X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=0e5675cbcdf985c29673216af4c7fb757bb230f5;hb=7720585dc8cc56cdad2486b330ed37ddd0133531;hp=3c53762ca21d7c0a0af0196a8f57a339e1f88ca4;hpb=f11efa71475b7bf825090716543a36b012db224a;p=jalview.git diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index 3c53762..0e5675c 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.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. * @@ -20,654 +20,354 @@ */ package jalview.gui; -import jalview.api.SequenceStructureBinding; -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.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 jalview.ws.dbsources.Pdb; - -import java.awt.Component; 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.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; import java.io.File; -import java.io.FileOutputStream; -import java.io.FileReader; -import java.io.IOException; -import java.io.PrintWriter; import java.util.ArrayList; +import java.util.Collections; import java.util.List; -import java.util.Vector; +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.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; -import javax.swing.event.MenuEvent; -import javax.swing.event.MenuListener; + +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureRenderer; +import jalview.bin.Cache; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.datamodel.StructureViewerModel; +import jalview.datamodel.StructureViewerModel.StructureData; +import jalview.ext.rbvi.chimera.JalviewChimeraBinding; +import jalview.gui.StructureViewer.ViewerType; +import jalview.io.DataSourceType; +import jalview.io.StructureFile; +import jalview.structures.models.AAStructureBindingModel; +import jalview.util.ImageMaker.TYPE; +import jalview.util.MessageManager; +import jalview.util.Platform; /** - * GUI elements for handlnig an external chimera display + * GUI elements for handling an external chimera display * * @author jprocter * */ -public class ChimeraViewFrame extends GStructureViewer implements Runnable, - ViewSetProvider, JalviewStructureDisplayI - +public class ChimeraViewFrame extends StructureViewerBase { - private JalviewChimeraBindingModel jmb; + private JalviewChimeraBinding jmb; /* - * list of sequenceSet ids associated with the view + * Path to Chimera session file. This is set when an open Jalview/Chimera + * session is saved, or on restore from a Jalview project (if it holds the + * filename of any saved Chimera sessions). */ - private ArrayList _aps = new ArrayList(); + private String chimeraSessionFile = null; - /* - * list of alignment panels to use for superposition - */ - private Vector _alignwith = new Vector(); + private int myWidth = 500; - /* - * list of alignment panels that are used for colouring structures by aligned - * sequences - */ - private Vector _colourwith = new Vector(); - - private boolean allChainsSelected = false; - - private boolean alignAddedStructures = false; - - AlignmentPanel ap; - - /* - * state flag for PDB retrieval thread - */ - private boolean _started = false; - - private boolean addingStructures = false; - - private IProgressIndicator progressBar = null; - - private String viewId = null; - - /* - * pdb retrieval thread. - */ - private Thread worker = null; + private int myHeight = 150; /** * Initialise menu options. */ - private void initMenus() + @Override + protected void initMenus() { - viewerActionMenu.setText(MessageManager.getString("label.chimera")); - viewerColour.setText(MessageManager - .getString("label.colour_with_chimera")); - viewerColour.setToolTipText(MessageManager - .getString("label.let_chimera_manage_structure_colours")); - helpItem.setText(MessageManager.getString("label.chimera_help")); - seqColour.setSelected(jmb.isColourBySequence()); - viewerColour.setSelected(!jmb.isColourBySequence()); - if (_colourwith == null) - { - _colourwith = new Vector(); - } - if (_alignwith == null) - { - _alignwith = new Vector(); - } + super.initMenus(); - ViewSelectionMenu 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 Chimera 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 