70fd4c40d0b2046c6d402e365e4d04f9cfbb68ef;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index fcb31eb..64ea4dc 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 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,68 +20,48 @@ */ package jalview.gui; -import jalview.api.structures.JalviewStructureDisplayI; -import jalview.bin.Cache; -import jalview.datamodel.Alignment; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.ext.jmol.JalviewJmolBinding; -import jalview.gui.ViewSelectionMenu.ViewSetProvider; -import jalview.io.AppletFormatAdapter; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.jbgui.GStructureViewer; -import jalview.schemes.BuriedColourScheme; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.HelixColourScheme; -import jalview.schemes.HydrophobicColourScheme; -import jalview.schemes.PurinePyrimidineColourScheme; -import jalview.schemes.StrandColourScheme; -import jalview.schemes.TaylorColourScheme; -import jalview.schemes.TurnColourScheme; -import jalview.schemes.ZappoColourScheme; -import jalview.util.MessageManager; -import jalview.util.Platform; +import java.util.Locale; import java.awt.BorderLayout; import java.awt.Color; -import java.awt.Component; import java.awt.Dimension; import java.awt.Font; import java.awt.Graphics; -import java.awt.Rectangle; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.io.BufferedReader; import java.io.File; -import java.io.FileOutputStream; -import java.io.FileReader; -import java.io.PrintWriter; -import java.util.ArrayList; -import java.util.Enumeration; -import java.util.Vector; +import java.util.List; +import java.util.Map; -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JColorChooser; -import javax.swing.JInternalFrame; -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JSplitPane; +import javax.swing.SwingUtilities; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; -import javax.swing.event.MenuEvent; -import javax.swing.event.MenuListener; -public class AppJmol extends GStructureViewer implements Runnable, - ViewSetProvider, JalviewStructureDisplayI +import jalview.api.AlignmentViewPanel; +import jalview.bin.Console; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.datamodel.StructureViewerModel; +import jalview.datamodel.StructureViewerModel.StructureData; +import jalview.fts.service.alphafold.AlphafoldRestClient; +import jalview.gui.ImageExporter.ImageWriterI; +import jalview.gui.StructureViewer.ViewerType; +import jalview.structure.StructureCommand; +import jalview.structures.models.AAStructureBindingModel; +import jalview.util.BrowserLauncher; +import jalview.util.ImageMaker; +import jalview.util.MessageManager; +import jalview.util.Platform; +public class AppJmol extends StructureViewerBase { + // ms to wait for Jmol to load files + private static final int JMOL_LOAD_TIMEOUT = 20000; + + private static final String SPACE = " "; + + private static final String QUOTE = "\""; + AppJmolBinding jmb; JPanel scriptWindow; @@ -90,45 +70,6 @@ public class AppJmol extends GStructureViewer implements Runnable, 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); - */ - @Deprecated - public AppJmol(String file, String id, SequenceI[] seq, - AlignmentPanel ap, String loadStatus, Rectangle bounds) - { - this(file, id, seq, ap, loadStatus, bounds, null); - } - - /** - * @deprecated - */ - @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 @@ -148,139 +89,84 @@ public class AppJmol extends GStructureViewer implements Runnable, * @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) + public AppJmol(StructureViewerModel viewerModel, AlignmentPanel ap, + String sessionFile, String viewid) { - PDBEntry[] pdbentrys = new PDBEntry[files.length]; - for (int i = 0; i < pdbentrys.length; i++) + Map pdbData = viewerModel.getFileData(); + PDBEntry[] pdbentrys = new PDBEntry[pdbData.size()]; + SequenceI[][] seqs = new SequenceI[pdbData.size()][]; + int i = 0; + for (StructureData data : pdbData.values()) { - PDBEntry pdbentry = new PDBEntry(); - pdbentry.setFile(files[i]); - pdbentry.setId(ids[i]); + PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null, + PDBEntry.Type.PDB, data.getFilePath()); pdbentrys[i] = pdbentry; + List sequencesForPdb = data.getSeqList(); + seqs[i] = sequencesForPdb + .toArray(new SequenceI[sequencesForPdb.size()]); + i++; } - // / TODO: check if protocol is needed to be set, and if chains are + + // TODO: check if protocol is needed to be set, and if chains are // autodiscovered. jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), - pdbentrys, seqs, null, null); + pdbentrys, seqs, null); jmb.setLoadingFromArchive(true); addAlignmentPanel(ap); - if (useToAlign) + if (viewerModel.isAlignWithPanel()) { useAlignmentPanelForSuperposition(ap); } - if (leaveColouringToJmol || !usetoColour) + initMenus(); + boolean useToColour = viewerModel.isColourWithAlignPanel(); + boolean leaveColouringToJmol = viewerModel.isColourByViewer(); + if (leaveColouringToJmol || !useToColour) { jmb.setColourBySequence(false); seqColour.setSelected(false); viewerColour.setSelected(true); } - if (usetoColour) + else if (useToColour) { useAlignmentPanelForColourbyseq(ap); jmb.setColourBySequence(true); seqColour.setSelected(true); viewerColour.setSelected(false); } - this.setBounds(bounds); - initMenus(); - viewId = viewid; - // jalview.gui.Desktop.addInternalFrame(this, "Loading File", - // bounds.width,bounds.height); + + this.setBounds(viewerModel.getX(), viewerModel.getY(), + viewerModel.getWidth(), viewerModel.getHeight()); + setViewId(viewid); this.addInternalFrameListener(new InternalFrameAdapter() { - public void internalFrameClosing(InternalFrameEvent internalFrameEvent) + @Override + public void internalFrameClosing( + InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); - initJmol(loadStatus); // pdbentry, seq, JBPCHECK! - + StringBuilder cmd = new StringBuilder(); + cmd.append("load FILES ").append(QUOTE) + .append(Platform.escapeBackslashes(sessionFile)).append(QUOTE); + initJmol(cmd.toString()); } - private void initMenus() + @Override + protected void initMenus() { - seqColour.setSelected(jmb.isColourBySequence()); - viewerColour.setSelected(!jmb.isColourBySequence()); - if (_colourwith == null) - { - _colourwith = new Vector(); - } - if (_alignwith == null) - { - _alignwith = new Vector(); - } - - seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith, - new ItemListener() - { - - @Override - public void itemStateChanged(ItemEvent e) - { - if (!seqColour.isSelected()) - { - seqColour.doClick(); - } - else - { - // update the jmol display now. - seqColour_actionPerformed(null); - } - } - }); - viewMenu.add(seqColourBy); - final ItemListener handler; - JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this, - _alignwith, handler = new ItemListener() - { - - @Override - public void itemStateChanged(ItemEvent e) - { - alignStructs.setEnabled(_alignwith.size() > 0); - alignStructs.setToolTipText(MessageManager - .formatMessage( - "label.align_structures_using_linked_alignment_views", - new String[] - { new Integer(_alignwith.size()).toString() })); - } - }); - handler.itemStateChanged(null); - viewerActionMenu.add(alpanels); - viewerActionMenu.addMenuListener(new MenuListener() - { - - @Override - public void menuSelected(MenuEvent e) - { - handler.itemStateChanged(null); - } - - @Override - public void menuDeselected(MenuEvent e) - { - // TODO Auto-generated method stub - - } - - @Override - public void menuCanceled(MenuEvent e) - { - // TODO Auto-generated method stub + super.initMenus(); - } - }); + viewerColour + .setText(MessageManager.getString("label.colour_with_jmol")); + viewerColour.setToolTipText(MessageManager + .getString("label.let_jmol_manage_structure_colours")); } - IProgressIndicator progressBar = null; - /** - * add a single PDB structure to a new or existing Jmol view + * display a single PDB structure in a new Jmol view * * @param pdbentry * @param seq @@ -290,355 +176,61 @@ public class AppJmol extends GStructureViewer implements Runnable, 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()); + setProgressIndicator(ap.alignFrame); - if (alreadyMapped != null) - { - int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.pdb_entry_is_already_displayed", new String[] - { pdbentry.getId() }), MessageManager.formatMessage( - "label.map_sequences_to_visible_window", new String[] - { pdbentry.getId() }), - JOptionPane.YES_NO_CANCEL_OPTION); - - if (option == JOptionPane.CANCEL_OPTION) - { - return; - } - 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, - MessageManager.formatMessage( - "label.add_pdbentry_to_view", new String[] - { pdbentry.getId(), topJmol.getTitle() }), - MessageManager - .getString("label.align_to_existing_structure_view"), - JOptionPane.YES_NO_CANCEL_OPTION); - if (option == JOptionPane.CANCEL_OPTION) - { - return; - } - 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 }); + openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry }, + new SequenceI[][] + { seq }); } - private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, - SequenceI[][] seqs) + private void openNewJmol(AlignmentPanel ap, boolean alignAdded, + PDBEntry[] pdbentrys, SequenceI[][] seqs) { - progressBar = ap.alignFrame; + setProgressIndicator(ap.alignFrame); jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), - pdbentrys, seqs, null, null); + pdbentrys, seqs, null); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); + + alignAddedStructures = alignAdded; 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; - { - addingStructures = false; - worker = new Thread(this); - worker.start(); - } + addingStructures = false; + worker = new Thread(this, "OpenJmol"); + worker.start(); + this.addInternalFrameListener(new InternalFrameAdapter() { - public void internalFrameClosing(InternalFrameEvent internalFrameEvent) + @Override + public void internalFrameClosing( + InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); } /** - * create a new Jmol containing several structures superimposed using the - * given alignPanel. + * create a new Jmol containing several structures optionally superimposed + * using the given alignPanel. * * @param ap + * @param alignAdded + * - true to superimpose * @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 _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 _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) - { - 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); - viewerColour.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 apanel) + public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe, + SequenceI[][] seqs) { - Vector result = new Vector(); - JInternalFrame[] frames = Desktop.instance.getAllFrames(); - - for (JInternalFrame frame : frames) - { - if (frame instanceof AppJmol) - { - if (((AppJmol) frame).isLinkedWith(apanel)) - { - result.addElement(frame); - } - } - } - return result; + openNewJmol(ap, alignAdded, pe, seqs); } void initJmol(String command) @@ -658,529 +250,213 @@ public class AppJmol extends GStructureViewer implements Runnable, scriptWindow = new JPanel(bl); scriptWindow.setVisible(false); } - ; + jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, null); - jmb.newJmolPopup(true, "Jmol", true); + // jmb.newJmolPopup("Jmol"); if (command == null) { command = ""; } - jmb.evalStateCommand(command); + jmb.executeCommand(new StructureCommand(command), false); + jmb.executeCommand(new StructureCommand("set hoverDelay=0.1"), false); jmb.setFinishedInit(true); } - void setChainMenuItems(Vector chains) + @Override + public void run() { - chainMenu.removeAll(); - if (chains == null) - { - return; - } - JMenuItem menuItem = new JMenuItem( - MessageManager.getString("label.all")); - menuItem.addActionListener(new ActionListener() + _started = true; + try { - public void actionPerformed(ActionEvent evt) + List files = jmb.fetchPdbFiles(this); + if (files.size() > 0) { - 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; + showFilesInViewer(files); } - }); - - chainMenu.add(menuItem); - - for (int c = 0; c < chains.size(); c++) + } finally { - menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true); - menuItem.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent evt) - { - if (!allChainsSelected) - { - centerViewer(); - } - } - }); - - chainMenu.add(menuItem); + _started = false; + worker = null; } } - 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); - } - - public 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 + * Either adds the given files to a structure viewer or opens a new viewer to + * show them + * + * @param files + * list of absolute paths to structure files */ - private boolean _started = false; - - public void run() + void showFilesInViewer(List files) { - _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(MessageManager.formatMessage("status.fetching_pdb", new String[]{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(MessageManager.getString("label.state_completed"), hdl); - } - if (pdbseq != null) - { - // just transfer the file name from the first sequence's first - // PDBEntry - file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId() - .elementAt(0)).getFile()).getAbsolutePath(); - jmb.pdbentry[pi].setFile(file); - - files.append(" \"" + Platform.escapeString(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(" \"" + Platform.escapeString(file) + "\""); - } - } - } - } catch (OutOfMemoryError