X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;fp=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=45ab9a94d358efe695168e6f7d48672377aabba6;hb=4f30214e8098748469c6a4269ac2ed6c5750e4b0;hp=c6d6e9785a69cceea7944d2bb40d9c29705edc02;hpb=0bc9297afd18a3e2b412364bf1af426570555b9a;p=jalview.git diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index c6d6e97..45ab9a9 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -20,43 +20,37 @@ */ 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.ImageMaker.TYPE; -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 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.Cache; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +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.ImageMaker.TYPE; +import jalview.util.MessageManager; +import jalview.util.Platform; + /** * GUI elements for handling an external chimera display * @@ -67,8 +61,6 @@ 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 @@ -76,8 +68,6 @@ public class ChimeraViewFrame extends StructureViewerBase */ private String chimeraSessionFile = null; - private Random random = new Random(); - private int myWidth = 500; private int myHeight = 150; @@ -92,11 +82,6 @@ public class ChimeraViewFrame extends StructureViewerBase 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); @@ -139,34 +124,21 @@ public class ChimeraViewFrame extends StructureViewerBase */ 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) - { - getChimeraAttributes(attName); - } - }); - attributesMenu.add(menuItem); - } + getChimeraAttributes(attName); + } + }); + attributesMenu.add(menuItem); } } @@ -184,9 +156,9 @@ public class ChimeraViewFrame extends StructureViewerBase /** * Send a command to Chimera to create residue attributes for Jalview features *

- * The syntax is: setattr r + * The syntax is: setattr r <attName> <attValue> <atomSpec> *

- * For example: setattr r jv:chain "Ferredoxin-1, Chloroplastic" #0:94.A + * For example: setattr r jv_chain "Ferredoxin-1, Chloroplastic" #0:94.A */ protected void sendFeaturesToChimera() { @@ -218,9 +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)); } } @@ -228,8 +200,7 @@ 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); @@ -257,6 +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 @@ -337,7 +315,8 @@ 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); this.dispose(); @@ -358,71 +337,6 @@ 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). */ @@ -550,8 +464,8 @@ public class ChimeraViewFrame extends StructureViewerBase pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos], jmb.getChains()[pos], pe.getFile(), protocol, - progressBar); - stashFoundChains(pdb, pe.getFile()); + getProgressIndicator()); + jmb.stashFoundChains(pdb, pe.getFile()); } catch (OutOfMemoryError oomerror) { @@ -585,7 +499,7 @@ 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); } @@ -597,7 +511,7 @@ public class ChimeraViewFrame extends StructureViewerBase @Override public void run() { - alignStructs_withAllAlignPanels(); + alignStructsWithAllAlignPanels(); } }).start(); } @@ -607,105 +521,6 @@ 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. TODO: refactor to common with Jmol ? duplication - * - * @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 - { - 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 makePDBImage(TYPE imageType) { @@ -714,14 +529,16 @@ public class ChimeraViewFrame extends StructureViewerBase } @Override - public void showHelp_actionPerformed(ActionEvent actionEvent) + public void showHelp_actionPerformed() { try { - BrowserLauncher - .openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide"); + String url = jmb.getHelpURL(); + BrowserLauncher.openURL(url); } catch (IOException ex) { + System.err + .println("Show Chimera help failed with: " + ex.getMessage()); } } @@ -731,76 +548,6 @@ 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() { @@ -818,26 +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; - } - - @Override - protected IProgressIndicator getIProgressIndicator() - { - return progressBar; - } }