Object[] - { new Integer(_alignwith.size()).toString() })); - } - }); - handler.itemStateChanged(null); - viewerActionMenu.add(alpanels); - viewerActionMenu.addMenuListener(new MenuListener() - { + savemenu.setVisible(false); // not yet implemented + viewMenu.add(fitToWindow); + JMenuItem writeFeatures = new JMenuItem( + MessageManager.getString("label.create_viewer_attributes")); + writeFeatures.setToolTipText(MessageManager + .getString("label.create_viewer_attributes_tip")); + writeFeatures.addActionListener(new ActionListener() + { @Override - public void menuSelected(MenuEvent e) + public void actionPerformed(ActionEvent e) { - handler.itemStateChanged(null); + sendFeaturesToChimera(); } + }); + viewerActionMenu.add(writeFeatures); - @Override - public void menuDeselected(MenuEvent e) - { - // TODO Auto-generated method stub - } + final JMenu fetchAttributes = new JMenu( + MessageManager.getString("label.fetch_chimera_attributes")); + fetchAttributes.setToolTipText( + MessageManager.getString("label.fetch_chimera_attributes_tip")); + fetchAttributes.addMouseListener(new MouseAdapter() + { @Override - public void menuCanceled(MenuEvent e) + public void mouseEntered(MouseEvent e) { - // TODO Auto-generated method stub + buildAttributesMenu(fetchAttributes); } }); + viewerActionMenu.add(fetchAttributes); } /** - * add a single PDB structure to a new or existing Chimera view + * Query Chimera for its residue attribute names and add them as items off the + * attributes menu * - * @param pdbentry - * @param seq - * @param chains - * @param ap + * @param attributesMenu */ - public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq, - String[] chains, final AlignmentPanel ap) + protected void buildAttributesMenu(JMenu attributesMenu) { - super(); - progressBar = ap.alignFrame; - // //////////////////////////////// - // Is the pdb file already loaded? - String alreadyMapped = ap.getStructureSelectionManager() - .alreadyMappedToFile(pdbentry.getId()); - - if (alreadyMapped != null) + List atts = jmb.getChimeraAttributes(); + attributesMenu.removeAll(); + Collections.sort(atts); + for (String attName : atts) { - int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.pdb_entry_is_already_displayed", new Object[] - { pdbentry.getId() }), MessageManager.formatMessage( - "label.map_sequences_to_visible_window", new Object[] - { pdbentry.getId() }), - JOptionPane.YES_NO_CANCEL_OPTION); - - if (option == JOptionPane.CANCEL_OPTION) - { - return; - } - if (option == JOptionPane.YES_OPTION) + JMenuItem menuItem = new JMenuItem(attName); + menuItem.addActionListener(new ActionListener() { - // TODO : Fix multiple seq to one chain issue here. - ap.getStructureSelectionManager().setMapping(seq, chains, - alreadyMapped, AppletFormatAdapter.FILE); - if (ap.seqPanel.seqCanvas.fr != null) + @Override + public void actionPerformed(ActionEvent e) { - ap.seqPanel.seqCanvas.fr.featuresAdded(); - ap.paintAlignment(true); + getChimeraAttributes(attName); } - - // Now this ChimeraViewFrame is mapped to new sequences. We must add - // them to the existing array - JInternalFrame[] frames = Desktop.instance.getAllFrames(); - - for (JInternalFrame frame : frames) - { - if (frame instanceof ChimeraViewFrame) - { - final ChimeraViewFrame topView = ((ChimeraViewFrame) frame); - // JBPNOTE: this looks like a binding routine, rather than a gui - // routine - for (int pe = 0; pe < topView.jmb.pdbentry.length; pe++) - { - if (topView.jmb.pdbentry[pe].getFile().equals(alreadyMapped)) - { - topView.jmb.addSequence(pe, seq); - topView.addAlignmentPanel(ap); - // add it to the set used for colouring - topView.useAlignmentPanelForColourbyseq(ap); - topView.buildChimeraActionMenu(); - ap.getStructureSelectionManager() - .sequenceColoursChanged(ap); - break; - } - } - } - } - - return; - } - } - // ///////////////////////////////// - // Check if there are other Chimera views involving this alignment - // and prompt user about adding this molecule to one of them - List existingViews = getChimeraWindowsFor(ap); - for (ChimeraViewFrame topView : existingViews) - { - // TODO: highlight topView in view somehow - int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - MessageManager.formatMessage("label.add_pdbentry_to_view", - new Object[] - { pdbentry.getId(), topView.