oomerror) - { - new OOMWarning("Retrieving PDB files: " + pdbid, oomerror); - } catch (Exception ex) + long lastnotify = jmb.getLoadNotifiesHandled(); + StringBuilder fileList = new StringBuilder(); + for (String s : files) { - ex.printStackTrace(); - errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid - + "'"); + fileList.append(SPACE).append(QUOTE) + .append(Platform.escapeBackslashes(s)).append(QUOTE); } - if (errormsgs.length() > 0) - { + String filesString = fileList.toString(); - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager - .formatMessage("label.pdb_entries_couldnt_be_retrieved", - new String[] - { errormsgs.toString() }), MessageManager - .getString("label.couldnt_load_file"), - JOptionPane.ERROR_MESSAGE); - - } - long lastnotify = jmb.getLoadNotifiesHandled(); - if (files.length() > 0) + if (!addingStructures) { - if (!addingStructures) + try { - - 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 + initJmol("load FILES " + filesString); + } catch (OutOfMemoryError oomerror) { - 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); - } + new OOMWarning("When trying to open the Jmol viewer!", oomerror); + Console.debug("File locations are " + filesString); + } catch (Exception ex) + { + Console.error("Couldn't open Jmol viewer!", ex); + ex.printStackTrace(); + return; } + } + else + { + StringBuilder cmd = new StringBuilder(); + cmd.append("loadingJalviewdata=true\nload APPEND "); + cmd.append(filesString); + cmd.append("\nloadingJalviewdata=null"); + final StructureCommand command = new StructureCommand(cmd.toString()); + lastnotify = jmb.getLoadNotifiesHandled(); - // need to wait around until script has finished - while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled() - : (jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb - .getPdbFile().length != jmb.pdbentry.length)) + try { - 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.executeCommand(command, false); + } catch (OutOfMemoryError oomerror) { - jmb.updateColours(ap); - } - // do superposition if asked to - if (alignAddedStructures) + new OOMWarning("When trying to add structures to the Jmol viewer!", + oomerror); + Console.debug("File locations are " + filesString); + return; + } catch (Exception ex) { - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - alignStructs_withAllAlignPanels(); - // jmb.superposeStructures(ap.av.getAlignment(), -1, null); - } - }); - alignAddedStructures = false; + Console.error("Couldn't add files to Jmol viewer!", ex); + ex.printStackTrace(); + return; } - addingStructures = false; - } - _started = false; - worker = null; - } - - @Override - public void pdbFile_actionPerformed(ActionEvent actionEvent) - { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file")); - chooser.setToolTipText(MessageManager.getString("action.save")); - int value = chooser.showSaveDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) + // need to wait around until script has finished + int waitMax = JMOL_LOAD_TIMEOUT; + int waitFor = 35; + int waitTotal = 0; + while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled() + : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null + && jmb.getStructureFiles().length == files.size())) { try { - // TODO: cope with multiple PDB files in view - BufferedReader in = new BufferedReader(new FileReader( - jmb.getPdbFile()[0])); - File outFile = chooser.getSelectedFile(); + Console.debug("Waiting around for jmb notify."); + waitTotal += waitFor; - PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); - String data; - while ((data = in.readLine()) != null) - { - if (!(data.indexOf("
") > -1 || data.indexOf("
") > -1)) - { - out.println(data); - } - } - out.close(); - } catch (Exception ex) + // Thread.sleep() throws an exception in JS + Thread.sleep(waitFor); + } catch (Exception e) { - ex.printStackTrace(); } - } - } - - @Override - public void viewMapping_actionPerformed(ActionEvent actionEvent) - { - jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); - try - { - for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++) + if (waitTotal > waitMax) { - cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile())); - cap.appendText("\n"); + System.err.println("Timed out waiting for Jmol to load files after " + + waitTotal + "ms"); + // System.err.println("finished: " + jmb.isFinishedInit() + // + "; loaded: " + Arrays.toString(jmb.getPdbFile()) + // + "; files: " + files.toString()); + jmb.getStructureFiles(); + break; } - } catch (OutOfMemoryError e) - { - new OOMWarning( - "composing sequence-structure alignments for display in text box.", - e); - cap.dispose(); - return; } - jalview.gui.Desktop.addInternalFrame(cap, - MessageManager.getString("label.pdb_sequence_mapping"), 550, - 600); - } - - @Override - public void eps_actionPerformed(ActionEvent e) - { - makePDBImage(jalview.util.ImageMaker.TYPE.EPS); - } - - @Override - public void png_actionPerformed(ActionEvent e) - { - makePDBImage(jalview.util.ImageMaker.TYPE.PNG); - } - - void makePDBImage(jalview.util.ImageMaker.TYPE type) - { - int width = getWidth(); - int height = getHeight(); - - jalview.util.ImageMaker im; - if (type == jalview.util.ImageMaker.TYPE.PNG) - { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.PNG, - "Make PNG image from view", width, height, null, null); - } - else if (type == jalview.util.ImageMaker.TYPE.EPS) + // refresh the sequence colours for the new structure(s) + for (AlignmentViewPanel ap : _colourwith) { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.EPS, - "Make EPS file from view", width, height, null, - this.getTitle()); + jmb.updateColours(ap); } - else - { - - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA", - width, height, null, this.getTitle()); - } - - if (im.getGraphics() != null) + // do superposition if asked to + if (alignAddedStructures) { - Rectangle rect = new Rectangle(width, height); - jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect); - im.writeImage(); + alignAddedStructures(); } + addingStructures = false; } - @Override - public void viewerColour_actionPerformed(ActionEvent actionEvent) - { - if (viewerColour.isSelected()) - { - // disable automatic sequence colouring. - jmb.setColourBySequence(false); - } - } - - @Override - public void seqColour_actionPerformed(ActionEvent actionEvent) + /** + * Queues a thread to align structures with Jalview alignments + */ + void alignAddedStructures() { - jmb.setColourBySequence(seqColour.isSelected()); - if (_colourwith == null) - { - _colourwith = new Vector(); - } - if (jmb.isColourBySequence()) + javax.swing.SwingUtilities.invokeLater(new Runnable() { - if (!jmb.isLoadingFromArchive()) + @Override + public void run() { - if (_colourwith.size() == 0 && ap != null) + if (jmb.jmolViewer.isScriptExecuting()) { - // Make the currently displayed alignment panel the associated view - _colourwith.add(ap.alignFrame.alignPanel); + SwingUtilities.invokeLater(this); + try + { + Thread.sleep(5); + } catch (InterruptedException q) + { + } + return; + } + else + { + alignStructsWithAllAlignPanels(); } } - // Set the colour using the current view for the associated alignframe - for (AlignmentPanel ap : _colourwith) - { - jmb.colourBySequence(ap.av.showSequenceFeatures, ap); - } - } - } - - @Override - public void chainColour_actionPerformed(ActionEvent actionEvent) - { - chainColour.setSelected(true); - jmb.colourByChain(); - } - - @Override - public void chargeColour_actionPerformed(ActionEvent actionEvent) - { - chargeColour.setSelected(true); - jmb.colourByCharge(); - } - - @Override - public void zappoColour_actionPerformed(ActionEvent actionEvent) - { - zappoColour.setSelected(true); - jmb.setJalviewColourScheme(new ZappoColourScheme()); - } - - @Override - public void taylorColour_actionPerformed(ActionEvent actionEvent) - { - taylorColour.setSelected(true); - jmb.setJalviewColourScheme(new TaylorColourScheme()); - } - - @Override - public void hydroColour_actionPerformed(ActionEvent actionEvent) - { - hydroColour.setSelected(true); - jmb.setJalviewColourScheme(new HydrophobicColourScheme()); - } - - @Override - public void helixColour_actionPerformed(ActionEvent actionEvent) - { - helixColour.setSelected(true); - jmb.setJalviewColourScheme(new HelixColourScheme()); - } - - @Override - public void strandColour_actionPerformed(ActionEvent actionEvent) - { - strandColour.setSelected(true); - jmb.setJalviewColourScheme(new StrandColourScheme()); - } - - @Override - public void turnColour_actionPerformed(ActionEvent actionEvent) - { - turnColour.setSelected(true); - jmb.setJalviewColourScheme(new TurnColourScheme()); - } - - @Override - public void buriedColour_actionPerformed(ActionEvent actionEvent) - { - buriedColour.setSelected(true); - jmb.setJalviewColourScheme(new BuriedColourScheme()); - } + }); - @Override - public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent) - { - setJalviewColourScheme(new PurinePyrimidineColourScheme()); - } - - @Override - public void userColour_actionPerformed(ActionEvent actionEvent) - { - userColour.setSelected(true); - new UserDefinedColours(this, null); } + /** + * Outputs the Jmol viewer image as an image file, after prompting the user to + * choose a file and (for EPS) choice of Text or Lineart character rendering + * (unless a preference for this is set) + * + * @param type + */ @Override - public void backGround_actionPerformed(ActionEvent actionEvent) + public void makePDBImage(ImageMaker.TYPE type) { - java.awt.Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_backgroud_colour"), null); - if (col != null) + int width = getWidth(); + int height = getHeight(); + ImageWriterI writer = new ImageWriterI() { - jmb.setBackgroundColour(col); - } + @Override + public void exportImage(Graphics g) throws Exception + { + jmb.jmolViewer.renderScreenImage(g, width, height); + } + }; + String view = MessageManager.getString("action.view") + .toLowerCase(Locale.ROOT); + ImageExporter exporter = new ImageExporter(writer, + getProgressIndicator(), type, getTitle()); + exporter.doExport(null, this, width, height, view); } @Override - public void showHelp_actionPerformed(ActionEvent actionEvent) + public void showHelp_actionPerformed() { try { - jalview.util.BrowserLauncher - .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/"); + BrowserLauncher // BH 2018 + .openURL("http://wiki.jmol.org");// http://jmol.sourceforge.net/docs/JmolUserGuide/"); } catch (Exception ex) { + System.err.println("Show Jmol help failed with: " + ex.getMessage()); } } + @Override public void showConsole(boolean showConsole) { - if (showConsole) { if (splitPane == null) @@ -1215,14 +491,12 @@ public class AppJmol extends GStructureViewer implements Runnable, { final Dimension currentSize = new Dimension(); - final Rectangle rectClip = new Rectangle(); - + @Override public void paintComponent(Graphics g) { getSize(currentSize); - g.getClipBounds(rectClip); - if (jmb.fileLoadingError != null) + if (jmb != null && jmb.hasFileLoadingError()) { g.setColor(Color.black); g.fillRect(0, 0, currentSize.width, currentSize.height); @@ -1232,23 +506,24 @@ public class AppJmol extends GStructureViewer implements Runnable, + "...", 20, currentSize.height / 2); StringBuffer sb = new StringBuffer(); int lines = 0; - for (int e = 0; e < jmb.pdbentry.length; e++) + for (int e = 0; e < jmb.getPdbCount(); e++) { - sb.append(jmb.pdbentry[e].getId()); - if (e < jmb.pdbentry.length - 1) + sb.append(jmb.getPdbEntry(e).getId()); + if (e < jmb.getPdbCount() - 1) { sb.append(","); } - if (e == jmb.pdbentry.length - 1 || sb.length() > 20) + if (e == jmb.getPdbCount() - 1 || sb.length() > 20) { lines++; - g.drawString(sb.toString(), 20, currentSize.height / 2 - lines - * g.getFontMetrics().getHeight()); + g.drawString(sb.toString(), 20, currentSize.height / 2 + - lines * g.getFontMetrics().getHeight()); } } } - else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit()) + else if (jmb == null || jmb.jmolViewer == null + || !jmb.isFinishedInit()) { g.setColor(Color.black); g.fillRect(0, 0, currentSize.width, currentSize.height); @@ -1259,173 +534,27 @@ public class AppJmol extends GStructureViewer implements Runnable, } 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) - { - viewerActionMenu.setVisible(true); - } - if (!jmb.isLoadingFromArchive()) - { - seqColour_actionPerformed(null); - } - } - - protected void buildJmolActionMenu() - { - if (_alignwith == null) - { - _alignwith = new Vector(); - } - if (_alignwith.size() == 0 && ap != null) - { - _alignwith.add(ap); - } - ; - for (Component c : viewerActionMenu.getMenuComponents()) - { - if (c != alignStructs) - { - viewerActionMenu.remove((JMenuItem) c); + jmb.jmolViewer.renderScreenImage(g, currentSize.width, + currentSize.height); } } - final ItemListener handler; } - /* - * (non-Javadoc) - * - * @see - * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event - * .ActionEvent) - */ @Override - protected void alignStructs_actionPerformed(ActionEvent actionEvent) + public AAStructureBindingModel getBinding() { - 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); - - } - + return this.jmb; } - 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() + @Override + public ViewerType getViewerType() { - return !jmb.isColourBySequence(); + return ViewerType.JMOL; } - public JalviewJmolBinding getBinding() + @Override + protected String getViewerName() { - return jmb; + return "Jmol"; } - }