/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.gui.StructureViewer.ViewerType;
import jalview.io.AppletFormatAdapter;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import java.awt.event.ItemListener;
import java.io.BufferedReader;
import java.io.File;
+import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
+import java.io.InputStream;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
+import java.util.Map;
+import java.util.Random;
+import java.util.Set;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.event.MenuListener;
/**
- * GUI elements for handlnig an external chimera display
+ * GUI elements for handling an external chimera display
*
* @author jprocter
*
private boolean allChainsSelected = false;
- private boolean alignAddedStructures = false;
-
- /*
- * state flag for PDB retrieval thread
- */
- private boolean _started = false;
-
- private boolean addingStructures = false;
-
private IProgressIndicator progressBar = null;
/*
- * pdb retrieval thread.
- */
- private Thread worker = 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
* filename of any saved Chimera sessions).
*/
private String chimeraSessionFile = null;
+ private Random random = new Random();
+
/**
* Initialise menu options.
*/
}
});
viewMenu.add(seqColourBy);
+ viewMenu.add(fitToWindow);
+
final ItemListener handler;
JMenu alpanels = new ViewSelectionMenu(
MessageManager.getString("label.superpose_with"), this,
alignStructs.setToolTipText(MessageManager
.formatMessage(
"label.align_structures_using_linked_alignment_views",
- new Object[]
- { new Integer(_alignwith.size()).toString() }));
+ new Object[] { new Integer(_alignwith
+ .size()).toString() }));
}
});
handler.itemStateChanged(null);
String[] chains, final AlignmentPanel ap)
{
super();
- progressBar = ap.alignFrame;
- // ////////////////////////////////
- // Is the pdb file already loaded?
- String alreadyMapped = ap.getStructureSelectionManager()
- .alreadyMappedToFile(pdbentry.getId());
+ String pdbId = pdbentry.getId();
- if (alreadyMapped != null)
+ /*
+ * 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))
{
- 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)
- {
- // TODO : Fix multiple seq to one chain issue here.
- ap.getStructureSelectionManager().setMapping(seq, chains,
- alreadyMapped, AppletFormatAdapter.FILE);
- if (ap.getSeqPanel().seqCanvas.fr != null)
- {
- ap.getSeqPanel().seqCanvas.fr.featuresAdded();
- ap.paintAlignment(true);
- }
+ return;
+ }
- // Now this ChimeraViewFrame is mapped to new sequences. We must add
- // them to the existing array
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
+ /*
+ * 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;
+ }
- 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.getPdbCount(); pe++)
- {
- if (topView.jmb.getPdbEntry(pe).getFile()
- .equals(
- alreadyMapped))
- {
- topView.jmb.addSequence(pe, seq);
- topView.addAlignmentPanel(ap);
- // add it to the set used for colouring
- topView.useAlignmentPanelForColourbyseq(ap);
- topView.buildActionMenu();
- ap.getStructureSelectionManager()
- .sequenceColoursChanged(ap);
- break;
- }
- }
- }
- }
+ /*
+ * 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 });
+ }
- return;
- }
- }
- // /////////////////////////////////
- // Check if there are other Chimera views involving this alignment
- // and prompt user about adding this molecule to one of them
- List<ChimeraViewFrame> existingViews = getChimeraWindowsFor(ap);
- for (ChimeraViewFrame topView : existingViews)
+ /**
+ * Create a helper to manage progress bar display
+ */
+ protected void createProgressBar()
+ {
+ if (progressBar == null)
{
- // 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;
- }
+ progressBar = new ProgressBar(statusPanel, statusBar);
}
- // /////////////////////////////////
- openNewChimera(ap, new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq });
+ }
+
+ /**
+ * Answers true if this viewer already involves the given PDB ID
+ */
+ @Override
+ protected boolean hasPdbId(String pdbId)
+ {
+ return jmb.hasPdbId(pdbId);
}
private void openNewChimera(AlignmentPanel ap, PDBEntry[] pdbentrys,
SequenceI[][] seqs)
{
- progressBar = ap.alignFrame;
+ createProgressBar();
+ String[][] chains = extractChains(seqs);
jmb = new JalviewChimeraBindingModel(this,
- ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
+ ap.getStructureSelectionManager(), pdbentrys, seqs, chains,
+ null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
if (pdbentrys.length > 1)
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
- closeViewer();
+ closeViewer(false);
}
});
}
/**
- * create a new viewer containing several structures superimposed using the
- * given alignPanel.
+ * Retrieve chains for sequences by inspecting their PDB refs. The hope is
+ * that the first will be to the sequence's own chain. Really need a more
+ * managed way of doing this.