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) - { - topView.useAlignmentPanelForSuperposition(ap); - topView.addStructure(pdbentry, seq, chains, true, ap.alignFrame); - return; - } - } - // ///////////////////////////////// - openNewChimera(ap, new PDBEntry[] - { pdbentry }, new SequenceI[][] - { seq }); - } - - private void openNewChimera(AlignmentPanel ap, PDBEntry[] pdbentrys, - SequenceI[][] seqs) - { - progressBar = ap.alignFrame; - jmb = new JalviewChimeraBindingModel(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; - { - addingStructures = false; - worker = new Thread(this); - worker.start(); + }); + attributesMenu.add(menuItem); } - this.addInternalFrameListener(new InternalFrameAdapter() - { - public void internalFrameClosing(InternalFrameEvent internalFrameEvent) - { - closeViewer(); - } - }); - } /** - * create a new viewer containing several structures superimposed using the - * given alignPanel. + * Read residues in Chimera with the given attribute name, and set as features + * on the corresponding sequence positions (if any) * - * @param ap - * @param pe - * @param seqs + * @param attName */ - public ChimeraViewFrame(AlignmentPanel ap, PDBEntry[] pe, - SequenceI[][] seqs) + protected void getChimeraAttributes(String attName) { - super(); - openNewChimera(ap, pe, seqs); + jmb.copyStructureAttributesToFeatures(attName, getAlignmentPanel()); } - public AlignmentPanel[] getAllAlignmentPanels() + /** + * Sends command(s) to the structure viewer to create residue attributes for + * visible Jalview features + */ + protected void sendFeaturesToChimera() { - 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; + // todo pull up? + int count = jmb.sendFeaturesToViewer(getAlignmentPanel()); + statusBar.setText( + MessageManager.formatMessage("label.attributes_set", count)); } /** - * set the primary alignmentPanel reference and add another alignPanel to the - * list of ones to use for colouring and aligning + * open a single PDB structure in a new Chimera view * - * @param nap + * @param pdbentry + * @param seq + * @param chains + * @param ap */ - public void addAlignmentPanel(AlignmentPanel nap) + public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq, + String[] chains, final AlignmentPanel ap) { - if (ap == null) - { - ap = nap; - } - if (!_aps.contains(nap.av.getSequenceSetId())) - { - _aps.add(nap.av.getSequenceSetId()); - } + this(); + + openNewChimera(ap, new PDBEntry[] { pdbentry }, + new SequenceI[][] + { seq }); } /** - * remove any references held to the given alignment panel - * - * @param nap + * Create a helper to manage progress bar display */ - public void removeAlignmentPanel(AlignmentPanel nap) + protected void createProgressBar() { - try + if (getProgressIndicator() == null) { - _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) - { - buildChimeraActionMenu(); + setProgressIndicator(new ProgressBar(statusPanel, statusBar)); } } - public void useAlignmentPanelForSuperposition(AlignmentPanel nap) + private void openNewChimera(AlignmentPanel ap, PDBEntry[] pdbentrys, + SequenceI[][] seqs) { - addAlignmentPanel(nap); - if (!_alignwith.contains(nap)) + createProgressBar(); + jmb = newBindingModel(ap, pdbentrys, seqs); + addAlignmentPanel(ap); + useAlignmentPanelForColourbyseq(ap); + + if (pdbentrys.length > 1) { - _alignwith.add(nap); + useAlignmentPanelForSuperposition(ap); } - } + jmb.setColourBySequence(true); + setSize(myWidth, myHeight); + initMenus(); - public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap) - { - if (_alignwith.contains(nap)) + addingStructures = false; + worker = new Thread(this); + worker.start(); + + this.addInternalFrameListener(new InternalFrameAdapter() { - _alignwith.remove(nap); - } + @Override + public void internalFrameClosing( + InternalFrameEvent internalFrameEvent) + { + closeViewer(false); + } + }); + } - public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, - boolean enableColourBySeq) + protected JalviewChimeraBindingModel newBindingModel(AlignmentPanel ap, + PDBEntry[] pdbentrys, SequenceI[][] seqs) { - useAlignmentPanelForColourbyseq(nap); - jmb.setColourBySequence(enableColourBySeq); - seqColour.setSelected(enableColourBySeq); - viewerColour.setSelected(!enableColourBySeq); + return new JalviewChimeraBindingModel(this, + ap.getStructureSelectionManager(), pdbentrys, seqs, null); } - public void useAlignmentPanelForColourbyseq(AlignmentPanel nap) - { - addAlignmentPanel(nap); - if (!