X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=3a17ea35bfeaa69b3551be289b53ce99988d936a;hb=b7cd96eaeb85474ee2ddec1de92181a3b88ceece;hp=ba360af3117fc953555dc98f06d739adc08e63ad;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index ba360af..3a17ea3 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -20,42 +20,38 @@ */ package jalview.gui; -import jalview.api.FeatureRenderer; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.ext.rbvi.chimera.ChimeraCommands; -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.BrowserLauncher; -import jalview.util.MessageManager; -import jalview.util.Platform; -import jalview.ws.dbsources.Pdb; - import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.io.File; -import java.io.FileInputStream; -import java.io.IOException; -import java.io.InputStream; import java.util.ArrayList; import java.util.Collections; import java.util.List; -import java.util.Random; +import java.util.Map; -import javax.swing.JCheckBoxMenuItem; import javax.swing.JInternalFrame; import javax.swing.JMenu; import javax.swing.JMenuItem; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureRenderer; +import jalview.bin.Console; +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 handling an external chimera display * @@ -66,8 +62,6 @@ public class ChimeraViewFrame extends StructureViewerBase { private JalviewChimeraBinding jmb; - private IProgressIndicator progressBar = null; - /* * 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 @@ -75,13 +69,14 @@ public class ChimeraViewFrame extends StructureViewerBase */ private String chimeraSessionFile = null; - private Random random = new Random(); - private int myWidth = 500; private int myHeight = 150; - /** + private JMenuItem writeFeatures=null; + + private JMenu fetchAttributes=null; +/** * Initialise menu options. */ @Override @@ -89,120 +84,91 @@ public class ChimeraViewFrame extends StructureViewerBase { super.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")); savemenu.setVisible(false); // not yet implemented viewMenu.add(fitToWindow); - /* - * exchange of Jalview features and Chimera attributes is for now - * an optionally enabled experimental feature - */ - if (Desktop.instance.showExperimental()) + writeFeatures = new JMenuItem( + MessageManager.getString("label.create_viewer_attributes")); + writeFeatures.setToolTipText(MessageManager + .getString("label.create_viewer_attributes_tip")); + writeFeatures.addActionListener(new ActionListener() { - JMenuItem writeFeatures = new JMenuItem( - MessageManager.getString("label.create_chimera_attributes")); - writeFeatures.setToolTipText(MessageManager - .getString("label.create_chimera_attributes_tip")); - writeFeatures.addActionListener(new ActionListener() + @Override + public void actionPerformed(ActionEvent e) { - @Override - public void actionPerformed(ActionEvent e) - { - sendFeaturesToChimera(); - } - }); - viewerActionMenu.add(writeFeatures); + sendFeaturesToChimera(); + } + }); + viewerActionMenu.add(writeFeatures); - final JMenu fetchAttributes = new JMenu( - MessageManager.getString("label.fetch_chimera_attributes")); - fetchAttributes.setToolTipText(MessageManager - .getString("label.fetch_chimera_attributes_tip")); - fetchAttributes.addMouseListener(new MouseAdapter() - { + fetchAttributes = new JMenu( + MessageManager.formatMessage("label.fetch_viewer_attributes",getViewerName())); + fetchAttributes.setToolTipText( + MessageManager.formatMessage("label.fetch_viewer_attributes_tip",getViewerName())); + fetchAttributes.addMouseListener(new MouseAdapter() + { - @Override - public void mouseEntered(MouseEvent e) - { - buildAttributesMenu(fetchAttributes); - } - }); - viewerActionMenu.add(fetchAttributes); - } + @Override + public void mouseEntered(MouseEvent e) + { + buildAttributesMenu(fetchAttributes); + } + }); + viewerActionMenu.add(fetchAttributes); } - + @Override + protected void buildActionMenu() + { + super.buildActionMenu(); + // add these back in after menu is refreshed + viewerActionMenu.add(writeFeatures); + viewerActionMenu.add(fetchAttributes); + + }; /** - * Query Chimera for its residue attribute names and add them as items off the - * attributes menu + * Query the structure viewer for its residue attribute names and add them as + * items off the attributes menu * * @param attributesMenu */ protected void buildAttributesMenu(JMenu attributesMenu) { - List atts = jmb.sendChimeraCommand("list resattr", true); - if (atts == null) - { - return; - } + List atts = jmb.getChimeraAttributes(); attributesMenu.removeAll(); Collections.sort(atts); - for (String att : atts) + for (String attName : atts) { - final String attName = att.split(" ")[1]; - - /* - * ignore 'jv_*' attributes, as these are Jalview features that have - * been transferred to residue attributes in Chimera! - */ - if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX)) + JMenuItem menuItem = new JMenuItem(attName); + menuItem.addActionListener(new ActionListener() { - JMenuItem menuItem = new JMenuItem(attName); - menuItem.addActionListener(new ActionListener() + @Override + public void actionPerformed(ActionEvent e) { - @Override - public void actionPerformed(ActionEvent e) + if (getBinding().copyStructureAttributesToFeatures(attName, + getAlignmentPanel()) > 0) { - getChimeraAttributes(attName); + getAlignmentPanel().getFeatureRenderer().featuresAdded(); } - }); - attributesMenu.add(menuItem); - } + } + }); + attributesMenu.add(menuItem); } } /** - * Read residues in Chimera with the given attribute name, and set as features - * on the corresponding sequence positions (if any) - * - * @param attName - */ - protected void getChimeraAttributes(String attName) - { - jmb.copyStructureAttributesToFeatures(attName, getAlignmentPanel()); - } - - /** - * Send a command to Chimera to create residue attributes for Jalview features - *

- * The syntax is: setattr r - *

- * For example: setattr r jv:chain "Ferredoxin-1, Chloroplastic" #0:94.A + * Sends command(s) to the structure viewer to create residue attributes for + * visible Jalview features */ protected void sendFeaturesToChimera() { + // todo pull up? int count = jmb.sendFeaturesToViewer(getAlignmentPanel()); statusBar.setText( - MessageManager.formatMessage("label.attributes_set", count)); + MessageManager.formatMessage("label.attributes_set", count, getViewerName())); } /** - * add a single PDB structure to a new or existing Chimera view + * open a single PDB structure in a new Chimera view * * @param pdbentry * @param seq @@ -213,30 +179,7 @@ public class ChimeraViewFrame extends StructureViewerBase String[] chains, final AlignmentPanel ap) { this(); - String pdbId = pdbentry.getId(); - /* - * If the PDB file is already loaded, the user may just choose to add to an - * existing viewer (or cancel) - */ - if (addAlreadyLoadedFile(seq, chains, ap, pdbId)) - { - return; - } - - /* - * Check if there are other Chimera views involving this alignment and give - * user the option to add and align this molecule to one of them (or cancel) - */ - if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId)) - { - return; - } - - /* - * If the options above are declined or do not apply, show the structure in - * a new viewer - */ openNewChimera(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq }); @@ -247,9 +190,9 @@ public class ChimeraViewFrame extends StructureViewerBase */ protected void createProgressBar() { - if (progressBar == null) + if (getProgressIndicator() == null) { - progressBar = new ProgressBar(statusPanel, statusBar); + setProgressIndicator(new ProgressBar(statusPanel, statusBar)); } } @@ -257,14 +200,12 @@ public class ChimeraViewFrame extends StructureViewerBase SequenceI[][] seqs) { createProgressBar(); - jmb = new JalviewChimeraBindingModel(this, - ap.getStructureSelectionManager(), pdbentrys, seqs, null); + jmb = newBindingModel(ap, pdbentrys, seqs); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); if (pdbentrys.length > 1) { - alignAddedStructures = true; useAlignmentPanelForSuperposition(ap); } jmb.setColourBySequence(true); @@ -287,6 +228,13 @@ public class ChimeraViewFrame extends StructureViewerBase } + protected JalviewChimeraBindingModel newBindingModel(AlignmentPanel ap, + PDBEntry[] pdbentrys, SequenceI[][] seqs) + { + return new JalviewChimeraBindingModel(this, + ap.getStructureSelectionManager(), pdbentrys, seqs, null); + } + /** * Create a new viewer from saved session state data including Chimera session * file @@ -299,22 +247,34 @@ public class ChimeraViewFrame extends StructureViewerBase * @param colourBySequence * @param newViewId */ - public ChimeraViewFrame(String chimeraSessionFile, - AlignmentPanel alignPanel, PDBEntry[] pdbArray, - SequenceI[][] seqsArray, boolean colourByChimera, - boolean colourBySequence, String newViewId) + public ChimeraViewFrame(StructureViewerModel viewerData, + AlignmentPanel alignPanel, String sessionFile, String vid) { this(); - setViewId(newViewId); - this.chimeraSessionFile = chimeraSessionFile; + 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 (colourByChimera) + if (viewerData.isColourByViewer()) { jmb.setColourBySequence(false); seqColour.setSelected(false); viewerColour.setSelected(true); } - else if (colourBySequence) + else if (viewerData.isColourWithAlignPanel()) { jmb.setColourBySequence(true); seqColour.setSelected(true); @@ -323,17 +283,19 @@ public class ChimeraViewFrame extends StructureViewerBase } /** - * create a new viewer containing several structures superimposed using the - * given alignPanel. + * create a new viewer containing several structures, optionally superimposed + * using the given alignPanel. * * @param pe * @param seqs * @param ap */ - public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs, + public ChimeraViewFrame(PDBEntry[] pe, boolean alignAdded, + SequenceI[][] seqs, AlignmentPanel ap) { this(); + setAlignAddedStructures(alignAdded); openNewChimera(ap, pe, seqs); } @@ -352,29 +314,6 @@ public class ChimeraViewFrame extends StructureViewerBase } /** - * Returns a list of any Chimera viewers in the desktop. The list is - * restricted to those linked to the given alignment panel if it is not null. - */ - @Override - protected List getViewersFor(AlignmentPanel ap) - { - List result = new ArrayList(); - JInternalFrame[] frames = Desktop.instance.getAllFrames(); - - for (JInternalFrame frame : frames) - { - if (frame instanceof ChimeraViewFrame) - { - if (ap == null || ((StructureViewerBase) frame).isLinkedWith(ap)) - { - result.add((StructureViewerBase) frame); - } - } - } - return result; - } - - /** * Launch Chimera. If we have a chimera session file name, send Chimera the * command to open its saved session file. */ @@ -388,9 +327,11 @@ public class ChimeraViewFrame extends StructureViewerBase if (!jmb.launchChimera()) { JvOptionPane.showMessageDialog(Desktop.desktop, - MessageManager.getString("label.chimera_failed"), + MessageManager.formatMessage("label.open_viewer_failed", + getViewerName()), MessageManager.getString("label.error_loading_file"), JvOptionPane.ERROR_MESSAGE); + jmb.closeViewer(true); this.dispose(); return; } @@ -409,71 +350,6 @@ public class ChimeraViewFrame extends StructureViewerBase } /** - * Show only the selected chain(s) in the viewer - */ - @Override - void showSelectedChains() - { - List toshow = new ArrayList(); - for (int i = 0; i < chainMenu.getItemCount(); i++) - { - if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) - { - JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i); - if (item.isSelected()) - { - toshow.add(item.getText()); - } - } - } - jmb.showChains(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. - * - * @param closeChimera - * if true, close any linked Chimera process; if false, prompt first - */ - @Override - public void closeViewer(boolean closeChimera) - { - if (jmb != null && jmb.isChimeraRunning()) - { - if (!closeChimera) - { - String prompt = MessageManager - .formatMessage("label.confirm_close_chimera", new Object[] - { jmb.getViewerTitle(getViewerName(), false) }); - prompt = JvSwingUtils.wrapTooltip(true, prompt); - int confirm = JvOptionPane.showConfirmDialog(this, prompt, - MessageManager.getString("label.close_viewer"), - JvOptionPane.YES_NO_CANCEL_OPTION); - /* - * abort closure if user hits escape or Cancel - */ - if (confirm == JvOptionPane.CANCEL_OPTION - || confirm == JvOptionPane.CLOSED_OPTION) - { - return; - } - closeChimera = confirm == JvOptionPane.YES_OPTION; - } - jmb.closeViewer(closeChimera); - } - setAlignmentPanel(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; - dispose(); - } - - /** * Open any newly added PDB structures in Chimera, having first fetched data * from PDB (if not already saved). */ @@ -484,8 +360,8 @@ public class ChimeraViewFrame extends StructureViewerBase // 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 @@ -532,7 +408,7 @@ public class ChimeraViewFrame extends StructureViewerBase { filePDB.add(thePdbEntry); filePDBpos.add(Integer.valueOf(pi)); - files.append(" \"" + Platform.escapeString(file) + "\""); + files.append(" \"" + Platform.escapeBackslashes(file) + "\""); } } } catch (OutOfMemoryError oomerror) @@ -566,9 +442,15 @@ public class ChimeraViewFrame extends StructureViewerBase initChimera(); } catch (Exception ex) { - Cache.log.error("Couldn't open Chimera viewer!", ex); + Console.error("Couldn't open Chimera viewer!", ex); } } + if (!jmb.isViewerRunning()) + { + // nothing to do + // TODO: ensure we tidy up JAL-3619 + return; + } int num = -1; for (PDBEntry pe : filePDB) { @@ -598,9 +480,12 @@ public class ChimeraViewFrame extends StructureViewerBase stopProgressBar("", startTime); } // Explicitly map to the filename used by Chimera ; + pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos], - jmb.getChains()[pos], pe.getFile(), protocol); - stashFoundChains(pdb, pe.getFile()); + jmb.getChains()[pos], pe.getFile(), protocol, + getProgressIndicator()); + jmb.stashFoundChains(pdb, pe.getFile()); + } catch (OutOfMemoryError oomerror) { new OOMWarning( @@ -608,12 +493,12 @@ public class ChimeraViewFrame extends StructureViewerBase oomerror); } catch (Exception ex) { - Cache.log.error( + Console.error( "Couldn't open " + pe.getFile() + " in Chimera viewer!", ex); } finally { - Cache.log.debug("File locations are " + files); + Console.debug("File locations are " + files); } } } @@ -624,7 +509,8 @@ public class ChimeraViewFrame extends StructureViewerBase /* * ensure that any newly discovered features (e.g. RESNUM) - * are added to any open feature settings dialog + * are notified to the FeatureRenderer (and added to any + * open feature settings dialog) */ FeatureRenderer fr = getBinding().getFeatureRenderer(null); if (fr != null) @@ -633,22 +519,21 @@ public class ChimeraViewFrame extends StructureViewerBase } // refresh the sequence colours for the new structure(s) - for (AlignmentPanel ap : _colourwith) + for (AlignmentViewPanel ap : _colourwith) { jmb.updateColours(ap); } // do superposition if asked to - if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures) + if (alignAddedStructures) { new Thread(new Runnable() { @Override public void run() { - alignStructs_withAllAlignPanels(); + alignStructsWithAllAlignPanels(); } }).start(); - alignAddedStructures = false; } addingStructures = false; } @@ -656,130 +541,11 @@ public class ChimeraViewFrame extends StructureViewerBase 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 void stashFoundChains(StructureFile pdb, String file) - { - for (int i = 0; i < pdb.getChains().size(); i++) - { - String chid = new String( - pdb.getId() + ":" + pdb.getChains().elementAt(i).id); - jmb.getChainNames().add(chid); - jmb.getChainFile().put(chid, file); - } - } - - private String fetchPdbFile(PDBEntry processingEntry) throws Exception - { - // FIXME: this is duplicated code with Jmol frame ? - String filePath = null; - Pdb pdbclient = new Pdb(); - AlignmentI pdbseq = null; - String pdbid = processingEntry.getId(); - long handle = System.currentTimeMillis() - + Thread.currentThread().hashCode(); - - /* - * Write 'fetching PDB' progress on AlignFrame as we are not yet visible - */ - String msg = MessageManager.formatMessage("status.fetching_pdb", - new Object[] - { pdbid }); - getAlignmentPanel().alignFrame.setProgressBar(msg, handle); - // long hdl = startProgressBar(MessageManager.formatMessage( - // "status.fetching_pdb", new Object[] - // { pdbid })); - try - { - pdbseq = pdbclient.getSequenceRecords(pdbid); - } catch (OutOfMemoryError oomerror) - { - new OOMWarning("Retrieving PDB id " + pdbid, oomerror); - } finally - { - msg = pdbid + " " + MessageManager.getString("label.state_completed"); - getAlignmentPanel().alignFrame.setProgressBar(msg, handle); - // stopProgressBar(msg, 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(pdbseq.getSequenceAt(0).getAllPDBEntries() - .elementAt(0).getFile()).getAbsolutePath(); - processingEntry.setFile(filePath); - } - return filePath; - } - - /** - * Convenience method to update the progress bar if there is one. Be sure to - * call stopProgressBar with the returned handle to remove the message. - * - * @param msg - * @param handle - */ - public long startProgressBar(String msg) - { - // TODO would rather have startProgress/stopProgress as the - // IProgressIndicator interface - long tm = random.nextLong(); - if (progressBar != null) - { - progressBar.setProgressBar(msg, tm); - } - return tm; - } - - /** - * End the progress bar with the specified handle, leaving a message (if not - * null) on the status bar - * - * @param msg - * @param handle - */ - public void stopProgressBar(String msg, long handle) - { - if (progressBar != null) - { - progressBar.setProgressBar(msg, handle); - } - } - @Override - public void eps_actionPerformed(ActionEvent e) + public void makePDBImage(TYPE imageType) { - 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 showHelp_actionPerformed(ActionEvent actionEvent) - { - try - { - BrowserLauncher - .openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide"); - } catch (IOException ex) - { - } + throw new UnsupportedOperationException( + "Image export for Chimera is not implemented"); } @Override @@ -788,82 +554,6 @@ public class ChimeraViewFrame extends StructureViewerBase return jmb; } - /** - * Ask Chimera to save its session to the designated file path, or to a - * temporary file if the path is null. Returns the file path if successful, - * else null. - * - * @param filepath - * @see getStateInfo - */ - protected String saveSession(String filepath) - { - String pathUsed = filepath; - try - { - if (pathUsed == null) - { - File tempFile = File.createTempFile("chimera", ".py"); - tempFile.deleteOnExit(); - pathUsed = tempFile.getPath(); - } - boolean result = jmb.saveSession(pathUsed); - if (result) - { - this.chimeraSessionFile = pathUsed; - return pathUsed; - } - } catch (IOException e) - { - } - return null; - } - - /** - * Returns a string representing the state of the Chimera session. This is - * done by requesting Chimera to save its session to a temporary file, then - * reading the file contents. Returns an empty string on any error. - */ - @Override - public String getStateInfo() - { - String sessionFile = saveSession(null); - if (sessionFile == null) - { - return ""; - } - InputStream is = null; - try - { - File f = new File(sessionFile); - byte[] bytes = new byte[(int) f.length()]; - is = new FileInputStream(sessionFile); - is.read(bytes); - return new String(bytes); - } catch (IOException e) - { - return ""; - } finally - { - if (is != null) - { - try - { - is.close(); - } catch (IOException e) - { - // ignore - } - } - } - } - - @Override - protected void fitToWindow_actionPerformed() - { - jmb.focusView(); - } - @Override public ViewerType getViewerType() { @@ -875,20 +565,4 @@ public class ChimeraViewFrame extends StructureViewerBase { return "Chimera"; } - - /** - * Sends commands to align structures according to associated alignment(s). - * - * @return - */ - @Override - protected String alignStructs_withAllAlignPanels() - { - String reply = super.alignStructs_withAllAlignPanels(); - if (reply != null) - { - statusBar.setText("Superposition failed: " + reply); - } - return reply; - } }