chainNames)
{
chainMenu.removeAll();
if (chainNames == null || chainNames.isEmpty())
{
return;
}
JMenuItem menuItem = new JMenuItem(
MessageManager.getString("label.all"));
menuItem.addActionListener(new ActionListener()
{
@Override
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);
}
}
showSelectedChains();
allChainsSelected = false;
}
});
chainMenu.add(menuItem);
for (String chain : chainNames)
{
menuItem = new JCheckBoxMenuItem(chain, true);
menuItem.addItemListener(new ItemListener()
{
@Override
public void itemStateChanged(ItemEvent evt)
{
if (!allChainsSelected)
{
showSelectedChains();
}
}
});
chainMenu.add(menuItem);
}
}
/**
* Action on selecting one of Jalview's registered colour schemes
*/
@Override
public void changeColour_actionPerformed(String colourSchemeName)
{
AlignmentI al = getAlignmentPanel().av.getAlignment();
ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(
colourSchemeName, getAlignmentPanel().av, al, null);
getBinding().colourByJalviewColourScheme(cs);
}
/**
* Builds the colour menu
*/
protected void buildColourMenu()
{
colourMenu.removeAll();
AlignmentI al = getAlignmentPanel().av.getAlignment();
/*
* add colour by sequence, by chain, by charge and cysteine
*/
colourMenu.add(seqColour);
colourMenu.add(chainColour);
colourMenu.add(chargeColour);
chargeColour.setEnabled(!al.isNucleotide());
/*
* add all 'simple' (per-residue) colour schemes registered to Jalview
*/
ButtonGroup itemGroup = ColourMenuHelper.addMenuItems(colourMenu, this,
al, true);
/*
* add 'colour by viewer' (menu item text is set in subclasses)
*/
viewerColour.setSelected(false);
viewerColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
viewerColour_actionPerformed();
}
});
colourMenu.add(viewerColour);
/*
* add 'set background colour'
*/
JMenuItem backGround = new JMenuItem();
backGround
.setText(MessageManager.getString("action.background_colour"));
backGround.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
background_actionPerformed();
}
});
colourMenu.add(backGround);
/*
* add colour buttons to a group so their selection is
* mutually exclusive (background colour is a separate option)
*/
itemGroup.add(seqColour);
itemGroup.add(chainColour);
itemGroup.add(chargeColour);
itemGroup.add(viewerColour);
}
/**
* Construct menu items
*/
protected void initMenus()
{
AAStructureBindingModel binding = getBinding();
seqColour = new JRadioButtonMenuItem();
seqColour.setText(MessageManager.getString("action.by_sequence"));
seqColour.setName(ViewerColour.BySequence.name());
seqColour.setSelected(binding.isColourBySequence());
seqColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
seqColour_actionPerformed();
}
});
chainColour = new JRadioButtonMenuItem();
chainColour.setText(MessageManager.getString("action.by_chain"));
chainColour.setName(ViewerColour.ByChain.name());
chainColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
chainColour_actionPerformed();
}
});
chargeColour = new JRadioButtonMenuItem();
chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
chargeColour.setName(ViewerColour.ChargeCysteine.name());
chargeColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
chargeColour_actionPerformed();
}
});
viewerColour = new JRadioButtonMenuItem();
viewerColour
.setText(MessageManager.getString("label.colour_with_viewer"));
viewerColour.setToolTipText(MessageManager
.getString("label.let_viewer_manage_structure_colours"));
viewerColour.setName(ViewerColour.ByViewer.name());
viewerColour.setSelected(!binding.isColourBySequence());
if (_colourwith == null)
{
_colourwith = new Vector<>();
}
if (_alignwith == null)
{
_alignwith = new Vector<>();
}
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 viewer display now.
seqColour_actionPerformed();
}
}
});
viewMenu.add(seqColourBy);
final ItemListener handler = new ItemListener()
{
@Override
public void itemStateChanged(ItemEvent e)
{
if (_alignwith.isEmpty())
{
alignStructs.setEnabled(false);
alignStructs.setToolTipText(null);
}
else
{
alignStructs.setEnabled(true);
alignStructs.setToolTipText(MessageManager.formatMessage(
"label.align_structures_using_linked_alignment_views",
_alignwith.size()));
}
}
};
viewSelectionMenu = new ViewSelectionMenu(
MessageManager.getString("label.superpose_with"), this,
_alignwith, handler);
handler.itemStateChanged(null);
viewerActionMenu.add(viewSelectionMenu, 0);
viewerActionMenu.addMenuListener(new MenuListener()
{
@Override
public void menuSelected(MenuEvent e)
{
handler.itemStateChanged(null);
}
@Override
public void menuDeselected(MenuEvent e)
{
}
@Override
public void menuCanceled(MenuEvent e)
{
}
});
viewerActionMenu.setText(getViewerName());
helpItem.setText(MessageManager.formatMessage("label.viewer_help",
getViewerName()));
buildColourMenu();
}
/**
* Sends commands to the structure viewer to superimpose structures based on
* currently associated alignments. May optionally return an error message for
* the operation.