_colourwith.contains(nap)) + /** + * Create a new viewer from saved session state data including Chimera session + * file + * + * @param chimeraSessionFile + * @param alignPanel + * @param pdbArray + * @param seqsArray + * @param colourByChimera + * @param colourBySequence + * @param newViewId + */ + public ChimeraViewFrame(StructureViewerModel viewerData, + AlignmentPanel alignPanel, String sessionFile, String vid) + { + this(); + setViewId(vid); + this.chimeraSessionFile = sessionFile; + Map pdbData = viewerData.getFileData(); + PDBEntry[] pdbArray = new PDBEntry[pdbData.size()]; + SequenceI[][] seqsArray = new SequenceI[pdbData.size()][]; + int i = 0; + for (StructureData data : pdbData.values()) + { + PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null, + PDBEntry.Type.PDB, data.getFilePath()); + pdbArray[i] = pdbentry; + List sequencesForPdb = data.getSeqList(); + seqsArray[i] = sequencesForPdb + .toArray(new SequenceI[sequencesForPdb.size()]); + i++; + } + openNewChimera(alignPanel, pdbArray, seqsArray); + if (viewerData.isColourByViewer()) { - _colourwith.add(nap); + jmb.setColourBySequence(false); + seqColour.setSelected(false); + viewerColour.setSelected(true); } - } - - public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap) - { - if (_colourwith.contains(nap)) + else if (viewerData.isColourWithAlignPanel()) { - _colourwith.remove(nap); + jmb.setColourBySequence(true); + seqColour.setSelected(true); + viewerColour.setSelected(false); } } /** - * add a new structure (with associated sequences and chains) to this viewer, - * retrieving it if necessary first. + * create a new viewer containing several structures, optionally superimposed + * using the given alignPanel. * - * @param pdbentry - * @param seq - * @param chains - * @param alignFrame - * @param align - * if true, new structure(s) will be align using associated alignment + * @param pe + * @param seqs + * @param ap */ - private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq, - final String[] chains, final boolean b, - final IProgressIndicator alignFrame) + public ChimeraViewFrame(PDBEntry[] pe, boolean alignAdded, + SequenceI[][] seqs, + AlignmentPanel ap) { - 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; + this(); + setAlignAddedStructures(alignAdded); + openNewChimera(ap, pe, seqs); } - private List getChimeraWindowsFor(AlignmentPanel apanel) + /** + * Default constructor + */ + public ChimeraViewFrame() { - List result = new ArrayList(); - JInternalFrame[] frames = Desktop.instance.getAllFrames(); + super(); - for (JInternalFrame frame : frames) - { - if (frame instanceof ChimeraViewFrame) - { - if (((ChimeraViewFrame) frame).isLinkedWith(apanel)) - { - result.add((ChimeraViewFrame) frame); - } - } - } - return result; + /* + * closeViewer will decide whether or not to close this frame + * depending on whether user chooses to Cancel or not + */ + setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE); } - void initChimera(String command) + /** + * Launch Chimera. If we have a chimera session file name, send Chimera the + * command to open its saved session file. + */ + void initChimera() { jmb.setFinishedInit(false); - // TODO: consider waiting until the structure/view is fully loaded before - // displaying - jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(true), - getBounds().width, getBounds().height); - if (command == null) - { - command = ""; - } - jmb.evalStateCommand(command, false); - jmb.setFinishedInit(true); - } - - void setChainMenuItems(List chainNames) - { - chainMenu.removeAll(); - if (chainNames == null) - { + Desktop.addInternalFrame(this, + jmb.getViewerTitle(getViewerName(), true), getBounds().width, + getBounds().height); + + if (!jmb.launchChimera()) + { + JvOptionPane.showMessageDialog(Desktop.desktop, + MessageManager.formatMessage("label.open_viewer_failed", + getViewerName()), + MessageManager.getString("label.error_loading_file"), + JvOptionPane.ERROR_MESSAGE); + this.dispose(); return; } - JMenuItem menuItem = new JMenuItem( - MessageManager.getString("label.