*
- * @param ap
- * @param pe
* @param seqs
+ * @return
*/
- public ChimeraViewFrame(AlignmentPanel ap, PDBEntry[] pe,
- SequenceI[][] seqs)
+ protected String[][] extractChains(SequenceI[][] seqs)
{
- super();
- openNewChimera(ap, pe, seqs);
+ String[][] chains = new String[seqs.length][];
+ for (int i = 0; i < seqs.length; i++)
+ {
+ chains[i] = new String[seqs[i].length];
+ int seqno = 0;
+ for (SequenceI seq : seqs[i])
+ {
+ String chain = null;
+ if (seq.getDatasetSequence() != null)
+ {
+ Vector<PDBEntry> pdbrefs = seq.getDatasetSequence()
+ .getAllPDBEntries();
+ if (pdbrefs != null && pdbrefs.size() > 0)
+ {
+ chain = pdbrefs.get(0).getChainCode();
+ }
+ }
+ chains[i][seqno++] = chain;
+ }
+ }
+ return chains;
}
/**
* Create a new viewer from saved session state data including Chimera session
- * file.
- *
- * @param chimeraSession
+ * file
*
+ * @param chimeraSessionFile
* @param alignPanel
* @param pdbArray
* @param seqsArray
* @param colourByChimera
* @param colourBySequence
+ * @param newViewId
*/
- public ChimeraViewFrame(String chimeraSession, AlignmentPanel alignPanel,
- PDBEntry[] pdbArray,
+ public ChimeraViewFrame(String chimeraSessionFile,
+ AlignmentPanel alignPanel, PDBEntry[] pdbArray,
SequenceI[][] seqsArray, boolean colourByChimera,
- boolean colourBySequence)
+ boolean colourBySequence, String newViewId)
{
super();
- this.chimeraSessionFile = chimeraSession;
+ setViewId(newViewId);
+ this.chimeraSessionFile = chimeraSessionFile;
openNewChimera(alignPanel, pdbArray, seqsArray);
if (colourByChimera)
{
}
/**
- * add a new structure (with associated sequences and chains) to this viewer,
- * retrieving it if necessary first.
+ * create a new viewer containing several structures 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, 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));
+ super();
+ openNewChimera(ap, pe, seqs);
+ }
- } catch (Exception e)
- {
- }
+ public ChimeraViewFrame(Map<PDBEntry, List<SequenceI>> toView,
+ AlignmentPanel alignPanel)
+ {
+ super();
- }
- // and call ourselves again.
- addStructure(pdbentry, seq, chains, b, alignFrame);
- }
- }).start();
- return;
- }
+ /*
+ * Convert the map of sequences per pdb entry into the tied arrays expected
+ * by openNewChimera
+ *
+ * TODO pass the Map down to openNewChimera and its callees instead
+ */
+ final Set<PDBEntry> pdbEntries = toView.keySet();
+ PDBEntry[] pdbs = pdbEntries.toArray(new PDBEntry[pdbEntries.size()]);
+ SequenceI[][] seqsForPdbs = new SequenceI[pdbEntries.size()][];
+ for (int i = 0; i < pdbs.length; i++)
+ {
+ final List<SequenceI> seqsForPdb = toView.get(pdbs[i]);
+ seqsForPdbs[i] = seqsForPdb.toArray(new SequenceI[seqsForPdb.size()]);
}
- // 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;
+
+ openNewChimera(alignPanel, pdbs, seqsForPdbs);
}
- private List<ChimeraViewFrame> getChimeraWindowsFor(AlignmentPanel apanel)
+ /**
+ * 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<StructureViewerBase> getViewersFor(AlignmentPanel ap)
{
- List<ChimeraViewFrame> result = new ArrayList<ChimeraViewFrame>();
+ List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
JInternalFrame[] frames = Desktop.instance.getAllFrames();
for (JInternalFrame frame : frames)
{
if (frame instanceof ChimeraViewFrame)
{
- if (((StructureViewerBase) frame).isLinkedWith(apanel))
+ if (ap == null || ((StructureViewerBase) frame).isLinkedWith(ap))
{
- result.add((ChimeraViewFrame) frame);
+ result.add((StructureViewerBase) frame);
}
}
}
void initChimera()
{
jmb.setFinishedInit(false);
- jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
- getBounds().width, getBounds().height);
+ jalview.gui.Desktop.addInternalFrame(this,
+ jmb.getViewerTitle("Chimera", true), getBounds().width,
+ getBounds().height);
- /*
- * Pass an empty 'command' to launch Chimera
- */
- jmb.evalStateCommand("", false);
+ if (!jmb.launchChimera())
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.chimera_failed"),
+ MessageManager.getString("label.error_loading_file"),
+ JOptionPane.ERROR_MESSAGE);
+ this.dispose();
+ return;
+ }
if (this.chimeraSessionFile != null)
{
}
}
jmb.setFinishedInit(true);
+
+ jmb.startChimeraListener();
}
+ /**
+ * If the list is not empty, add menu items for 'All' and each individual
+ * chain to the "View | Show Chain" sub-menu. Multiple selections are allowed.
