*/
package jalview.gui;
+import jalview.api.AlignmentViewPanel;
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 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;
{
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
*/
private String chimeraSessionFile = null;
- private Random random = new Random();
-
private int myWidth = 500;
private int myHeight = 150;
viewerActionMenu.setText(MessageManager.getString("label.chimera"));
- viewerColour.setText(MessageManager
- .getString("label.colour_with_chimera"));
+ viewerColour
+ .setText(MessageManager.getString("label.colour_with_chimera"));
viewerColour.setToolTipText(MessageManager
.getString("label.let_chimera_manage_structure_colours"));
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())
+ JMenuItem writeFeatures = new JMenuItem(
+ MessageManager.getString("label.create_chimera_attributes"));
+ writeFeatures.setToolTipText(MessageManager
+ .getString("label.create_chimera_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()
- {
+ 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 mouseEntered(MouseEvent e)
- {
- buildAttributesMenu(fetchAttributes);
- }
- });
- viewerActionMenu.add(fetchAttributes);
- }
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ buildAttributesMenu(fetchAttributes);
+ }
+ });
+ viewerActionMenu.add(fetchAttributes);
}
/**
*/
protected void buildAttributesMenu(JMenu attributesMenu)
{
- List<String> atts = jmb.sendChimeraCommand("list resattr", true);
- if (atts == null)
- {
- return;
- }
+ List<String> 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);
}
}
protected void sendFeaturesToChimera()
{
int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
- statusBar.setText(MessageManager.formatMessage("label.attributes_set",
- count));
+ statusBar.setText(
+ MessageManager.formatMessage("label.attributes_set", count));
}
/**
- * 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
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 });
+ new SequenceI[][]
+ { seq });
}
/**
*/
protected void createProgressBar()
{
- if (progressBar == null)
+ if (getProgressIndicator() == null)
{
- progressBar = new ProgressBar(statusPanel, statusBar);
+ setProgressIndicator(new ProgressBar(statusPanel, statusBar));
}
}
if (pdbentrys.length > 1)
{
- alignAddedStructures = true;
useAlignmentPanelForSuperposition(ap);
}
jmb.setColourBySequence(true);
this.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ public void internalFrameClosing(
+ InternalFrameEvent internalFrameEvent)
{
closeViewer(false);
}
}
/**
- * 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);
}
}
/**
- * 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<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
- 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.
*/
boolean opened = jmb.openSession(chimeraSessionFile);
if (!opened)
{
- System.err
- .println("An error occurred opening Chimera session file "
- + chimeraSessionFile);
+ System.err.println("An error occurred opening Chimera session file "
+ + chimeraSessionFile);
}
}
}
/**
- * Show only the selected chain(s) in the viewer
- */
- @Override
- void showSelectedChains()
- {
- List<String> toshow = new ArrayList<String>();
- 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.
{
if (!closeChimera)
{
- String prompt = MessageManager.formatMessage(
- "label.confirm_close_chimera",
- new Object[] { jmb.getViewerTitle(getViewerName(),
- false) });
+ 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"),
// todo - record which pdbids were successfully imported.
StringBuilder errormsgs = new StringBuilder(128);
StringBuilder files = new StringBuilder(128);
- List<PDBEntry> filePDB = new ArrayList<PDBEntry>();
- List<Integer> filePDBpos = new ArrayList<Integer>();
+ List<PDBEntry> filePDB = new ArrayList<>();
+ List<Integer> filePDBpos = new ArrayList<>();
PDBEntry thePdbEntry = null;
StructureFile pdb = null;
try
{
filePDB.add(thePdbEntry);
filePDBpos.add(Integer.valueOf(pi));
- files.append(" \"" + Platform.escapeString(file) + "\"");
+ files.append(" \"" + Platform.escapeBackslashes(file) + "\"");
}
}
} catch (OutOfMemoryError oomerror)
} 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)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
- .formatMessage("label.pdb_entries_couldnt_be_retrieved",
- new Object[] { errormsgs.toString() }),
+ 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);
}
stopProgressBar("", startTime);
}
// Explicitly map to the filename used by Chimera ;
+
pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
- jmb.getChains()[pos], pe.getFile(), protocol);
+ jmb.getChains()[pos], pe.getFile(), protocol,
+ getProgressIndicator());
stashFoundChains(pdb, pe.getFile());
+
} catch (OutOfMemoryError oomerror)
{
new OOMWarning(
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);
}
// 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;
}
/**
* Fetch PDB data and save to a local file. Returns the full path to the file,
- * or null if fetch fails.
+ * or null if fetch fails. TODO: refactor to common with Jmol ? duplication
*
* @param processingEntry
* @return
{
for (int i = 0; i < pdb.getChains().size(); i++)
{
- String chid = new String(pdb.getId() + ":"
- + pdb.getChains().elementAt(i).id);
+ String chid = new String(
+ pdb.getId() + ":" + pdb.getChains().elementAt(i).id);
jmb.getChainNames().add(chid);
- jmb.getChainFile().put(chid, file);
+ jmb.addChainFile(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;
* Write 'fetching PDB' progress on AlignFrame as we are not yet visible
*/
String msg = MessageManager.formatMessage("status.fetching_pdb",
- new Object[] { pdbid });
+ new Object[]
+ { pdbid });
getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
// long hdl = startProgressBar(MessageManager.formatMessage(
// "status.fetching_pdb", new Object[]
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 eps_actionPerformed()
{
- throw new Error(
- MessageManager
- .getString("error.eps_generation_not_implemented"));
+ throw new Error(MessageManager
+ .getString("error.eps_generation_not_implemented"));
}
@Override
- public void png_actionPerformed(ActionEvent e)
+ public void png_actionPerformed()
{
- throw new Error(
- MessageManager
- .getString("error.png_generation_not_implemented"));
+ throw new Error(MessageManager
+ .getString("error.png_generation_not_implemented"));
}
@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.isChimeraX()
+ ? "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html"
+ : "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
+ BrowserLauncher.openURL(url);
} catch (IOException ex)
{
+ System.err
+ .println("Show Chimera help failed with: " + ex.getMessage());
}
}
{
if (pathUsed == null)
{
- File tempFile = File.createTempFile("chimera", ".py");
+ String suffix = jmb.isChimeraX() ? ".cxs" : ".py";
+ File tempFile = File.createTempFile("chimera", suffix);
tempFile.deleteOnExit();
pathUsed = tempFile.getPath();
}
* @return
*/
@Override
- protected String alignStructs_withAllAlignPanels()
+ protected String alignStructsWithAllAlignPanels()
{
- String reply = super.alignStructs_withAllAlignPanels();
+ String reply = super.alignStructsWithAllAlignPanels();
if (reply != null)
{
statusBar.setText("Superposition failed: " + reply);
git://source.jalview.org / jalview.git / blobdiff