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 (String chainName : chainNames) - { - menuItem = new JCheckBoxMenuItem(chainName, true); - menuItem.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent evt) - { - if (!allChainsSelected) - { - centerViewer(); - } - } - }); - - chainMenu.add(menuItem); - } - } - void centerViewer() - { - List toshow = new ArrayList(); - for (int i = 0; i < chainMenu.getItemCount(); i++) + if (this.chimeraSessionFile != null) { - if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) + boolean opened = jmb.openSession(chimeraSessionFile); + if (!opened) { - JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i); - if (item.isSelected()) - { - toshow.add(item.getText()); - } + System.err.println("An error occurred opening Chimera session file " + + chimeraSessionFile); } } - jmb.centerViewer(toshow); - } - /** - * Close down this instance of Jalview's Chimera viewer, giving the user the - * option to close the associated Chimera window (process). They may wish to - * keep it open until they have had an opportunity to save any work. - */ - public void closeViewer() - { - if (jmb.isChimeraRunning()) - { - String prompt = MessageManager - .formatMessage("label.confirm_close_chimera", new Object[] - { jmb.getViewerTitle(false) }); - prompt = JvSwingUtils.wrapTooltip(true, prompt); - int confirm = JOptionPane.showConfirmDialog(this, prompt, - MessageManager.getString("label.close_viewer"), - JOptionPane.YES_NO_OPTION); - jmb.closeViewer(confirm == JOptionPane.YES_OPTION); - } - 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; + jmb.startChimeraListener(); } /** * Open any newly added PDB structures in Chimera, having first fetched data * from PDB (if not already saved). */ + @Override public void run() { _started = true; // todo - record which pdbids were successfully imported. StringBuilder errormsgs = new StringBuilder(128); StringBuilder files = new StringBuilder(128); - List filePDB = new ArrayList(); - List filePDBpos = new ArrayList(); + List filePDB = new ArrayList<>(); + List filePDBpos = new ArrayList<>(); PDBEntry thePdbEntry = null; + StructureFile pdb = null; try { - String[] curfiles = jmb.getPdbFile(); // files currently in viewer + String[] curfiles = jmb.getStructureFiles(); // files currently in viewer // TODO: replace with reference fetching/transfer code (validate PDBentry // as a DBRef?) - for (int pi = 0; pi < jmb.pdbentry.length; pi++) + for (int pi = 0; pi < jmb.getPdbCount(); pi++) { String file = null; - thePdbEntry = jmb.pdbentry[pi]; + thePdbEntry = jmb.getPdbEntry(pi); if (thePdbEntry.getFile() == null) { /* @@ -703,7 +403,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, { filePDB.add(thePdbEntry); filePDBpos.add(Integer.valueOf(pi)); - files.append(" \"" + Platform.escapeString(file) + "\""); + files.append(" \"" + Platform.escapeBackslashes(file) + "\""); } } } catch (OutOfMemoryError oomerror) @@ -713,27 +413,28 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, } catch (Exception ex) { ex.printStackTrace(); - errormsgs.append("When retrieving pdbfiles for '" - + thePdbEntry.getId() + "'"); + errormsgs.append( + "When retrieving pdbfiles for '" + thePdbEntry.getId() + "'"); } if (errormsgs.length() > 0) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager - .formatMessage("label.pdb_entries_couldnt_be_retrieved", - new Object[] - { errormsgs.toString() }), MessageManager - .getString("label.couldnt_load_file"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.formatMessage( + "label.pdb_entries_couldnt_be_retrieved", new