+ *
+ * @param chainNames
+ */
void setChainMenuItems(List<String> chainNames)
{
chainMenu.removeAll();
- if (chainNames == null)
+ if (chainNames == null || chainNames.isEmpty())
{
return;
}
((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
}
}
- centerViewer();
+ showSelectedChains();
allChainsSelected = false;
}
});
{
if (!allChainsSelected)
{
- centerViewer();
+ showSelectedChains();
}
}
});
}
}
- void centerViewer()
+ /**
+ * Show only the selected chain(s) in the viewer
+ */
+ void showSelectedChains()
{
List<String> toshow = new ArrayList<String>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
}
}
}
- jmb.centerViewer(toshow);
+ 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
*/
- public void closeViewer()
+ public void closeViewer(boolean closeChimera)
{
- if (jmb.isChimeraRunning())
+ if (jmb != null && jmb.isChimeraRunning())
{
- String prompt = MessageManager
- .formatMessage("label.confirm_close_chimera", new Object[]
- { jmb.getViewerTitle("Chimera", 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);
+ if (!closeChimera)
+ {
+ String prompt = MessageManager.formatMessage(
+ "label.confirm_close_chimera",
+ new Object[] { jmb.getViewerTitle("Chimera", false) });
+ prompt = JvSwingUtils.wrapTooltip(true, prompt);
+ int confirm = JOptionPane.showConfirmDialog(this, prompt,
+ MessageManager.getString("label.close_viewer"),
+ JOptionPane.YES_NO_OPTION);
+ closeChimera = confirm == JOptionPane.YES_OPTION;
+ }
+ jmb.closeViewer(closeChimera);
}
setAlignmentPanel(null);
_aps.clear();
JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
- new Object[]
- { errormsgs.toString() }), MessageManager
- .getString("label.couldnt_load_file"),
+ new Object[] { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
JOptionPane.ERROR_MESSAGE);
}
try
{
int pos = filePDBpos.get(num).intValue();
+ long startTime = startProgressBar("Chimera "
+ + MessageManager.getString("status.opening_file"));
jmb.openFile(pe);
jmb.addSequence(pos, jmb.getSequence()[pos]);
File fl = new File(pe.getFile());
}
} catch (Throwable e)
{
+ } finally
+ {
+ stopProgressBar("", startTime);
}
// Explicitly map to the filename used by Chimera ;
- // TODO: use pe.getId() instead of pe.getFile() ?
- jmb.getSsm().setMapping(jmb.getSequence()[pos], null,
- pe.getFile(),
- protocol);
+ jmb.getSsm().setMapping(jmb.getSequence()[pos],
+ jmb.getChains()[pos], pe.getFile(), protocol);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning(
jmb.updateColours(ap);
}
// do superposition if asked to
- if (alignAddedStructures)
+ if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
{
new Thread(new Runnable()
{
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);
- }
+ 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);
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
} finally
{
- if (progressBar != null)
- {
- progressBar
- .setProgressBar(
- pdbid
- + " "
- + MessageManager
- .getString("label.state_completed"),
- hdl);
- }
+ 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
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();
+ 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 pdbFile_actionPerformed(ActionEvent actionEvent)
{
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
try
{
- for (int pdbe = 0; pdbe < jmb.getPdbCount(); pdbe++)
- {
- cap.appendText(jmb.printMapping(jmb.getPdbEntry(pdbe).getFile()));
- cap.appendText("\n");
- }
+ cap.appendText(jmb.printMappings());
} catch (OutOfMemoryError e)
{
new OOMWarning(
{
return;
}
- ;
+
if (_alignwith.size() == 0)
{
_alignwith.add(getAlignmentPanel());
}
- ;
+
try
{
AlignmentI[] als = new Alignment[_alignwith.size()];
}
Cache.log.info("Couldn't align structures with the " + sp.toString()
+ "associated alignment panels.", e);
-
}
-
}
public void setJalviewColourScheme(ColourSchemeI ucs)
}
/**
- * Ask Chimera to save its session to the designated file path. Returns true
- * if successful, else false.
+ * 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
*/
- public boolean saveSession(String filepath)
+ protected String saveSession(String filepath)
{
- boolean result = jmb.saveSession(filepath);
- if (result)
+ 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)
{
- this.chimeraSessionFile = filepath;
}
- return result;
+ return null;
}
/**
- * Returns the file path of the Chimera session file the last time it was
- * saved. If it was never saved, returns an empty string. There is no
- * guarantee that the Chimera session has not changed since it was saved.
+ * 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()
{
- return this.chimeraSessionFile;
+ 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()
+ {
+ return ViewerType.CHIMERA;
+ }
+
+ @Override
+ protected AAStructureBindingModel getBindingModel()
+ {
+ return jmb;
}
}
git://source.jalview.org / jalview.git / blobdiff