*/
@Override
protected String alignStructsWithAllAlignPanels()
{
if (getAlignmentPanel() == null)
{
return null;
}
if (_alignwith.size() == 0)
{
_alignwith.add(getAlignmentPanel());
}
String reply = null;
try
{
reply = getBinding().superposeStructures(_alignwith);
if (reply != null && !reply.isEmpty())
{
String text = MessageManager
.formatMessage("error.superposition_failed", reply);
statusBar.setText(text);
}
} catch (Exception e)
{
StringBuffer sp = new StringBuffer();
for (AlignmentViewPanel alignPanel : _alignwith)
{
sp.append("'" + alignPanel.getViewName() + "' ");
}
Console.info("Couldn't align structures with the " + sp.toString()
+ "associated alignment panels.", e);
}
return reply;
}
/**
* Opens a colour chooser dialog, and applies the chosen colour to the
* background of the structure viewer
*/
@Override
public void background_actionPerformed()
{
String ttl = MessageManager.getString("label.select_background_colour");
ColourChooserListener listener = new ColourChooserListener()
{
@Override
public void colourSelected(Color c)
{
getBinding().setBackgroundColour(c);
}
};
JalviewColourChooser.showColourChooser(this, ttl, null, listener);
}
@Override
public void viewerColour_actionPerformed()
{
if (viewerColour.isSelected())
{
// disable automatic sequence colouring.
getBinding().setColourBySequence(false);
}
}
@Override
public void chainColour_actionPerformed()
{
chainColour.setSelected(true);
getBinding().colourByChain();
}
@Override
public void chargeColour_actionPerformed()
{
chargeColour.setSelected(true);
getBinding().colourByCharge();
}
@Override
public void seqColour_actionPerformed()
{
AAStructureBindingModel binding = getBinding();
binding.setColourBySequence(seqColour.isSelected());
if (_colourwith == null)
{
_colourwith = new Vector<>();
}
if (binding.isColourBySequence())
{
if (!binding.isLoadingFromArchive())
{
if (_colourwith.size() == 0 && getAlignmentPanel() != null)
{
// Make the currently displayed alignment panel the associated view
_colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
}
}
// Set the colour using the current view for the associated alignframe
for (AlignmentViewPanel alignPanel : _colourwith)
{
binding.colourBySequence(alignPanel);
}
seqColoursApplied = true;
}
}
@Override
public void pdbFile_actionPerformed()
{
// TODO: JAL-3048 not needed for Jalview-JS - save PDB file
JalviewFileChooser chooser = new JalviewFileChooser(
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(getBinding().getStructureFiles()[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)
{
// ignore
}
}
}
}
}
@Override
public void viewMapping_actionPerformed()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
{
cap.appendText(getBinding().printMappings());
} catch (OutOfMemoryError e)
{
new OOMWarning(
"composing sequence-structure alignments for display in text box.",
e);
cap.dispose();
return;
}
Desktop.addInternalFrame(cap,
MessageManager.getString("label.pdb_sequence_mapping"), 550,
600);
}
protected abstract String getViewerName();
/**
* Configures the title and menu items of the viewer panel.
*/
@Override
public void updateTitleAndMenus()
{
AAStructureBindingModel binding = getBinding();
if (binding.hasFileLoadingError())
{
repaint();
return;
}
setChainMenuItems(binding.getChainNames());
this.setTitle(binding.getViewerTitle(getViewerName(), true));
/*
* enable 'Superpose with' if more than one mapped structure
*/
viewSelectionMenu.setEnabled(false);
if (getBinding().getMappedStructureCount() > 1
&& getBinding().getSequence().length > 1)
{
viewSelectionMenu.setEnabled(true);
}
/*
* Show action menu if it has any enabled items
*/
viewerActionMenu.setVisible(false);
for (int i = 0; i < viewerActionMenu.getItemCount(); i++)
{
if (viewerActionMenu.getItem(i).isEnabled())
{
viewerActionMenu.setVisible(true);
break;
}
}
if (!binding.isLoadingFromArchive())
{
seqColour_actionPerformed();
}
}
@Override
public String toString()
{
return getTitle();
}
@Override
public boolean hasMapping()
{
if (worker != null && (addingStructures || _started))
{
return false;
}
if (getBinding() == null)
{
if (_aps == null || _aps.size() == 0)
{
// viewer has been closed, but we did at some point run.