Object[] + { errormsgs.toString() }), + MessageManager.getString("label.couldnt_load_file"), + JvOptionPane.ERROR_MESSAGE); } if (files.length() > 0) { + jmb.setFinishedInit(false); if (!addingStructures) { try { - initChimera(""); + initChimera(); } catch (Exception ex) { Cache.log.error("Couldn't open Chimera viewer!", ex); @@ -748,23 +449,32 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, try { int pos = filePDBpos.get(num).intValue(); + long startTime = startProgressBar(getViewerName() + " " + + MessageManager.getString("status.opening_file_for") + + " " + pe.getId()); jmb.openFile(pe); - jmb.addSequence(pos, jmb.sequence[pos]); + jmb.addSequence(pos, jmb.getSequence()[pos]); File fl = new File(pe.getFile()); - String protocol = AppletFormatAdapter.URL; + DataSourceType protocol = DataSourceType.URL; try { if (fl.exists()) { - protocol = AppletFormatAdapter.FILE; + protocol = DataSourceType.FILE; } } catch (Throwable e) { + } finally + { + stopProgressBar("", startTime); } // Explicitly map to the filename used by Chimera ; - // TODO: use pe.getId() instead of pe.getFile() ? - jmb.ssm.setMapping(jmb.sequence[pos], null, pe.getFile(), - protocol); + + pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos], + jmb.getChains()[pos], pe.getFile(), protocol, + getProgressIndicator()); + jmb.stashFoundChains(pdb, pe.getFile()); + } catch (OutOfMemoryError oomerror) { new OOMWarning( @@ -772,19 +482,32 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, oomerror); } catch (Exception ex) { - Cache.log.error("Couldn't open " + pe.getFile() - + " in Chimera viewer!", ex); + Cache.log.error( + "Couldn't open " + pe.getFile() + " in Chimera viewer!", + ex); } finally { Cache.log.debug("File locations are " + files); } } } + + jmb.refreshGUI(); jmb.setFinishedInit(true); jmb.setLoadingFromArchive(false); + /* + * ensure that any newly discovered features (e.g. RESNUM) + * are added to any open feature settings dialog + */ + FeatureRenderer fr = getBinding().getFeatureRenderer(null); + if (fr != null) + { + fr.featuresAdded(); + } + // refresh the sequence colours for the new structure(s) - for (AlignmentPanel ap : _colourwith) + for (AlignmentViewPanel ap : _colourwith) { jmb.updateColours(ap); } @@ -793,12 +516,12 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, { new Thread(new Runnable() { + @Override public void run() { - alignStructs_withAllAlignPanels(); + alignStructsWithAllAlignPanels(); } }).start(); - alignAddedStructures = false; } addingStructures = false; } @@ -806,440 +529,34 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, worker = null; } - /** - * Fetch PDB data and save to a local file. Returns the full path to the file, - * or null if fetch fails. - * - * @param processingEntry - * @return - * @throws Exception - */ - private String fetchPdbFile(PDBEntry processingEntry) throws Exception - { - String filePath = null; - Pdb pdbclient = new Pdb(); - AlignmentI pdbseq = null; - String pdbid = processingEntry.getId(); - long hdl = pdbid.hashCode() - System.currentTimeMillis(); - if (progressBar != null) - { - progressBar.setProgressBar(MessageManager.formatMessage( - "status.fetching_pdb", new Object[] - { pdbid }), hdl); - } - try - { - pdbseq = pdbclient.getSequenceRecords(pdbid); - } catch (OutOfMemoryError oomerror) - { - new OOMWarning("Retrieving PDB id " + pdbid, oomerror); - } finally - { - if (progressBar != null) - { - progressBar.setProgressBar( - MessageManager.getString("label.state_completed"), hdl); - } - } - /* - * If PDB data were saved and are not invalid (empty alignment), return the - * file path. - */ - if (pdbseq != null && pdbseq.getHeight() > 0) - { - // just use the file name from the first sequence's first PDBEntry - filePath = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId() - .elementAt(0)).getFile()).getAbsolutePath(); - processingEntry.setFile(filePath); - } - return filePath; - } - - @Override - public void pdbFile_actionPerformed(ActionEvent actionEvent) - { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file")); - chooser.setToolTipText(MessageManager.getString("action.save")); - - int value = chooser.showSaveDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - BufferedReader in = null; - try - { - // TODO: cope with multiple PDB files in view - in = new BufferedReader(new FileReader(jmb.getPdbFile()[0])); - File outFile = chooser.getSelectedFile(); - - PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); - String data; - while ((data = in.readLine()) != null) - { - if (!(data.indexOf("
") > -1 || data.indexOf("
") > -1)) - { - out.println(data); - } - } - out.close(); - } catch (Exception ex) - { - ex.printStackTrace(); - } finally - { - if (in != null) - { - try - { - in.close(); - } catch (IOException e) - { - e.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++) - { - 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, - MessageManager.getString("label.pdb_sequence_mapping"), 550, - 600); - } - - @Override - public void eps_actionPerformed(ActionEvent e) - { - throw new Error( - MessageManager - .getString("error.eps_generation_not_implemented")); - } - - @Override - public void png_actionPerformed(ActionEvent e) - { - throw new Error( - MessageManager - .getString("error.png_generation_not_implemented")); - } - - @Override - public void viewerColour_actionPerformed(ActionEvent actionEvent) - { - if (viewerColour.isSelected()) - { - // disable automatic sequence colouring. - jmb.setColourBySequence(false); - } - } - - @Override - public void seqColour_actionPerformed(ActionEvent actionEvent) - { - jmb.setColourBySequence(seqColour.isSelected()); - if (_colourwith == null) - { - _colourwith = new Vector(); - } - if (jmb.isColourBySequence()) - { - if (!jmb.isLoadingFromArchive()) - { - if (_colourwith.size() == 0 && 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); - } - } - } - - @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) + public void makePDBImage(TYPE imageType) { - hydroColour.setSelected(true); - jmb.setJalviewColourScheme(new HydrophobicColourScheme()); + throw new UnsupportedOperationException( + "Image export for Chimera is not implemented"); } @Override - public void helixColour_actionPerformed(ActionEvent actionEvent) + public AAStructureBindingModel getBinding() { - 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); + return jmb; } @Override - public void backGround_actionPerformed(ActionEvent actionEvent) + protected void fitToWindow_actionPerformed() { - java.awt.Color col = JColorChooser - .showDialog(this, MessageManager - .getString("label.select_backgroud_colour"), null); - if (col != null) - { - jmb.setBackgroundColour(col); - } + jmb.focusView(); } @Override - public void showHelp_actionPerformed(ActionEvent actionEvent) - { - try - { - jalview.util.BrowserLauncher - .openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide"); - } catch (Exception ex) - { - } - } - - public String getViewId() - { - if (viewId == null) - { - viewId = System.currentTimeMillis() + "." + this.hashCode(); - } - return viewId; - } - - public void updateTitleAndMenus() + public ViewerType getViewerType() { - if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) - { - repaint(); - return; - } - setChainMenuItems(jmb.chainNames); - - this.setTitle(jmb.getViewerTitle(true)); - if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1) - { - viewerActionMenu.setVisible(true); - } - if (!jmb.isLoadingFromArchive()) - { - seqColour_actionPerformed(null); - } + return ViewerType.CHIMERA; } - protected void buildChimeraActionMenu() - { - 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); - } - } - } - - /* - * (non-Javadoc) - * - * @see - * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event - * .ActionEvent) - */ @Override - protected void alignStructs_actionPerformed(ActionEvent actionEvent) + protected String getViewerName() { - alignStructs_withAllAlignPanels(); + return "Chimera"; } - - 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 Chimera 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 isColouredByChimera() - { - return !jmb.isColourBySequence(); - } - - public SequenceStructureBinding getBinding() - { - return jmb; - } - }