return true;
}
return false;
}
String[] pdbids = getBinding().getStructureFiles();
if (pdbids == null)
{
return false;
}
int p = 0;
for (String pdbid : pdbids)
{
StructureMapping sm[] = getBinding().getSsm().getMapping(pdbid);
if (sm != null && sm.length > 0 && sm[0] != null)
{
p++;
}
}
// only return true if there is a mapping for every structure file we have
// loaded
if (p == 0 || p != pdbids.length)
{
return false;
}
// and that coloring has been applied
return seqColoursApplied;
}
@Override
public void raiseViewer()
{
toFront();
}
@Override
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;
}
@Override
public void stopProgressBar(String msg, long handle)
{
if (progressBar != null)
{
progressBar.setProgressBar(msg, handle);
}
}
protected IProgressIndicator getProgressIndicator()
{
return progressBar;
}
protected void setProgressIndicator(IProgressIndicator pi)
{
progressBar = pi;
}
public void setProgressMessage(String message, long id)
{
if (progressBar != null)
{
progressBar.setProgressBar(message, id);
}
}
@Override
public void showConsole(boolean show)
{
// default does nothing
}
/**
* Show only the selected chain(s) in the viewer
*/
protected 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());
}
}
}
getBinding().showChains(toshow);
}
/**
* Tries to fetch a PDB file and save to a temporary local file. Returns the
* saved file path if successful, or null if not.
*
* @param processingEntry
* @return
*/
protected String fetchPdbFile(PDBEntry processingEntry)
{
String filePath = null;
Pdb pdbclient = new Pdb();
EBIAlfaFold afclient = new EBIAlfaFold();
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
{
if (afclient.isValidReference(pdbid))
{
pdbseq = afclient.getSequenceRecords(pdbid,
processingEntry.getRetrievalUrl());
}
else
{
if (processingEntry.hasRetrievalUrl())
{
String safePDBId = java.net.URLEncoder.encode(pdbid, "UTF-8")
.replace("%", "__");
// retrieve from URL to new local tmpfile
File tmpFile = File.createTempFile(safePDBId,
"." + (PDBEntry.Type.MMCIF.toString().equals(
processingEntry.getType().toString()) ? "cif"
: "pdb"));
String fromUrl = processingEntry.getRetrievalUrl();
UrlDownloadClient.download(fromUrl, tmpFile);
// may not need this check ?
String file = tmpFile.getAbsolutePath();
if (file != null)
{
pdbseq = EBIAlfaFold.importDownloadedStructureFromUrl(fromUrl,
tmpFile, pdbid, null, null, null);
}
}
else
{
pdbseq = pdbclient.getSequenceRecords(pdbid);
}
}
} catch (Exception e)
{
System.err.println(
"Error retrieving PDB id " + pdbid + ": " + e.getMessage());
} 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;
}
/**
* If supported, saves the state of the structure viewer to a temporary file
* and returns the file, else returns null
*
* @return
*/
public File saveSession()
{
if (getBinding() == null)
{
return null;
}
File session = getBinding().saveSession();
long l = session.length();
int wait = 50;
do
{
try
{
Thread.sleep(5);
} catch (InterruptedException e)
{
}
long nextl = session.length();
if (nextl != l)
{
wait = 50;
l = nextl;
}
} while (--wait > 0);
return session;
}
/**
* 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 forceClose
* if true, close any linked Chimera process; if false, prompt first
*/
@Override
public void closeViewer(boolean forceClose)
{
AAStructureBindingModel binding = getBinding();
if (binding != null && binding.isViewerRunning())
{
if (!forceClose)
{
String viewerName = getViewerName();
String prompt = MessageManager
.formatMessage("label.confirm_close_viewer", new Object[]
{ binding.getViewerTitle(viewerName, false), viewerName });
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;
}
forceClose = confirm == JvOptionPane.YES_OPTION;
}
}
if (binding != null)
{
binding.closeViewer(forceClose);
}
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();
}
@Override
public void showHelp_actionPerformed()
{
/*
try
{
*/
String url = getBinding().getHelpURL();
if (url != null)
{
BrowserLauncher.openURL(url);
}
/*
}
catch (IOException ex)
{
System.err
.println("Show " + getViewerName() + " failed with: "
+ ex.getMessage());
}
*/
}
@Override
public boolean hasViewerActionsMenu()
{
return viewerActionMenu != null && viewerActionMenu.isEnabled()
&& viewerActionMenu.getItemCount() > 0
&& viewerActionMenu.isVisible();
}
}